Contacts of the strand formed by residues 72 - 76 (chain B) in PDB entry 1EV2
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 ARG 72 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ILE* 4.4 1.8 - - + +
35B HIS 3.9 6.3 - - - -
36B PRO 2.6 28.6 + - - -
37B ASP* 3.9 16.2 + - - +
38B GLY* 3.4 14.1 - - - +
66B LYS* 3.3 3.8 - - - +
67B GLY* 2.8 28.0 + - - -
70B ALA* 3.1 16.2 + - + +
71B ASN* 1.3 79.3 - - - +
73B TYR* 1.3 66.6 + - - +
84B ALA* 2.9 36.9 + - + -
85B SER* 3.3 12.3 - - - +
86B LYS* 3.7 22.5 - - + +
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Residues in contact with TYR 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B SER* 4.3 18.2 - - - -
65B ILE 3.5 3.8 - - - +
66B LYS* 3.8 48.6 + - + +
71B ASN 5.3 0.7 - - - -
72B ARG* 1.3 74.3 - - - +
74B LEU* 1.3 66.0 + - - +
75B ALA* 3.5 0.5 + - - +
84B ALA* 3.1 2.8 - - - -
85B SER* 2.7 48.1 + - - +
86B LYS 3.9 15.7 - - - -
87B SER* 4.8 0.4 - - - -
88B VAL* 3.3 34.1 - - + -
92B CYS* 4.1 18.8 - - + -
317F VAL* 3.6 26.6 + - + +
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 4.5 10.3 - - + -
34B ILE* 4.0 19.1 - - + +
40B VAL* 3.9 36.1 - - + -
65B ILE* 2.8 49.7 + - + +
73B TYR* 1.3 74.0 - - - +
75B ALA* 1.3 67.4 + - - +
82B LEU* 4.5 11.9 - - + -
83B LEU 3.6 4.0 - - - +
84B ALA* 4.3 0.7 - - - +
92B CYS* 3.4 20.8 - - - +
94B PHE* 3.8 22.5 - - + -
116B VAL* 4.0 21.5 - - + -
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Residues in contact with ALA 75 (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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73B TYR 4.1 2.7 - - - +
74B LEU* 1.3 78.3 - - - +
76B MET* 1.3 61.6 + - - +
81B ARG 3.8 0.3 - - - +
82B LEU* 3.4 9.7 - - - +
83B LEU* 2.7 51.7 + - + +
85B SER* 4.9 2.0 - - - -
89B THR* 4.9 3.6 - - + -
91B GLU* 3.1 21.1 - - + +
92B CYS* 3.7 15.7 - - - -
94B PHE* 4.1 4.0 - - - -
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Residues in contact with MET 76 (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 ALA* 1.3 74.5 - - - +
77B LYS* 1.3 70.5 + - - +
80B GLY* 4.1 10.1 - - - -
81B ARG 3.4 5.8 - - - +
82B LEU* 3.5 23.6 - - + -
91B GLU* 3.0 28.1 + - - +
94B PHE* 4.1 11.4 - - + -
108B SER* 4.2 21.0 + - - +
110B LYS* 5.9 1.4 - - - +
111B TYR* 4.9 6.1 - - + -
114B TRP* 3.5 31.9 - - + +
115B TYR 3.4 35.4 - - - +
116B VAL* 4.0 6.5 - - + +
127B GLY* 4.1 9.6 - - - -
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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