Contacts of the strand formed by residues 3 - 13 (chain J) in PDB entry 1S7X
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 HIS 3 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1J GLY 3.3 19.7 + - - -
2J PRO* 1.3 78.7 + - + +
4J SER* 1.3 64.4 + - - +
29J ASP* 3.3 18.4 + - - +
102J ASP* 3.6 2.9 - - - +
103J LEU* 2.9 38.9 + - + +
104J GLY 4.8 2.2 - - - -
107J TRP* 3.9 28.7 + + - -
168J LEU* 4.6 2.2 - - + -
172J LEU* 3.2 47.7 - - + +
176J ASN* 6.3 0.7 - - - -
179J LEU 5.8 0.7 - - - -
180J LEU* 4.2 24.2 - - + +
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Residues in contact with SER 4 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3J HIS* 1.3 78.9 - - - +
5J MET* 1.3 62.5 + - - +
6J ARG* 3.9 7.0 + - - +
28J VAL* 3.5 3.6 - - - -
29J ASP* 2.9 35.6 + - - -
30J ASN* 3.8 21.5 + - - -
101J CYS 3.3 6.7 - - - -
102J ASP* 3.2 24.0 - - - -
168J LEU* 3.6 12.2 - - - +
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Residues in contact with MET 5 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J SER* 1.3 74.5 - - - +
6J ARG* 1.3 75.1 + - - +
7J TYR* 4.1 15.7 - - + -
27J TYR 3.2 13.5 - - - +
28J VAL* 4.4 2.0 - - + -
33J PHE* 4.2 4.0 - - + -
100J GLY* 3.2 2.9 - - - -
101J CYS* 3.0 33.3 + - - -
159J TYR* 4.4 1.8 - - - +
164J CYS* 3.2 44.9 - - - +
167J TRP* 4.6 1.6 - - + -
168J LEU* 3.9 23.5 - - + +
171J TYR* 3.6 30.7 - - - -
1L LYS 3.9 23.6 - - - +
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Residues in contact with ARG 6 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J SER* 3.9 10.4 - - - +
5J MET* 1.3 88.7 + - - +
7J TYR* 1.3 65.4 + - - +
8J PHE* 3.6 30.1 - - + -
26J GLY* 3.4 2.3 - - - -
27J TYR* 2.8 45.4 + - + +
30J ASN* 5.0 10.8 - - - +
98J MET* 5.6 2.8 - - - +
99J SER 3.3 20.0 - - - +
100J GLY* 4.3 0.9 - - - +
101J CYS 3.2 14.8 + - - +
102J ASP* 3.0 27.3 + - - -
113J TYR* 3.1 44.9 + - - +
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Residues in contact with TYR 7 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J MET* 4.1 17.3 - - + -
6J ARG* 1.3 76.8 - - - +
8J PHE* 1.3 63.6 + - - +
9J GLU* 4.1 13.2 + - - +
24J SER* 3.9 7.9 - - - +
25J VAL 3.4 2.9 - - - -
26J GLY* 3.7 9.4 - - - -
33J PHE* 3.5 18.1 - + - -
34J VAL* 3.8 21.5 - - + +
45J TYR* 3.6 26.5 - + - -
59J TYR* 4.4 2.1 + - - -
63J GLU* 4.2 2.9 + - - -
97J GLN 3.6 1.6 - - - +
98J MET* 3.5 4.5 - - - -
99J SER* 2.8 46.3 + - - +
100J GLY* 6.0 0.2 - - - -
159J TYR* 4.2 7.4 - - - -
171J TYR* 4.3 0.5 + - - -
1L LYS* 2.8 43.1 + - - -
2L ALA* 3.6 24.4 + - + -
3L VAL 5.1 0.9 - - - +
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Residues in contact with PHE 8 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J ARG* 3.6 33.9 - - + -
7J TYR* 1.3 80.6 - - - +
9J GLU* 1.3 61.0 + - - +
23J ILE* 3.8 1.0 - - - +
24J SER* 3.7 1.0 - - - -
25J VAL* 2.9 34.3 + - + +
27J TYR* 3.9 29.8 - + + +
97J GLN 3.3 3.8 - - - -
98J MET* 3.8 26.0 - - + -
56K PHE* 3.2 60.7 - + + +
57K SER* 4.4 4.9 - - - -
58K LYS* 4.7 5.4 - - + -
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Residues in contact with GLU 9 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J TYR* 4.3 12.6 - - + +
8J PHE* 1.3 74.8 - - - +
10J THR* 1.3 64.5 + - - +
22J TYR* 2.5 25.2 + - + +
23J ILE 3.3 4.3 - - - +
24J SER* 3.3 24.2 - - - +
45J TYR* 5.6 0.4 - - - -
70J GLN* 2.8 30.3 + - - +
74J PHE* 3.6 19.2 - - + -
95J LEU 4.7 0.2 - - - -
96J GLN* 3.3 4.9 - - - -
97J GLN* 2.9 51.5 + - + +
99J SER* 4.4 0.9 + - - -
56K PHE* 3.7 2.4 - - - -
2L ALA* 5.5 1.6 - - - +
3L VAL* 4.2 10.3 - - - +
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Residues in contact with THR 10 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J GLU* 1.3 71.9 + - - +
11J ALA* 1.3 64.5 + - - +
12J VAL* 3.4 27.6 - - + -
21J ARG 3.6 1.3 - - - +
22J TYR* 3.3 8.9 - - - -
23J ILE* 2.8 43.6 + - + -
74J PHE* 4.7 0.9 - - - -
94J THR* 4.4 11.4 - - + -
95J LEU 3.6 4.0 - - - -
96J GLN* 3.9 3.0 - - + +
54K MET* 4.6 10.1 - - + -
56K PHE* 3.2 31.0 - - - -
62K PHE* 4.2 12.3 - - + -
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Residues in contact with ALA 11 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J THR* 1.3 75.3 - - - +
12J VAL* 1.3 62.6 + - - +
20J PRO* 4.8 4.5 - - + -
21J ARG 3.2 7.9 - - - +
22J TYR* 4.6 4.9 - - + -
74J PHE* 3.5 37.2 - - + -
78J LEU* 3.7 18.9 - - + +
93J HIS 4.0 0.2 - - - +
94J THR* 3.4 4.2 - - - +
95J LEU* 2.9 33.9 + - + +
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Residues in contact with VAL 12 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J THR* 3.4 23.6 - - + -
11J ALA* 1.3 79.0 - - - +
13J SER* 1.3 70.5 + - - +
14J ARG* 5.4 4.8 - - + +
20J PRO* 3.1 7.8 - - - +
21J ARG* 3.0 38.7 + - + +
78J LEU* 5.1 0.2 - - - -
92J SER* 6.0 1.8 - - - -
93J HIS 3.4 9.4 - - - +
94J THR* 4.3 7.9 - - + +
32K PRO* 5.8 1.6 - - + -
33K PRO* 3.9 28.9 - - + -
34K HIS* 6.0 2.2 - - + +
54K MET* 4.6 9.2 - - + -
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Residues in contact with SER 13 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J VAL* 1.3 79.2 - - - +
14J ARG* 1.3 63.1 + - - +
17J LEU 6.2 0.2 - - - -
19J GLU 5.7 1.1 - - - -
20J PRO* 4.4 17.7 - - - -
78J LEU* 4.9 9.2 - - - +
91J GLY 4.3 2.0 + - - -
92J SER* 3.3 7.7 + - - -
93J HIS* 2.9 59.6 + - - +
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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