Contacts of the helix formed by residues 70 - 84 (chain D) in PDB entry 3V5I
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 SER 70 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D ILE* 2.9 14.3 + - - +
37D ASP* 4.4 6.5 - - - -
38D ASP* 4.3 3.8 + - - -
69D GLY* 1.3 72.0 - - - +
71D VAL* 1.3 58.7 + - - +
72D THR* 3.4 10.0 + - - -
73D ALA* 3.0 31.8 + - - +
74D GLY* 3.0 24.3 + - - -
99D MET* 3.9 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D GLY 3.3 5.3 + - - +
70D SER* 1.3 70.4 + - - +
72D THR* 1.3 65.9 + - + +
74D GLY* 3.2 2.6 + - - -
75D PHE* 2.9 47.2 + - + -
99D MET* 3.7 29.7 - - + +
125D PRO* 4.4 16.2 - - + -
126D LEU 6.0 0.9 - - - +
146D THR* 3.7 26.7 - - + -
150D LEU* 4.3 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ASP* 4.6 5.4 + - - -
70D SER* 3.4 8.0 + - - -
71D VAL* 1.3 77.4 - - + +
73D ALA* 1.3 68.2 + - - +
75D PHE* 3.1 8.2 + - + +
76D ALA 3.0 18.0 + - - -
142D HIS* 6.0 1.6 - - + -
65E ASN* 4.8 2.0 + - - -
94E GLY* 3.2 18.4 - - - +
95E MET* 3.7 39.0 - - + +
119E GLU* 4.1 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D ILE* 3.9 6.1 - - + -
37D ASP 3.6 21.8 - - - +
38D ASP* 3.6 19.3 - - - +
41D ALA* 3.5 16.7 - - + +
70D SER* 3.0 23.9 + - - +
72D THR* 1.3 80.2 + - - +
74D GLY* 1.3 62.4 + - - +
76D ALA* 3.1 14.0 + - - +
77D ILE* 3.3 9.7 + - - +
65E ASN* 4.4 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D ILE* 3.9 8.7 - - - +
70D SER 3.0 16.0 + - - -
71D VAL 3.5 4.0 - - - -
73D ALA* 1.3 77.2 - - - +
75D PHE* 1.3 56.9 + - - +
77D ILE* 3.1 8.3 + - - +
78D TYR* 2.8 24.9 + - - +
99D MET* 3.7 21.1 - - - -
103D LEU* 3.6 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D VAL* 2.9 42.9 + - + -
72D THR* 3.1 11.2 + - + +
74D GLY* 1.3 73.0 - - - +
76D ALA* 1.3 67.8 + - - +
78D TYR* 4.0 15.7 - + + -
79D ASP* 2.8 28.6 + - - +
99D MET* 5.2 0.9 - - - -
102D PHE* 3.7 22.9 - + - -
146D THR* 5.2 0.9 - - + -
149D LYS* 3.6 36.6 - - + -
150D LEU* 3.7 26.0 - - + -
153D ILE* 3.8 16.6 - - + -
94E GLY* 4.5 7.9 - - - +
117E ASN* 3.8 28.9 - - + +
119E GLU* 5.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D ALA* 4.5 3.8 - - + -
45D VAL* 3.6 8.0 - - + +
72D THR 3.0 9.5 + - - +
73D ALA 3.1 10.3 + - - +
75D PHE* 1.3 75.7 - - - +
77D ILE* 1.3 61.3 + - - +
79D ASP* 4.3 1.3 - - - +
80D THR* 2.9 30.0 + - - -
65E ASN* 4.0 16.2 - - - +
93E ILE* 4.1 20.3 - - + +
94E GLY* 3.7 24.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D LEU* 5.1 4.7 - - + -
36D ILE* 4.4 11.2 - - + -
40D VAL* 4.9 2.0 - - + -
41D ALA* 3.9 33.7 - - + +
44D ILE* 3.9 38.4 - - + -
45D VAL* 4.2 6.1 - - + -
48D LEU* 4.7 1.3 - - + -
62D LEU* 5.0 3.8 - - + -
73D ALA 3.3 9.4 + - - +
74D GLY 3.1 7.4 + - - +
76D ALA* 1.3 74.1 - - - +
78D TYR* 1.3 66.6 + - - +
80D THR* 3.1 4.2 + - - -
81D ILE* 2.9 41.6 + - + +
103D LEU* 4.0 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D GLY 2.8 19.0 + - - +
75D PHE* 3.7 15.9 - + + +
77D ILE* 1.3 75.2 - - - +
79D ASP* 1.3 83.0 + - - +
81D ILE* 3.1 8.0 + - - +
82D GLN* 3.1 45.0 + - + +
102D PHE* 3.6 18.4 - + + -
103D LEU* 3.8 10.5 - - + +
106D ALA* 3.4 33.4 - - + -
153D ILE* 3.1 33.8 - - + +
156D GLU* 5.2 2.3 + - - -
157D ARG* 3.3 19.5 + - - -
117E ASN* 3.7 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 79 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D PHE 2.8 22.5 + - - +
76D ALA* 4.3 2.5 - - - +
78D TYR* 1.3 84.1 - - - +
80D THR* 1.3 57.5 + - - +
82D GLN* 3.2 6.2 + - - +
83D HIS* 2.9 29.8 + - - +
93E ILE* 5.8 0.9 - - + -
94E GLY 5.6 1.5 + - - +
115E LEU* 3.2 33.5 - - + +
116E PRO* 4.0 8.8 - - + +
117E ASN* 2.8 53.2 + - - +
118E ALA* 3.6 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D VAL* 3.6 29.8 - - + +
48D LEU* 3.9 27.6 - - + -
49D LEU* 4.4 10.8 - - + -
76D ALA 2.9 19.8 + - - -
77D ILE 3.1 4.9 + - - -
79D ASP* 1.3 76.4 - - - +
81D ILE* 1.3 64.2 + - - +
83D HIS* 3.0 15.9 + - + +
84D ILE* 3.1 22.9 + - + +
63E TYR* 6.1 0.3 - - - -
93E ILE* 4.5 5.4 - - - +
115E LEU* 4.1 8.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D LEU* 3.8 17.0 - - + -
62D LEU* 4.1 20.0 - - + -
77D ILE* 2.9 35.2 + - + +
78D TYR* 3.1 10.3 + - - +
80D THR* 1.3 77.2 - - - +
82D GLN* 1.3 78.9 + - - +
84D ILE* 3.4 22.3 + - - +
86D PRO 4.8 1.6 - - - +
88D VAL* 3.9 33.2 - - + +
90D THR* 5.3 1.1 - - + -
103D LEU* 4.8 9.9 - - + +
106D ALA* 3.9 20.4 - - + +
107D GLY* 5.1 0.9 - - - -
108D ALA 5.5 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D TYR* 3.1 51.4 + - + +
79D ASP* 3.2 6.5 + - - +
81D ILE* 1.3 85.0 + - - +
83D HIS* 1.3 61.9 + - - +
84D ILE 3.9 4.5 - - - +
106D ALA* 3.1 23.0 + - - +
107D GLY 6.0 0.4 - - - -
108D ALA* 6.0 1.2 - - - +
157D ARG* 3.6 21.3 + - - +
192E PRO* 4.1 28.2 - - + +
193E GLU 4.4 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D LEU* 5.3 7.6 - - + +
52D GLN* 4.6 3.5 + - - -
79D ASP 2.9 16.7 + - - +
80D THR* 3.0 9.2 + - - +
82D GLN* 1.3 76.6 - - - +
84D ILE* 1.3 70.8 + - - +
63E TYR* 5.4 7.0 - + - -
115E LEU* 4.5 14.2 - - + +
116E PRO* 6.5 0.4 - - + -
190E MET* 3.4 42.5 - - + +
191E VAL 4.7 11.2 - - - -
192E PRO* 4.9 3.1 - - + -
193E GLU* 4.0 32.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D LEU* 4.2 21.3 - - + +
49D LEU* 4.3 19.3 - - + -
52D GLN* 3.4 28.9 - - + +
60D ILE* 3.8 28.9 - - + -
80D THR* 3.1 16.4 + - + +
81D ILE* 3.4 21.0 - - - +
82D GLN 3.9 4.9 - - - +
83D HIS* 1.3 85.1 - - - +
85D LYS* 1.3 63.6 + - - +
86D PRO* 3.9 13.5 - - + +
88D VAL* 3.9 15.5 - - + -
193E GLU* 5.9 2.8 - - - -
----------------------------------------------------------
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