Contacts of the helix formed by residues 91 - 104 (chain B) in PDB entry 3ECS
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 LYS 91 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B LEU* 3.7 22.2 + - - +
35B LYS* 5.1 2.0 + - - +
37B ASP 4.5 5.3 + - - -
38B LYS* 3.0 48.2 - - - +
46B ARG* 6.1 1.0 - - - +
88B LYS* 3.0 39.9 - - - +
89B CYS* 2.8 5.8 + - - +
90B LYS* 1.3 81.0 - - - +
92B ILE* 1.3 61.6 + - - +
93B MSE 2.8 9.3 + - + +
94B ILE* 3.4 33.2 + - + +
95B GLU* 3.7 3.3 + - - +
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Residues in contact with ILE 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B CYS 3.9 15.3 - - - +
90B LYS* 3.2 2.0 - - - -
91B LYS* 1.3 78.9 - - - +
93B MSE 1.3 79.6 + - + +
95B GLU* 2.9 44.5 - - + +
96B ARG* 3.1 18.3 + - + +
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Residues in contact with MSE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 3.9 19.7 - - + -
47B ALA* 6.2 4.5 - - - -
76B ILE* 3.4 36.4 - - + +
77B SER* 4.3 25.8 - - - +
90B LYS* 2.8 52.3 - - + +
91B LYS* 2.8 0.6 - - + -
92B ILE* 1.3 87.3 - - + +
94B ILE* 1.3 67.9 + - + +
96B ARG* 2.6 24.1 + - - +
97B GLY* 2.7 11.8 + - - -
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Residues in contact with ILE 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.8 17.5 - - + +
34B LEU* 3.3 40.8 - - + +
35B LYS* 3.4 28.5 - - + +
91B LYS* 3.5 29.8 - - + +
93B MSE 1.3 78.5 - - + +
95B GLU* 1.3 53.7 + - - +
97B GLY* 4.2 1.1 - - - +
98B GLU* 2.8 63.1 + - + +
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Residues in contact with GLU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LYS 3.7 2.5 + - - +
92B ILE* 2.9 47.8 + - + +
93B MSE 2.7 3.8 + - - -
94B ILE* 1.3 79.7 - - - +
96B ARG* 1.3 60.7 + - + +
98B GLU* 3.4 13.2 + - - +
99B LEU* 3.3 18.7 + - - +
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Residues in contact with ARG 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B PHE* 3.2 46.1 + - + +
76B ILE* 3.3 12.7 - - + +
77B SER* 2.6 52.5 + - - +
92B ILE* 3.1 18.5 + - + +
93B MSE 2.6 16.1 + - - +
95B GLU* 1.3 80.9 - - + +
97B GLY* 1.3 57.7 + - - +
98B GLU 3.0 1.8 - - - -
99B LEU* 3.4 12.8 - - + -
100B PHE* 2.9 23.6 + - - +
307B ALA* 4.8 16.8 + - - +
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Residues in contact with GLY 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.2 22.3 - - - +
72B PHE* 3.8 28.3 - - - -
76B ILE* 4.0 8.5 - - - +
93B MSE 2.7 18.0 + - - -
94B ILE* 3.5 4.5 - - - -
96B ARG* 1.3 73.0 - - - +
98B GLU* 1.3 59.9 + - - +
100B PHE* 4.5 1.1 - - - -
101B LEU* 3.5 16.3 + - - +
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Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LEU* 3.5 20.9 - - + -
35B LYS* 3.7 12.3 + - - -
94B ILE* 2.8 45.5 + - + +
95B GLU* 3.5 11.2 - - - +
97B GLY* 1.3 79.7 - - - +
99B LEU* 1.3 60.1 + - - +
100B PHE 3.4 0.2 - - - -
101B LEU* 3.9 4.4 - - - +
102B ARG* 3.5 36.3 + - - +
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B PHE* 4.7 15.5 - - + -
95B GLU 3.3 11.5 + - - +
96B ARG* 3.1 16.9 + - + +
98B GLU* 1.3 79.0 - - - +
100B PHE* 1.3 59.1 + - - +
101B LEU 3.2 0.4 - - - -
102B ARG* 3.3 19.1 + - + +
103B ARG* 3.0 31.1 + - + +
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Residues in contact with PHE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ILE* 3.5 30.1 - - + -
68B GLY 4.4 0.7 - - - -
71B LEU* 3.8 37.9 - - + -
72B PHE* 3.5 32.8 - + + -
75B PHE* 3.5 31.4 - + + -
96B ARG 2.9 16.7 + - - +
97B GLY* 4.1 6.5 - - - +
98B GLU 3.4 0.2 - - - -
99B LEU* 1.3 78.2 - - - +
101B LEU* 1.3 58.3 + - - +
102B ARG 3.4 0.2 - - - -
103B ARG* 4.0 13.4 - - - +
104B ILE* 3.1 47.9 + - + +
233B PHE* 5.4 2.9 - - + -
303B LEU* 6.5 0.9 - - + -
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B VAL* 4.5 13.0 - - + -
27B ILE* 4.1 14.1 - - + -
28B ARG* 3.5 58.8 - - + +
31B LEU* 4.0 17.9 - - + -
97B GLY 3.5 13.1 + - - +
98B GLU* 4.3 5.8 - - - +
99B LEU 3.2 0.4 - - - -
100B PHE* 1.3 78.8 - - - +
102B ARG* 1.3 63.0 + - - +
104B ILE* 3.6 8.9 - - + +
105B SER* 3.2 23.2 + - - -
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Residues in contact with ARG 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLU* 3.5 30.1 + - - +
99B LEU* 3.3 19.4 + - + +
101B LEU* 1.3 77.4 - - - +
103B ARG* 1.3 63.3 + - - +
105B SER* 2.5 24.4 + - - +
106B LEU* 3.0 26.3 - - + +
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Residues in contact with ARG 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 3.0 20.6 + - + +
100B PHE* 4.0 15.2 - - - +
101B LEU 3.3 0.2 - - - -
102B ARG* 1.3 77.9 - - - +
104B ILE* 1.3 75.5 - - - +
105B SER 3.1 4.7 + - - -
106B LEU* 3.2 26.3 + - - +
107B SER* 3.9 4.6 + - - -
110B LYS* 5.8 5.6 - - - +
232B SER* 4.0 6.4 + - - -
287B ASP* 3.3 27.5 + - - +
288B LEU* 3.6 26.9 - - - +
303B LEU* 4.2 10.3 - - - +
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Residues in contact with ILE 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B VAL* 3.9 29.7 - - + +
27B ILE* 3.3 33.4 - - + -
100B PHE* 3.1 35.2 + - + +
101B LEU* 3.6 13.0 - - - +
103B ARG* 1.3 90.8 - - - +
105B SER* 1.3 57.7 + - - +
106B LEU 3.2 2.7 - - - -
107B SER* 3.6 21.5 + - - +
232B SER* 5.6 3.1 - - - +
233B PHE* 4.0 30.9 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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