Contacts of the strand formed by residues 25 - 32 (chain A) in PDB entry 1J71
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 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A VAL* 3.3 1.8 - - - -
20A VAL 2.9 36.7 + - - +
23A ASN* 3.0 34.0 + - - +
24A GLN* 1.3 70.4 - - - +
26A LYS* 1.3 60.1 + - - +
27A GLN* 3.2 18.5 - - - +
64A THR 3.7 5.6 - - - +
65A PHE* 3.5 22.5 - - + -
66A ASP* 2.8 38.3 + - - +
69A SER* 3.0 21.7 + - - -
70A SER* 4.3 2.4 - - - -
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Residues in contact with LYS 26 (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 ASP* 6.5 1.1 - - + -
18A ILE 3.4 6.5 - - - +
19A VAL* 4.0 13.9 - - + -
24A GLN* 3.2 13.5 + - - +
25A GLN* 1.3 71.7 - - - +
27A GLN* 1.3 69.9 + - - +
63A GLY* 3.6 14.0 - - - -
64A THR 4.3 1.4 + - - +
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Residues in contact with GLN 27 (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 ASP* 3.4 4.3 - - - +
18A ILE* 2.8 43.0 + - + +
20A VAL* 4.1 19.2 - - + +
25A GLN* 3.2 26.3 - - - +
26A LYS* 1.3 78.3 - - - +
28A THR* 1.3 61.0 + - - +
29A VAL* 4.0 12.3 - - + -
40A VAL* 4.2 15.8 - - + +
41A VAL 4.7 1.6 + - - +
62A GLU 3.8 4.9 - - - +
63A GLY 3.3 6.7 + - - -
64A THR* 2.9 48.2 - - - +
65A PHE* 3.8 10.8 + - - +
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Residues in contact with THR 28 (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 ILE* 5.2 7.9 - - + -
10A GLU* 3.5 23.8 - - - +
15A ALA* 3.6 14.4 - - + -
16A ALA 3.4 6.7 - - - +
17A ASP* 2.7 23.3 + - - +
27A GLN* 1.3 72.6 - - - +
29A VAL* 1.3 63.4 + - - +
62A GLU* 3.1 40.9 + - - +
121A GLN* 3.0 18.5 + - - +
122A GLY 4.5 1.2 + - - -
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Residues in contact with VAL 29 (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 ALA* 3.0 6.1 - - - +
16A ALA* 2.8 35.2 + - - +
18A ILE* 4.0 35.7 - - + -
27A GLN* 4.3 10.5 - - + -
28A THR* 1.3 77.2 - - - +
30A VAL* 1.3 62.3 + - - +
31A ILE* 3.6 3.2 + - + +
38A LEU* 4.7 1.6 - - + -
39A TRP 4.4 5.6 - - - +
40A VAL* 4.6 4.3 - - + -
121A GLN* 4.2 0.7 - - - +
122A GLY* 3.3 30.3 - - - +
123A ILE 4.0 3.6 - - - +
124A MET* 4.0 24.0 - - + +
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Residues in contact with VAL 30 (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 GLU* 4.2 2.5 - - - +
13A SER* 3.6 31.9 - - - +
14A TYR 3.4 12.8 - - - +
15A ALA* 4.0 0.4 - - + +
29A VAL* 1.3 71.7 - - - +
31A ILE* 1.3 73.1 + - - +
32A ASP* 3.4 8.2 + - + +
120A ASP* 5.7 0.9 - - - +
121A GLN* 3.7 23.1 - - + +
122A GLY 3.0 5.5 + - - -
123A ILE* 3.3 29.3 - - + +
124A MET* 2.7 31.2 + - - -
219A SER 5.3 0.4 - - - +
220A GLY* 4.9 9.4 - - - -
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Residues in contact with ILE 31 (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 THR* 5.8 0.7 - - + -
7A LEU* 3.4 30.5 - - + -
14A TYR* 2.9 17.2 + - + +
16A ALA* 3.8 26.7 - - + +
29A VAL* 4.5 2.5 - - + +
30A VAL* 1.3 76.6 - - - +
32A ASP* 1.3 60.2 + - - +
33A THR* 5.4 0.7 - - + -
124A MET* 3.9 31.4 - - + +
126A ILE* 3.7 25.8 - - + -
158A LEU* 5.1 7.0 - - + -
170A ILE* 3.8 19.5 - - + -
172A PHE* 5.3 3.6 - - + -
219A SER* 2.8 21.7 + - - +
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Residues in contact with ASP 32 (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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30A VAL* 4.4 5.8 - - + +
31A ILE* 1.3 75.5 - - - +
33A THR* 1.3 59.0 + - - +
34A GLY* 2.8 20.9 + - - -
35A SER* 2.6 35.4 + - - +
84A TYR* 4.2 8.8 - - - -
123A ILE* 3.7 25.0 - - + +
124A MET 3.1 10.4 + - - +
126A ILE* 3.0 27.0 + - - -
218A ASP* 2.9 16.2 - - - +
219A SER* 3.4 1.1 - - - -
220A GLY* 3.1 12.6 + - - -
336B THR 5.2 2.4 + - - -
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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