Contacts of the helix formed by residues 70 - 96 (chain D) in PDB entry 5YWB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 70 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D PRO* 1.3 73.0 - - - +
71D HIS* 1.3 53.0 + - - +
72D ASN 3.4 2.5 - - - -
73D LEU* 3.2 17.2 + - - +
74D ARG* 2.6 38.6 + - - +
124D TYR* 5.1 1.1 - - - -
185D VAL* 4.1 15.2 - - - +
188D ASN* 5.1 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D HIS* 4.0 29.1 + + + +
68D PHE* 3.2 24.1 + - - +
69D PRO 3.3 0.4 + - - -
70D GLY* 1.3 76.0 - - - +
72D ASN* 1.3 71.9 + - - +
74D ARG* 3.0 7.0 + - - +
75D TRP* 2.9 61.7 + + - -
124D TYR* 3.1 32.6 + + + -
128D GLU* 4.6 12.9 - - + +
223D ASN* 4.0 10.7 - - + -
224D LEU* 3.4 21.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D GLY 3.4 0.4 - - - -
71D HIS* 1.3 90.2 - - - +
73D LEU* 1.3 60.5 + - - +
75D TRP* 3.3 1.9 + - - +
76D ILE* 2.9 42.7 + - + +
224D LEU* 4.4 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D GLY* 3.2 17.0 + - - +
72D ASN* 1.3 79.3 - - - +
74D ARG* 1.3 63.2 + - - +
76D ILE* 4.5 13.2 - - + +
77D LEU* 2.9 53.2 + - + +
181D MET* 5.6 11.9 - - + -
185D VAL* 3.8 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D GLY 2.6 21.0 + - - +
71D HIS 3.0 6.9 + - - +
73D LEU* 1.3 73.7 - - - +
75D TRP* 1.3 61.8 + - + +
77D LEU* 3.4 2.8 + - - +
78D THR* 2.8 37.2 + - - +
120D SER* 5.3 5.1 + - - +
124D TYR* 3.3 55.3 + - + -
136D LEU* 6.0 0.2 - - - +
139D LEU* 4.8 3.2 - - - +
143D TRP* 4.1 10.7 - - + +
182D LEU* 4.0 24.9 + - + +
185D VAL* 3.3 29.1 - - + +
186D GLU* 2.8 43.4 + - - +
189D VAL* 4.2 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D HIS* 2.9 58.2 + + - +
72D ASN 3.9 1.6 - - - +
74D ARG* 1.3 78.7 - - + +
76D ILE* 1.3 67.8 + - + +
78D THR* 3.1 5.3 + - - -
79D PHE* 2.9 50.4 + + + -
121D VAL* 3.7 48.2 - - + -
124D TYR* 4.2 10.5 - + + -
125D HIS* 5.4 10.8 - + + -
223D ASN* 4.5 15.3 - - + -
224D LEU* 3.2 24.5 - - + -
225D LEU* 2.9 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D ASN* 2.9 29.8 + - + +
73D LEU* 3.8 13.7 - - + +
75D TRP* 1.3 76.8 - - + +
77D LEU* 1.3 65.1 + - + +
79D PHE* 3.1 9.1 + - - +
80D ILE* 3.0 42.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D LEU* 2.9 47.2 + - + +
74D ARG 3.8 3.6 - - - +
76D ILE* 1.3 76.3 - - + +
78D THR* 1.3 58.7 + - - +
80D ILE* 3.2 21.6 + - + +
81D LEU* 2.9 32.5 + - - +
178D LEU* 4.0 19.7 - - + +
181D MET* 3.9 37.5 - - + +
182D LEU* 4.0 31.2 - - + +
185D VAL* 4.6 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D ARG* 2.8 30.5 + - - +
75D TRP* 3.1 9.8 + - + -
77D LEU* 1.3 78.1 - - - +
79D PHE* 1.3 59.5 + - + +
81D LEU* 3.2 12.8 + - + +
82D LEU* 2.9 25.3 + - - +
117D ALA* 4.4 20.7 - - + +
120D SER* 5.4 4.6 + - - +
121D VAL* 3.6 30.9 - - + +
143D TRP* 6.0 1.4 - - - -
182D LEU* 4.6 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D TRP* 2.9 55.2 + + + -
76D ILE* 3.1 8.9 + - - +
78D THR* 1.3 75.5 - - + +
80D ILE* 1.3 66.8 + - + +
82D LEU* 3.2 28.6 + - + +
83D PHE* 3.0 22.0 + - - +
225D LEU* 4.2 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D ILE* 3.0 34.0 + - + +
77D LEU* 3.6 25.4 - - + +
79D PHE* 1.3 76.8 - - + +
81D LEU* 1.3 57.7 + - - +
83D PHE* 3.2 10.6 + - + +
84D VAL* 3.0 38.6 + - + +
178D LEU* 3.8 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D LEU 2.9 16.9 + - - +
78D THR* 3.4 14.1 - - + +
80D ILE* 1.3 74.5 - - - +
82D LEU* 1.3 65.4 + - - +
84D VAL* 3.3 2.2 + - - +
85D LEU* 2.9 34.2 + - + +
117D ALA* 4.7 19.3 - - + -
143D TRP* 4.3 15.5 - - + -
175D LEU* 4.3 20.4 - - + +
178D LEU* 3.7 32.1 - - + -
179D TYR* 4.6 12.1 - - + +
182D LEU* 3.5 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D THR* 2.9 13.5 + - + +
79D PHE* 3.3 33.2 - - + +
81D LEU* 1.3 76.6 - - - +
83D PHE* 1.3 62.5 + - - +
85D LEU* 3.2 9.3 + - - +
86D VAL* 3.0 32.3 + - + +
114D PHE* 3.4 34.5 - - + -
117D ALA* 5.8 2.1 - - - +
118D ILE* 5.5 6.5 - - + -
364D LEU* 5.9 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D PHE 3.0 13.3 + - - +
80D ILE* 3.5 14.1 - - + +
81D LEU 3.2 0.2 - - - -
82D LEU* 1.3 77.7 - - - +
84D VAL* 1.3 74.6 + - + +
86D VAL* 3.1 12.5 + - + +
87D CYS* 3.0 46.4 + - - -
361D LEU* 4.8 20.4 - - + -
364D LEU* 3.8 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D ILE* 3.0 20.6 + - + +
81D LEU* 4.0 4.9 - - - +
83D PHE* 1.3 87.8 - - + +
85D LEU* 1.3 58.2 + - - +
87D CYS* 3.2 8.0 + - - +
88D GLU* 2.9 26.9 + - + +
171D LEU* 3.8 35.9 - - + +
174D LEU* 4.8 14.4 - - + -
175D LEU* 4.1 21.1 - - + +
178D LEU* 3.9 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D LEU* 2.9 28.2 + - + +
82D LEU* 3.6 7.4 - - - +
83D PHE 3.1 0.2 - - - -
84D VAL* 1.3 74.6 - - - +
86D VAL* 1.3 64.4 + - - +
88D GLU* 3.2 26.0 + - - +
89D ILE* 2.9 30.4 + - + +
110D ALA* 4.0 11.4 - - - +
113D ALA* 3.5 45.5 - - + +
114D PHE* 3.5 22.9 - - + +
117D ALA* 4.6 9.2 - - + -
175D LEU* 4.7 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D LEU* 3.0 26.4 + - + +
83D PHE* 3.4 11.2 - - + +
85D LEU* 1.3 77.3 - - - +
87D CYS* 1.3 62.3 + - - +
89D ILE* 3.2 13.8 + - + +
90D ALA* 3.0 21.7 + - + +
114D PHE* 5.6 5.8 - - + -
360D VAL* 3.9 28.0 - - + -
361D LEU* 4.8 12.3 - - + -
364D LEU* 5.2 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D PHE* 3.0 49.5 + - - -
84D VAL* 3.2 8.9 + - - +
86D VAL* 1.3 79.3 - - - +
88D GLU* 1.3 57.6 + - - +
90D ALA* 3.1 10.4 + - - +
91D GLU* 3.0 25.5 + - - +
171D LEU* 3.8 29.6 - - + +
357D VAL* 6.3 1.6 - - - -
361D LEU* 5.4 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D VAL* 2.9 14.5 + - + +
85D LEU* 3.2 31.5 + - - +
87D CYS* 1.3 75.8 - - - +
89D ILE* 1.3 58.5 + - - +
91D GLU* 3.1 9.8 + - - +
92D GLY* 2.9 24.6 + - - -
107D TYR* 5.4 1.0 - - - +
109D PRO* 4.9 2.7 - - - +
110D ALA* 3.6 21.2 + - + +
113D ALA* 5.3 0.3 - - - +
150D LYS* 3.6 7.9 + - - -
168D ARG* 4.9 9.2 + - - +
171D LEU* 4.3 22.3 - - + +
172D THR* 4.8 8.7 - - - +
175D LEU* 2.8 33.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 89 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D LEU 2.9 23.2 + - - +
86D VAL* 3.6 13.2 - - + +
88D GLU* 1.3 75.5 - - - +
90D ALA* 1.3 62.3 + - - +
92D GLY* 3.2 2.4 + - - +
93D ILE* 2.9 34.9 + - + +
107D TYR* 5.6 11.1 - - + +
110D ALA* 3.8 20.4 - - + +
111D GLY* 4.7 11.4 - - - +
114D PHE* 5.3 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D VAL* 3.0 13.8 + - + +
87D CYS* 3.1 13.2 + - - +
89D ILE* 1.3 78.3 - - - +
91D GLU* 1.3 63.0 + - - +
93D ILE* 3.2 9.0 + - - +
94D LEU* 2.9 33.1 + - + +
357D VAL* 4.4 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D CYS 3.0 8.1 + - - +
88D GLU* 3.1 12.0 + - - +
90D ALA* 1.3 75.2 - - - +
92D GLY* 1.3 57.7 + - - +
94D LEU* 3.1 10.2 + - + +
95D SER* 2.9 30.0 + - - -
167D LEU* 3.0 47.9 - - + +
168D ARG* 2.9 45.5 + - - +
171D LEU* 2.7 38.5 - - + +
172D THR* 6.0 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D GLU 2.9 13.2 + - - -
89D ILE 3.2 2.9 + - - -
91D GLU* 1.3 76.2 - - - +
93D ILE* 1.3 64.1 + - - +
95D SER* 4.1 5.4 - - - -
96D ASP* 3.2 25.6 + - - +
106D LEU 5.7 0.7 - - - -
107D TYR* 3.5 33.7 - - - +
168D ARG* 4.7 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D ILE* 2.9 30.2 + - + +
90D ALA* 3.2 9.6 + - - +
92D GLY* 1.3 78.0 - - - +
94D LEU* 1.3 70.7 + - + +
95D SER 3.4 0.3 + - - -
96D ASP* 3.6 15.3 + - + +
107D TYR* 5.4 14.6 - - + -
356D TYR* 6.1 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D ALA* 2.9 22.8 + - + +
91D GLU* 3.1 12.3 + - + +
93D ILE* 1.3 82.6 - - + +
95D SER* 1.3 64.1 + - - +
96D ASP 4.6 1.4 - - - -
167D LEU* 4.8 17.0 - - + -
354D ASN* 4.8 26.0 - - - +
357D VAL* 6.4 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D GLU 2.9 16.4 + - - -
92D GLY* 4.1 6.1 - - - -
93D ILE 3.2 0.2 - - - -
94D LEU* 1.3 80.1 - - - +
96D ASP* 1.3 62.6 + - - +
103D HIS* 5.8 4.3 - - - +
106D LEU* 5.0 14.9 - - - +
168D ARG* 5.9 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D GLY 3.2 16.8 + - - +
93D ILE* 3.6 12.5 + - + +
94D LEU 3.5 2.2 - - - -
95D SER* 1.3 85.1 - - - +
103D HIS* 4.8 34.9 - - + +
107D TYR* 4.9 9.6 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il