Contacts of the strand formed by residues 4 - 12 (chain A) in PDB entry 2A4X
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 4 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A SER 4.9 2.0 + - - +
3A ALA* 1.3 77.9 - - - +
5A ILE* 1.3 68.4 + - - +
6A SER* 3.2 1.9 + - - +
244B ASP* 3.2 38.0 + - - +
277B PHE* 4.1 5.6 - - - -
278B GLU* 2.8 46.6 + - + +
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Residues in contact with ILE 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ARG* 1.3 76.2 - - - +
6A SER* 1.3 61.2 + - - +
7A LEU 4.2 5.4 - - - +
8A PHE* 3.6 31.4 - - + -
47A ILE* 3.8 16.8 - - + +
227B VAL* 4.7 5.2 - - + -
243B LEU* 3.8 32.4 - - + +
244B ASP* 4.6 6.3 + - - +
249B LEU* 3.8 29.4 - - + -
275B ILE* 4.1 14.1 - - + -
276B ALA 3.6 6.5 - - - +
277B PHE* 3.5 34.7 - - + +
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Residues in contact with SER 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ARG* 3.2 3.9 + - - -
5A ILE* 1.3 74.6 - - - +
7A LEU* 1.3 60.8 + - - +
46A GLY 4.4 1.0 - - - +
47A ILE* 3.5 10.9 - - - +
48A ARG* 2.9 47.9 + - - -
276B ALA 2.9 6.9 + - - -
278B GLU* 4.0 19.3 + - - -
326B PHE* 3.7 23.4 - - - -
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Residues in contact with LEU 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ILE* 3.8 3.5 - - - +
6A SER* 1.3 83.8 - - - +
8A PHE* 1.3 82.5 + - - +
9A ALA* 3.8 14.8 - - + +
38A HIS* 5.3 2.2 - - + -
40A GLU* 4.3 6.3 - - - +
47A ILE* 4.3 1.8 - - - -
48A ARG* 3.3 50.3 - - + +
50A ALA* 4.1 17.5 - - + -
274B ALA 5.8 0.2 - - - -
275B ILE* 3.7 1.9 - - - -
276B ALA* 2.8 53.3 + - + +
324B ASP* 5.5 1.8 - - - +
326B PHE* 5.7 1.3 - - + -
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Residues in contact with PHE 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ILE* 3.6 25.4 - - + -
7A LEU* 1.3 77.9 - - - +
9A ALA* 1.3 59.8 + - - +
47A ILE* 3.7 22.2 - - + -
48A ARG 3.0 6.8 + - - +
49A LEU* 3.4 6.3 - - + +
50A ALA 2.8 24.1 + - - -
208B PHE* 3.4 63.3 - + + -
243B LEU* 3.7 21.3 - - + -
247B ILE* 4.6 1.3 - - + -
248B ARG 5.3 0.2 - - - -
249B LEU* 4.3 10.1 - - + -
273B PHE* 3.6 24.9 - + + -
274B ALA 3.4 3.1 - - - -
275B ILE* 3.9 25.1 - - + -
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Residues in contact with ALA 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 3.8 15.0 - - + +
8A PHE* 1.3 75.6 - - - +
10A VAL* 1.3 65.2 + - - +
11A VAL* 5.9 0.7 - - - -
50A ALA* 3.3 16.4 - - + +
52A ASP* 4.1 15.0 - - - +
271B HIS* 5.7 0.2 - - - -
273B PHE* 3.2 9.0 - - - -
274B ALA* 2.8 44.9 + - + +
324B ASP* 5.6 1.6 - - - +
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Residues in contact with VAL 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ALA* 1.3 81.7 - - - +
11A VAL* 1.3 63.2 + - - +
12A VAL* 3.8 6.9 + - + -
18A SER* 5.0 0.7 - - - +
22A TYR* 5.2 5.8 - - + +
49A LEU* 4.7 7.4 - - + -
50A ALA 2.9 12.1 + - - +
51A TRP* 3.3 35.7 - - + +
52A ASP* 3.1 24.2 + - - +
73A PHE* 4.2 15.5 - - + -
75A ILE* 4.1 24.7 - - + -
117A ASP* 5.5 0.7 - - - +
121A ASN* 4.6 11.9 - - - +
272B ARG 3.2 11.0 - - - +
273B PHE* 4.4 2.9 - - + -
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Residues in contact with VAL 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ALA 5.8 0.4 - - - +
10A VAL* 1.3 75.8 - - - +
12A VAL* 1.3 61.7 + - - +
52A ASP* 3.3 11.7 - - + +
54A VAL* 3.9 18.8 - - + -
57A VAL* 3.8 22.9 - - + -
64A TRP* 3.8 20.9 - - + +
119A ASP* 4.0 3.6 - - - +
121A ASN* 4.9 1.0 + - - -
271B HIS* 3.5 47.6 - - + +
272B ARG* 2.7 40.0 + - - +
273B PHE* 5.6 0.2 - - - -
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Residues in contact with VAL 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A VAL* 4.1 9.2 - - + +
11A VAL* 1.3 79.2 - - - +
13A GLU* 1.3 62.8 + - - +
14A ASP 4.0 2.0 - - - +
15A MET* 4.0 34.3 - - + +
18A SER* 3.3 30.1 - - - +
51A TRP* 3.8 15.0 - - + -
52A ASP 2.9 24.3 + - - +
53A THR* 3.3 5.8 - - - -
54A VAL* 3.2 24.6 + - - -
117A ASP* 6.0 0.7 - - - +
119A ASP* 3.5 13.7 - - - +
121A ASN* 6.1 0.7 - - - +
272B ARG* 4.5 0.2 - - - -
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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