Contacts of the helix formed by residues 80 - 92 (chain D) in PDB entry 4GDK
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 THR 80 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D THR 4.2 7.9 - - - +
79D ARG* 1.3 76.7 - - - +
81D ILE* 1.3 66.0 + - - +
82D GLN* 3.9 2.8 + - - +
83D GLY* 3.1 28.9 + - - -
84D LEU* 3.1 18.0 + - - +
112D PRO 3.4 13.3 + - - +
113D ASP* 3.5 23.1 - - - +
114D GLN 3.2 6.1 - - - +
115D GLU* 4.6 4.7 - - + -
116D VAL* 5.0 1.6 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
80D THR* 1.3 72.5 - - - +
82D GLN* 1.3 58.0 + - - +
84D LEU* 3.0 12.2 + - + +
85D ILE* 2.9 42.8 + - + +
102D ILE* 4.2 13.6 - - + +
110D PRO* 3.7 38.6 - - + +
111D SER 3.7 17.3 - - - +
112D PRO* 3.6 8.9 + - + -
114D GLN 3.1 11.6 + - - +
115D GLU 5.8 0.2 - - - -
116D VAL* 5.2 4.2 - - + +
119D LEU* 3.7 22.7 - - + -
131D LEU* 4.3 23.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
80D THR* 4.2 3.1 - - - +
81D ILE* 1.3 77.9 - - - +
83D GLY* 1.3 62.4 + - - +
85D ILE* 3.2 20.5 + - - +
86D ASP* 3.1 62.6 + - - +
89D LYS* 5.7 1.4 - - - +
112D PRO* 3.0 41.7 + - + +
113E LEU* 5.5 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D ARG* 4.5 4.9 + - - -
80D THR* 3.1 22.8 + - - -
82D GLN* 1.3 77.9 - - - +
84D LEU* 1.3 59.6 + - - +
86D ASP* 4.1 6.3 - - - +
87D PHE* 3.1 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D ILE* 4.0 11.0 - - + -
59D LEU* 5.6 4.0 - - + -
75D VAL* 5.0 5.4 - - + -
79D ARG* 3.9 41.7 - - + +
80D THR 3.1 15.9 + - - +
81D ILE* 3.0 12.6 + - + +
83D GLY* 1.3 78.5 - - - +
85D ILE* 1.3 55.8 + - - +
86D ASP 3.3 0.2 - - - -
87D PHE* 3.2 10.2 - - + +
88D ILE* 2.7 44.5 + - + +
102D ILE* 4.2 9.2 - - + -
116D VAL* 3.8 24.0 - - + -
131D LEU* 3.8 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D ILE* 2.9 29.5 + - + +
82D GLN* 3.5 26.0 - - - +
84D LEU* 1.3 77.3 - - - +
86D ASP* 1.3 62.4 + - - +
88D ILE* 3.8 1.4 - - - +
89D LYS* 2.9 60.7 + - + +
100D LEU* 3.6 28.7 - - + +
101D PHE* 5.4 0.4 - - - -
102D ILE* 3.7 25.4 - - + +
112D PRO* 5.6 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D GLN* 3.1 43.0 + - - +
83D GLY* 4.2 5.6 - - - +
85D ILE* 1.3 78.2 - - - +
87D PHE* 1.3 63.7 + - - +
89D LYS* 4.0 16.8 + - - +
90D LYS* 3.2 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D LEU* 5.2 2.2 - - + -
68D MET* 4.3 6.3 - - + -
73D TRP* 3.6 46.9 - + - -
75D VAL* 6.4 1.8 - - + -
79D ARG* 3.7 26.5 - - - +
83D GLY 3.1 20.9 + - - +
84D LEU* 3.1 12.9 + - + +
86D ASP* 1.3 79.4 - - - +
88D ILE* 1.3 72.7 + - + +
90D LYS* 3.7 9.8 + - - +
91D PHE* 3.2 49.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D LEU* 3.7 35.9 - - + -
68D MET* 3.8 13.5 - - + -
84D LEU* 2.7 26.0 + - + +
85D ILE 3.9 2.5 - - - +
87D PHE* 1.3 83.3 - - + +
89D LYS* 1.3 65.5 + - - +
90D LYS 3.1 2.2 - - - -
91D PHE* 2.9 19.3 + - - +
92D LEU* 3.1 29.5 + - + +
100D LEU* 3.6 19.5 - - + -
102D ILE* 4.5 17.5 - - + -
133D TYR* 4.5 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 89 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D GLN* 5.7 0.8 - - - +
85D ILE* 2.9 43.0 + - + +
86D ASP* 4.0 18.0 + - - +
87D PHE 3.5 0.2 - - - -
88D ILE* 1.3 74.8 - - - +
90D LYS* 1.3 61.9 + - + +
92D LEU* 3.3 3.3 + - - +
93D LYS 3.2 3.5 + - - -
94D LEU* 2.8 49.7 + - + +
95D VAL 3.9 13.9 - - - +
96D ALA* 3.1 20.6 + - - +
98D GLU 2.9 28.0 + - - -
99D GLN* 4.7 1.6 - - - +
100D LEU* 4.1 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 90 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D ASP* 3.2 23.1 + - - +
87D PHE* 3.8 8.1 - - - +
88D ILE 3.1 0.4 - - - -
89D LYS* 1.3 77.9 - - + +
91D PHE* 1.3 65.8 + - + +
93D LYS* 3.1 16.1 + - - +
94D LEU 4.9 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D MET* 3.5 29.8 - - + -
69D LYS* 6.0 6.3 - - + +
73D TRP* 4.0 23.3 - + - -
87D PHE* 3.2 53.2 - + - -
88D ILE 2.9 6.8 + - - +
90D LYS* 1.3 81.8 - - + +
92D LEU* 1.3 63.0 + - - +
93D LYS* 3.2 10.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D THR* 3.9 17.3 - - + -
66D PRO* 3.3 54.7 - - + +
67D ILE 4.1 7.4 - - - +
68D MET* 4.0 21.3 - - + -
88D ILE* 3.1 32.2 + - + +
89D LYS 4.0 0.7 - - - +
90D LYS 3.2 0.4 - - - -
91D PHE* 1.3 79.5 - - - +
93D LYS* 1.3 72.6 + - - +
94D LEU* 3.3 30.2 - - + +
100D LEU* 4.2 4.7 - - + -
133D TYR* 4.0 7.0 - - + -
----------------------------------------------------------
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