Contacts of the strand formed by residues 2 - 13 (chain S) in PDB entry 2JA7
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 PHE 2 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48P ILE 3.6 0.7 - - - +
49P ALA* 3.8 0.3 - - - -
50P LEU* 2.9 49.3 + - + +
52P LEU* 3.7 30.5 - - + -
55P ALA* 4.0 15.7 - - + -
59P ILE* 5.2 0.4 - - + -
144P THR* 3.8 29.8 - - + -
147P TYR* 4.5 9.9 - + - -
148P LEU* 3.9 12.3 - - + -
1S MET* 1.3 87.1 + - + +
3S PHE* 1.3 64.3 + - - +
46S LEU* 4.0 7.6 - - + -
77S VAL* 4.3 15.9 - - + -
78S VAL 3.4 3.8 - - - -
79S PHE* 3.7 33.9 - + + -
103S VAL* 6.2 0.7 - - + -
104S GLY* 5.7 0.2 - - - -
105S PRO* 4.7 6.5 - - + -
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Residues in contact with PHE 3 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29P LEU* 3.6 30.3 - - + -
33P PHE* 3.9 10.5 - + + -
47P LEU* 3.0 39.3 - - + -
48P ILE 3.3 7.0 - - - +
49P ALA* 5.4 3.1 - - + -
50P LEU* 4.9 1.5 - - - +
175P PHE* 4.4 7.6 - + + -
1S MET* 2.5 49.4 - - + -
2S PHE* 1.3 74.2 - - - +
4S ILE* 1.3 66.3 + - - +
5S LYS* 3.9 1.6 - - + +
77S VAL* 3.2 8.7 - - - +
78S VAL* 2.5 50.0 + - + +
80S LYS* 2.7 40.2 - - + +
82S PHE* 4.1 1.6 - + - -
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Residues in contact with ILE 4 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P GLN* 4.3 6.6 + - - -
47P LEU* 6.4 0.2 - - - -
48P ILE* 3.3 44.7 + - + +
50P LEU* 3.8 25.1 - - + -
58P VAL* 4.1 11.2 - - + -
3S PHE* 1.3 75.2 - - - +
5S LYS* 1.3 59.0 + - - +
6S ASP* 5.3 1.0 - - - +
49S LEU* 3.9 16.8 - - + -
75S ARG* 3.9 34.6 + - + +
76S ALA 3.1 9.9 - - - +
77S VAL* 3.4 23.1 - - + -
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Residues in contact with LYS 5 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7P THR* 3.4 21.1 - - - +
8P PHE* 6.3 1.3 - - - -
32P GLU* 3.2 34.5 + - - +
33P PHE* 4.4 15.0 - - + +
37P GLN* 2.4 54.0 + - - +
38P ILE 5.1 1.7 + - - +
47P LEU* 5.6 0.2 - - + -
3S PHE* 5.2 1.8 - - + -
4S ILE* 1.3 75.6 - - - +
6S ASP* 1.3 67.2 + - - +
7S LEU* 3.8 23.9 + - + +
42S PHE* 4.8 4.5 - - + -
75S ARG* 3.7 3.6 - - - +
76S ALA 3.3 28.6 + - - +
78S VAL* 3.7 20.4 - - + +
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Residues in contact with ASP 6 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7P THR* 4.0 4.3 + - - -
8P PHE* 3.8 21.9 + - + +
37P GLN* 3.9 12.0 + - - +
38P ILE 3.9 12.7 - - - +
39P ASN* 3.6 25.5 - - - +
40P HIS* 4.4 3.5 + - - +
45P GLU* 4.1 2.6 - - - +
4S ILE 5.3 0.8 - - - +
5S LYS* 1.3 79.6 - - + +
7S LEU* 1.3 64.8 + - - +
73S LYS* 3.7 23.3 + - - +
74S TYR 3.9 2.2 - - - -
75S ARG* 3.0 40.1 + - - +
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Residues in contact with LEU 7 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5P THR* 3.8 9.2 - - + +
6P SER 3.7 7.4 - - - +
7P THR* 4.5 1.1 - - - +
8P PHE 5.5 0.7 - - - -
5S LYS* 3.8 23.0 + - + +
6S ASP* 1.3 79.4 - - - +
8S SER* 1.3 61.8 + - - +
42S PHE* 3.3 40.4 - - + -
45S ILE* 3.2 29.6 - - + -
73S LYS* 2.9 12.7 - - - -
74S TYR* 2.7 61.1 + - + +
76S ALA* 4.9 5.2 - - + +
78S VAL* 5.2 3.1 - - + -
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Residues in contact with SER 8 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5P THR* 3.1 29.5 + - - -
6P SER* 2.9 31.9 + - - -
8P PHE* 5.0 6.0 + - - -
7S LEU* 1.3 76.5 - - - +
9S LEU* 1.3 60.2 + - - +
71S ASN* 3.5 19.0 + - - -
72S VAL 3.3 9.2 - - - -
73S LYS* 3.9 15.3 - - - -
74S TYR* 3.9 2.9 - - - -
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Residues in contact with LEU 9 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4P SER 3.6 29.2 - - - +
5P THR* 4.3 7.6 - - - +
6P SER* 5.3 1.1 - - - +
8S SER* 1.3 76.9 - - - +
10S ASN* 1.3 90.7 + - - +
11S ILE* 4.1 11.9 - - + -
30S LEU* 3.8 33.9 - - + +
33S GLU* 4.7 19.5 - - + +
34S VAL* 4.0 17.0 - - + -
70S PHE 3.6 0.3 - - - +
71S ASN* 3.5 2.9 - - - -
72S VAL* 2.8 34.9 + - - +
74S TYR* 5.0 2.0 - - + -
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Residues in contact with ASN 10 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M ARG* 5.7 7.5 - - - +
6P SER* 6.0 0.4 + - - -
9S LEU* 1.3 88.8 - - + +
11S ILE* 1.3 62.7 + - - +
12S THR* 4.2 1.8 + - - -
33S GLU* 5.7 0.9 - - - +
69S GLU* 4.4 26.8 + - + +
70S PHE 3.4 3.2 - - - +
71S ASN* 3.0 44.0 + - - +
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Residues in contact with ILE 11 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9S LEU* 4.2 13.5 - - + -
10S ASN* 1.3 75.8 - - - +
12S THR* 1.3 72.1 + - - +
13S LEU* 3.7 1.9 + - + -
26S LEU* 4.2 28.0 - - + +
29S LYS* 4.4 26.7 - - + -
30S LEU* 4.1 31.9 - - + +
33S GLU* 5.4 6.5 - - - +
68S ALA 3.6 1.0 - - - +
69S GLU* 3.3 4.0 - - - -
70S PHE* 3.0 33.8 + - + +
72S VAL* 3.6 29.6 - - + -
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Residues in contact with THR 12 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10S ASN 4.2 1.8 + - - -
11S ILE* 1.3 78.7 - - - +
13S LEU* 1.3 60.0 + - - +
14S HIS 3.9 2.1 + - - -
29S LYS* 5.5 4.3 + - - -
62S LEU* 4.4 12.8 - - + +
67S SER* 3.7 26.9 - - - +
68S ALA 3.2 6.3 - - - +
69S GLU* 3.9 21.0 + - - +
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Residues in contact with LEU 13 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11S ILE* 3.7 2.3 + - + -
12S THR* 1.3 72.5 - - - +
14S HIS* 1.3 86.4 + - - +
17S PHE* 3.2 42.0 - - + +
18S PHE* 3.7 4.1 - - + -
22S MET* 3.4 39.9 - - + +
25S TYR* 5.1 6.3 - - + -
26S LEU* 3.9 23.3 - - + -
67S SER* 2.9 5.3 - - - -
68S ALA 2.8 35.4 + - - -
70S PHE* 3.8 20.9 - - + -
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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