Contacts of the strand formed by residues 85 - 98 (chain B) in PDB entry 3EVS
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 CYS 85 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B CYS* 2.0 54.5 - - + -
20B SER 3.7 2.2 - - - -
48B CYS* 3.6 19.6 - - - +
49B GLU* 3.5 26.9 - - - -
50B GLY 3.7 15.4 + - - +
52B CYS* 3.7 3.9 - - - -
83B THR 4.2 0.2 + - - -
84B CYS* 1.3 79.9 - - - +
86B VAL* 1.3 62.1 + - - +
118B GLY 3.3 5.6 - - - -
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Residues in contact with VAL 86 (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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48B CYS* 3.5 6.5 - - - -
84B CYS* 3.9 20.0 - - + +
85B CYS* 1.3 80.4 - - - +
87B PRO* 1.3 79.9 - - + +
88B THR* 3.7 0.5 - - - +
117B CYS* 3.4 0.9 - - - -
118B GLY 2.9 29.1 + - - +
120B ARG* 3.7 36.1 - - + -
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Residues in contact with PRO 87 (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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48B CYS* 3.6 12.3 - - + +
86B VAL* 1.3 98.6 - - + +
88B THR* 1.3 61.6 + - - +
89B ARG 4.5 0.4 - - - +
90B LEU* 3.7 27.6 - - + +
114B VAL* 3.7 28.7 - - + -
116B SER 3.4 9.6 - - - +
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Residues in contact with THR 88 (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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60B LEU 5.1 0.2 - - - +
61B GLU* 3.9 13.3 + - - +
86B VAL 3.7 2.7 - - - +
87B PRO* 1.3 78.1 - - - +
89B ARG* 1.3 69.5 + - - +
90B LEU* 4.7 2.9 - - - -
116B SER* 2.6 35.0 + - - -
117B CYS 3.9 3.3 + - - -
118B GLY* 3.7 23.6 - - - +
120B ARG* 3.8 42.3 + - + +
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Residues in contact with ARG 89 (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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61B GLU* 2.9 42.4 + - - -
87B PRO* 4.5 0.3 - - - +
88B THR* 1.3 86.8 + - - +
90B LEU* 1.3 68.8 + - - +
114B VAL* 3.9 2.1 - - - -
115B GLU* 2.9 31.2 + - + -
116B SER* 3.3 33.5 + - - +
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Residues in contact with LEU 90 (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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87B PRO* 3.7 34.5 - - + +
88B THR 4.7 1.3 - - - -
89B ARG* 1.3 84.2 - - - +
91B SER* 1.3 61.6 + - - +
111B ASP* 3.6 49.0 - - + +
112B MET 4.9 1.3 - - - -
113B VAL 3.1 23.1 - - - +
114B VAL* 4.1 8.3 - - + +
115B GLU* 4.0 4.4 - - - +
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Residues in contact with SER 91 (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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90B LEU* 1.3 74.4 - - - +
92B PRO* 1.3 75.2 + - - +
111B ASP 4.2 3.1 - - - -
112B MET 2.8 22.1 + - - -
113B VAL* 2.9 25.3 + - - +
115B GLU* 2.2 34.8 + - - -
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Residues in contact with PRO 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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91B SER* 1.3 93.3 - - - +
93B ILE* 1.3 69.8 + - - +
108B GLN* 3.4 38.4 - - + +
109B TYR 3.0 22.0 - - - +
110B GLU* 4.0 16.2 - - - +
111B ASP 4.5 0.2 - - - -
112B MET 4.4 0.2 - - - +
113B VAL* 4.5 1.6 - - - +
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Residues in contact with ILE 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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40B PRO* 4.7 9.0 - - + -
43B TYR* 3.8 38.6 - - + -
92B PRO* 1.3 80.6 - - - +
94B SER* 1.3 64.7 + - - +
95B ILE* 4.0 18.6 + - + -
108B GLN* 4.4 2.0 - - - -
109B TYR* 2.8 29.8 + - - +
112B MET* 3.8 28.4 - - + +
113B VAL* 3.5 25.8 - - + -
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Residues in contact with SER 94 (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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40B PRO* 3.7 14.9 - - - +
93B ILE* 1.3 78.5 - - - +
95B ILE* 1.3 65.2 + - - +
106B TYR* 3.4 39.2 + - - -
107B LYS 3.1 11.4 - - - -
108B GLN* 3.7 23.1 + - - +
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Residues in contact with ILE 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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28B PHE* 4.0 27.4 - - + -
36B TRP* 5.5 0.9 - - + -
37B ILE* 3.8 35.0 - - + -
39B ALA 3.7 5.8 - - - +
40B PRO* 4.7 3.6 - - + -
93B ILE* 4.0 11.0 - - + -
94B SER* 1.3 79.9 - - - +
96B LEU* 1.3 66.4 + - - +
97B PHE* 3.8 10.8 - - + -
105B VAL 3.4 3.1 - - - +
106B TYR* 3.8 3.8 - - - -
107B LYS 2.9 29.5 + - - -
109B TYR* 3.8 30.7 - - + -
112B MET* 4.2 7.9 - - + -
66C PHE* 4.1 16.8 - - + -
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Residues in contact with LEU 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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38B ILE* 3.0 58.2 + - + -
39B ALA* 2.8 26.9 + - + +
95B ILE* 1.3 73.5 - - - +
97B PHE* 1.3 63.1 + - - +
104B VAL* 3.4 28.3 - - + -
105B VAL 3.2 14.8 - - - +
106B TYR* 3.9 24.3 - - + +
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Residues in contact with PHE 97 (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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36B TRP* 3.2 38.4 - + + +
37B ILE* 4.1 3.6 - - - -
38B ILE* 4.3 5.2 - - - +
95B ILE* 3.8 14.4 - - + -
96B LEU* 1.3 78.3 - - - +
98B ILE* 1.3 76.9 + - - +
99B ASP* 3.9 21.5 - - + -
104B VAL* 3.3 3.9 - - - +
105B VAL* 2.7 63.8 + - + +
107B LYS* 3.8 26.2 - - + -
109B TYR* 3.4 26.2 - + - -
65C ASP* 4.6 6.7 - - - -
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Residues in contact with ILE 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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35B ASP 4.9 4.7 - - - +
36B TRP* 2.8 38.8 + - + +
38B ILE* 3.9 23.8 - - + -
97B PHE* 1.3 84.3 - - - +
99B ASP* 1.3 72.0 + - - +
102B ASN* 4.0 24.0 - - - +
103B ASN 3.3 9.9 - - - +
104B VAL* 4.4 11.0 - - + -
69C ARG* 5.6 0.9 + - - -
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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