Contacts of the strand formed by residues 75 - 79 (chain B) in PDB entry 3EXG
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 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ASP* 3.3 26.2 - - - -
22B LYS* 3.0 29.1 + - + +
23B VAL* 3.8 29.6 - - + +
24B PHE 3.9 0.5 + - - -
73B GLY 4.5 4.7 + - - +
74B LEU* 1.3 79.7 - - - +
76B PRO* 1.3 65.8 - - - +
77B ILE* 3.6 3.6 + - - +
111B PRO* 3.7 22.1 - - + +
161B ILE* 3.3 20.8 + - + +
162B ARG* 3.4 11.1 + - - +
163B ASP 3.0 21.6 + - - -
164B ASN* 2.9 29.1 + - - -
1003B K 4.7 0.2 - - - -
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Residues in contact with PRO 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 3.4 39.3 - - + +
26B LEU* 4.3 9.2 - - + -
66B ALA* 3.4 28.3 - - + +
70B ALA* 3.7 11.4 - - + +
74B LEU 3.3 9.9 - - - +
75B ARG* 1.3 92.1 - - - +
77B ILE* 1.3 59.4 + - - +
78B CYS 3.7 0.4 - - - -
111B PRO 3.5 8.5 - - - +
112B ILE* 3.7 8.9 - - + +
113B VAL* 3.1 26.0 + - - +
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Residues in contact with ILE 77 (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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13B MET* 4.2 22.7 - - + +
17B LEU* 5.2 3.4 - - + -
23B VAL* 4.3 14.6 - - + -
24B PHE 2.8 11.9 + - - +
25B LEU* 3.3 27.0 - - + +
26B LEU* 2.9 27.7 + - - +
75B ARG 4.4 5.8 - - - +
76B PRO* 1.3 72.1 - - - +
78B CYS* 1.3 60.4 + - - +
113B VAL* 3.6 13.2 - - + +
115B ARG* 4.2 26.9 - - + -
157B ILE* 5.5 1.3 - - + -
161B ILE* 3.4 38.6 - - + -
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Residues in contact with CYS 78 (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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26B LEU* 3.4 8.7 - - + -
62B PHE* 4.3 16.4 - - - -
63B ALA* 4.2 14.1 - - - -
66B ALA* 3.8 28.7 - - + -
76B PRO 3.7 0.2 - - - -
77B ILE* 1.3 73.7 - - - +
79B GLU* 1.3 60.1 + - - +
80B PHE* 3.9 12.0 + - - -
112B ILE* 4.3 2.9 - - + -
113B VAL 2.7 15.0 + - - +
114B PHE* 3.3 28.3 - - + +
115B ARG 3.2 20.8 + - - -
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Residues in contact with GLU 79 (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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25B LEU* 4.5 7.4 - - + +
26B LEU 2.8 15.5 + - - +
27B GLY* 3.6 16.3 - - - -
28B GLU 4.5 5.7 + - - +
30B VAL* 3.4 29.4 - - + +
35B GLY* 5.7 0.3 - - - -
36B ALA* 4.7 16.0 + - - +
37B TYR* 5.2 4.3 + - - -
39B VAL* 5.2 4.8 - - - +
40B SER* 4.9 4.2 + - - -
62B PHE* 4.0 10.9 - - - -
77B ILE 3.9 1.4 + - - -
78B CYS* 1.3 73.7 - - - +
80B PHE* 1.3 74.0 + - - +
81B MET* 4.1 10.9 + - + +
115B ARG* 2.8 51.1 + - - +
116B GLY* 4.9 0.7 - - - -
117B PRO* 5.3 1.7 - - - +
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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