Contacts of the strand formed by residues 4 - 9 (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 LYS 4 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C GLU* 5.5 1.8 - - - -
3C VAL* 1.3 75.8 - - - +
5C ILE* 1.3 62.2 + - - +
34C LYS* 3.5 20.6 - - + +
36C PHE* 4.2 26.3 - - + -
57C ARG 4.5 13.6 + - - +
58C GLY 4.2 13.7 - - - +
59C VAL* 4.0 11.4 - - - -
60C ASP* 2.8 43.2 + - - +
61C VAL 3.3 5.7 + - - -
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Residues in contact with ILE 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C VAL* 4.2 12.1 - - + -
4C LYS* 1.3 80.1 - - - +
6C GLY* 1.3 67.2 + - - +
24C PHE* 4.1 13.5 - - + -
28C ALA* 4.1 17.7 - - + -
33C ALA* 3.8 22.4 - - + -
34C LYS 2.8 14.2 + - - +
35C VAL* 3.4 8.7 - - + -
36C PHE* 2.8 30.8 + - - +
59C VAL* 3.9 3.8 - - - -
61C VAL* 3.3 13.2 - - + +
63C VAL* 3.6 28.7 - - + -
255C ALA* 3.9 20.6 - - + -
256C VAL* 4.4 6.7 - - + -
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Residues in contact with GLY 6 (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* 1.3 71.9 - - - +
7C MET* 1.3 56.6 + - - -
8C ALA 3.8 0.7 + - - -
36C PHE* 3.4 6.7 - - - -
54C MET* 3.6 20.9 - - - -
59C VAL* 3.6 14.3 - - - +
61C VAL 2.8 12.9 + - - -
62C LEU* 3.4 6.9 - - - +
63C VAL* 2.7 32.9 + - - +
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Residues in contact with MET 7 (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 4.0 0.8 + - - -
6C GLY* 1.3 72.1 - - - -
8C ALA* 1.3 57.7 + - - +
9C ILE* 3.6 23.4 + - + -
20C ASP 4.2 4.5 - - - +
21C ARG* 4.1 29.6 - - - +
24C PHE* 3.9 43.1 - - + -
25C VAL* 4.9 0.2 - - - -
35C VAL* 3.9 16.2 - - + -
36C PHE 2.7 10.0 + - - +
37C VAL* 3.4 11.8 - - + +
38C GLN 3.1 26.5 + - - +
54C MET* 3.5 2.2 - - - +
63C VAL* 3.2 26.7 - - + +
65C ILE* 4.7 9.4 - - + -
89C TYR* 4.7 10.1 - - + -
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Residues in contact with ALA 8 (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 3.8 1.0 + - - +
7C MET* 1.3 70.0 - - - +
9C ILE* 1.3 64.5 + - - +
38C GLN 3.7 4.9 - - - -
47C GLN* 3.5 12.1 + - + +
50C GLN* 5.3 5.4 - - + +
51C ILE* 3.7 32.8 - - + +
54C MET* 4.1 15.5 - - + -
62C LEU* 5.4 0.2 - - + -
63C VAL 2.9 7.9 + - - -
64C ILE* 3.4 11.0 - - + -
65C ILE 2.9 23.7 + - - -
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Residues in contact with ILE 9 (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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7C MET* 3.9 33.2 - - + +
8C ALA* 1.3 78.6 - - - +
10C ASP* 1.3 58.7 + - - +
11C ASP 3.7 20.4 - - - +
12C LEU* 3.7 26.5 - - + -
17C TRP* 5.2 4.0 - - + +
21C ARG* 4.8 9.9 - - + -
37C VAL* 4.7 12.3 - - + -
38C GLN 2.9 20.2 + - - +
39C SER* 3.8 13.0 - - - +
40C ALA* 3.0 22.9 + - - +
47C GLN* 3.5 7.2 + - - -
50C GLN* 4.6 0.3 - - - +
65C ILE* 3.6 31.4 - - + -
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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