Contacts of the strand formed by residues 61 - 64 (chain C) in PDB entry 3MA0
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 VAL 61 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C VAL* 4.2 8.3 - - + -
4C LYS 3.3 1.4 + - - +
5C ILE* 3.3 12.4 - - + +
6C GLY* 2.8 31.5 + - - -
59C VAL* 3.5 2.7 - - - +
60C ASP* 1.3 88.5 - - + +
62C LEU* 1.3 69.9 + - - +
63C VAL* 4.1 11.9 - - + -
84C ILE* 4.2 1.1 - - - -
85C LYS* 3.4 15.9 - - + +
87C LEU* 4.9 0.7 - - + +
255C ALA* 3.3 33.4 - - + +
258C LEU* 4.2 9.9 - - + -
259C GLY* 3.4 21.1 - - - +
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Residues in contact with LEU 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C GLY 3.4 3.6 - - - +
51C ILE* 4.1 31.2 - - + +
54C MET* 3.9 39.5 - - + -
55C ILE* 4.3 5.6 - - + +
59C VAL* 4.2 7.2 - - + -
61C VAL* 1.3 74.9 - - - +
63C VAL* 1.3 62.6 + - - +
64C ILE* 4.0 17.3 - - + -
75C VAL 5.3 0.2 - - - +
76C VAL* 6.0 0.9 - - - -
79C ALA* 3.6 31.4 - - + -
84C ILE* 3.9 10.3 - - + +
85C LYS 2.8 12.2 + - - +
86C VAL* 3.5 8.4 - - + +
87C LEU 2.8 27.7 + - - +
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Residues in contact with VAL 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ILE* 3.6 22.4 - - + -
6C GLY 2.7 10.6 + - - +
7C MET* 3.2 20.0 - - + +
8C ALA 2.9 24.1 + - - +
24C PHE* 3.8 20.2 - - + -
61C VAL* 4.1 3.6 - - + -
62C LEU* 1.3 77.4 - - - +
64C ILE* 1.3 61.4 + - - +
65C ILE* 4.1 0.8 + - + -
87C LEU* 3.4 20.9 - - + -
89C TYR* 3.9 30.3 - - + -
255C ALA* 4.0 13.7 - - + -
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Residues in contact with ILE 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ALA* 3.4 17.9 - - + +
47C GLN* 4.0 2.9 - - - +
51C ILE* 3.8 29.8 - - + -
62C LEU* 4.2 21.3 - - + -
63C VAL* 1.3 77.2 - - - +
65C ILE* 1.3 64.5 + - - +
66C PRO* 3.4 18.6 - - - +
72C LEU* 3.9 21.5 - - + -
76C VAL* 4.8 8.5 - - + -
86C VAL* 4.0 24.2 - - + -
87C LEU 3.0 6.9 + - - -
88C ALA* 3.8 2.6 - - - -
89C TYR* 3.0 23.5 + - - -
93C ILE* 3.9 16.3 - - + +
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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