Contacts of the strand formed by residues 31 - 35 (chain B) in PDB entry 3MX0
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 31 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU 6.0 0.2 + - - -
28B VAL* 3.4 25.3 - - - +
29B ALA 4.0 1.0 - - - +
30B ASP* 1.3 78.8 - - + +
32B TYR* 1.3 64.8 + - - +
33B ALA* 3.8 3.1 + - + +
57B TYR* 2.9 61.9 - - + +
58B LEU 4.3 0.4 - - - +
59B ASP* 2.5 50.7 + - - +
113B LYS* 4.6 7.9 - - - +
115B SER* 4.4 10.7 + - - -
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Residues in contact with TYR 32 (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 VAL* 4.2 26.6 + - + -
29B ALA* 4.2 15.5 + - - -
30B ASP 4.2 2.7 - - - -
31B ARG* 1.3 73.5 - - - +
33B ALA* 1.3 61.8 + - - +
34B VAL* 6.1 0.4 - - + -
50B ILE* 4.8 17.7 - - + -
51B ASP 3.3 27.2 + - - -
52B VAL* 4.3 20.0 - - + -
56B ASP* 4.1 19.5 + - + -
57B TYR 2.9 20.5 + - - +
58B LEU* 3.3 18.7 - - + +
59B ASP* 2.8 24.0 + - - -
159B ARG* 3.4 17.0 + - - -
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Residues in contact with ALA 33 (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 VAL* 4.8 5.4 - - + +
31B ARG 3.8 4.4 + - - +
32B TYR* 1.3 73.5 - - - +
34B VAL* 1.3 74.0 + - - +
35B TYR* 4.8 12.4 - - + +
48B TYR* 4.6 1.0 + - - -
59B ASP* 3.4 9.9 - - + +
61B PHE* 3.6 26.9 - - + -
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Residues in contact with VAL 34 (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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32B TYR* 5.4 1.1 - - + -
33B ALA* 1.3 87.3 - - - +
35B TYR* 1.3 63.5 + - - +
36B TRP* 3.9 7.3 + - + +
40B ASN* 5.4 0.7 - - - +
43B PHE* 3.5 36.1 - - + -
48B TYR* 3.1 32.3 - - + +
50B ILE* 5.3 5.6 - - + -
58B LEU* 5.0 9.2 - - + -
59B ASP 3.1 8.4 + - - +
60B VAL* 3.5 7.3 - - + +
61B PHE* 2.8 31.8 + - - -
154B LEU* 4.9 14.8 - - + -
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Residues in contact with TYR 35 (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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33B ALA* 4.8 8.6 - - + +
34B VAL* 1.3 84.1 - - - +
36B TRP* 1.3 59.9 + - - +
37B ASN* 3.3 9.7 + - - +
40B ASN* 2.6 31.3 + - - +
43B PHE* 3.8 4.0 - - - -
61B PHE* 3.2 42.3 - + + +
62B CYS 5.0 2.2 - - - +
111B PRO* 5.4 6.7 - - + -
1E NAG 4.0 33.0 - - - +
2E NAG 3.7 38.5 + - - -
3E NAG 3.5 28.4 + - + +
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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