Contacts of the strand formed by residues 9 - 21 (chain A) in PDB entry 3JTC
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 GLN 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A GLY 3.2 15.9 + - - +
8A LEU* 1.3 69.7 - - - +
10A ARG* 1.4 63.2 + - - +
102A GLU* 3.5 0.2 - - - -
103A LEU* 2.8 53.9 + - + +
173A VAL* 3.6 17.9 - - + +
174A GLN* 4.6 4.5 - - - +
177A ILE* 2.9 42.8 - - + +
178A SER 3.3 21.0 + - - +
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Residues in contact with ARG 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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8A LEU* 3.8 18.0 + - + +
9A GLN* 1.4 79.3 - - - +
11A LEU* 1.3 60.2 + - - +
12A HIS* 3.3 43.2 + - + +
32A SER* 5.9 0.6 - - - -
33A LEU* 3.4 10.0 - - - +
34A GLY* 3.1 61.9 + - - +
35A GLY* 4.6 3.6 - - - +
101A CYS 3.2 13.9 - - - +
102A GLU* 3.9 16.2 - - + -
173A VAL* 3.9 8.2 - - - +
177A ILE* 4.5 2.4 - - - +
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Residues in contact with LEU 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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10A ARG* 1.3 73.9 - - - +
12A HIS* 1.3 69.5 + - - +
13A MET* 3.9 12.8 - - + -
31A ALA* 4.3 12.3 - - + -
32A SER 3.4 19.3 - - - +
33A LEU* 3.9 16.2 - - + -
38A THR* 4.6 2.7 - - - +
39A HIS* 5.3 0.4 - - - +
100A GLY* 3.1 5.0 - - - -
101A CYS 3.0 31.4 + - - -
169A CYS* 3.8 10.8 - - - -
172A TYR* 4.0 15.5 - - + -
173A VAL* 3.6 18.6 - - + +
606A PTY 3.7 46.4 - - + -
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Residues in contact with HIS 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 ARG* 3.3 43.0 + - + +
11A LEU* 1.3 85.9 - - - +
13A MET* 1.3 62.6 + - - +
31A ALA* 3.1 6.2 - - - +
32A SER* 2.9 39.6 + - - +
98A PHE* 3.8 25.4 - + + -
99A LEU 3.5 2.7 - - - -
102A GLU* 2.8 29.0 + - + -
113A PHE* 3.7 25.3 - + - -
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Residues in contact with MET 13 (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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11A LEU* 3.9 24.5 - - + -
12A HIS* 1.3 78.3 - - - +
14A LEU* 1.4 60.3 + - - +
30A ASN 3.4 4.3 - - - -
31A ALA* 3.8 15.7 - - + -
98A PHE* 3.5 6.3 - - - -
99A LEU* 2.8 63.8 + - + +
100A GLY* 4.1 12.3 - - - -
164A PHE* 3.9 28.9 - - + -
165A LEU* 5.1 0.7 - - + -
169A CYS* 4.0 16.6 - - - -
606A PTY 3.9 37.5 - - + -
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Residues in contact with LEU 14 (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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13A MET* 1.4 75.1 - - - +
15A GLN* 1.3 61.1 + - - +
16A ILE* 4.0 3.6 - - + -
29A GLY* 2.9 22.7 - - - -
30A ASN* 2.8 24.3 + - - +
96A ARG* 3.4 47.1 - - + +
97A CYS 3.4 15.5 - - - +
98A PHE* 4.0 20.6 - - + -
603A NAG 3.0 41.5 - - - +
606A PTY 3.6 6.1 - - - +
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Residues in contact with GLN 15 (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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14A LEU* 1.3 75.0 - - - +
16A ILE* 1.4 66.5 + - - +
17A SER* 3.1 23.1 + - - +
27A TYR* 3.7 7.0 - - + -
28A GLN 3.7 3.8 - - - +
29A GLY* 4.1 1.6 - - - -
41A LEU* 5.4 3.8 - - + -
72A TYR* 2.7 31.8 + - - -
73A LEU* 3.6 22.1 - - + +
76A PHE* 3.6 24.9 - - - -
95A ILE 3.7 1.0 - - - +
96A ARG* 3.4 2.8 - - - -
97A CYS* 2.8 55.1 + - + +
99A LEU* 5.3 0.2 - - - +
606A PTY 4.2 18.2 - - + +
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Residues in contact with ILE 16 (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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14A LEU* 4.0 4.5 - - + -
15A GLN* 1.4 76.1 - - - +
17A SER* 1.3 64.4 + - - +
18A TYR* 3.6 35.3 - - + +
26A TRP 3.7 0.7 - - - +
27A TYR* 3.4 4.3 - - - +
28A GLN* 2.7 35.2 + - + +
94A THR* 3.6 19.3 - - + -
95A ILE 3.4 3.6 - - - +
96A ARG* 3.3 55.0 - - + +
603A NAG 2.0 34.1 - - - +
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Residues in contact with SER 17 (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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15A GLN* 3.1 30.1 + - - +
16A ILE* 1.3 75.0 - - - +
18A TYR* 1.4 62.9 + - - +
19A PHE* 3.6 24.9 + - - -
25A VAL* 3.7 8.5 - - - -
26A TRP 3.5 5.2 - - - -
27A TYR* 3.2 5.6 - - - -
76A PHE* 3.3 13.9 - - - -
94A THR* 3.3 4.4 - - - -
95A ILE* 2.8 38.7 + - - -
97A CYS* 5.8 0.2 - - - -
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Residues in contact with TYR 18 (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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16A ILE* 3.6 24.4 - - + +
17A SER* 1.4 72.4 - - - +
19A PHE* 1.3 61.7 + - - +
20A ARG* 3.7 4.8 + - + +
25A VAL* 3.2 4.2 - - - +
26A TRP* 2.8 61.8 + + + +
28A GLN* 3.4 38.2 + - + -
93A LEU 3.8 4.5 - - - -
94A THR* 3.7 26.5 - - + +
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Residues in contact with PHE 19 (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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17A SER* 3.6 29.8 - - - -
18A TYR* 1.3 72.1 - - - +
20A ARG* 1.3 63.2 + - - +
21A ASP 3.2 12.6 - - - +
22A PRO 4.5 2.2 - - - -
24A HIS 3.6 3.6 - - - -
25A VAL* 3.8 18.8 - - + -
76A PHE* 3.7 19.1 - + - -
77A HIS* 3.6 31.2 - + - -
80A VAL* 3.7 24.2 - - + -
91A PHE* 3.7 18.9 - + + -
92A PRO* 3.2 5.9 - - - +
93A LEU* 2.9 48.0 + - + +
95A ILE* 3.7 17.7 - - + -
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Residues in contact with ARG 20 (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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18A TYR* 3.7 5.0 + - + +
19A PHE* 1.3 72.0 - - - +
21A ASP* 1.3 70.6 + - - +
24A HIS* 3.3 18.8 + - + +
25A VAL* 6.2 0.4 - - - -
26A TRP 6.3 0.2 - - - +
91A PHE* 3.7 11.7 - - - +
92A PRO* 3.9 14.9 - - - +
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Residues in contact with ASP 21 (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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19A PHE* 3.2 6.3 - - - +
20A ARG* 1.3 84.9 - - - +
22A PRO* 1.3 75.7 - - + +
23A TYR* 3.0 26.4 + - + +
24A HIS* 2.9 46.1 + - - +
91A PHE* 3.5 22.8 - - + -
106B GLU* 5.8 3.5 - - - +
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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