Contacts of the strand formed by residues 30 - 37 (chain A) in PDB entry 1OBA
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 ASN 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A VAL* 4.3 15.1 - - - +
6A ASP* 4.9 7.1 + - - +
7A LEU 3.1 20.5 + - - +
8A PHE* 3.5 11.1 - - + -
9A VAL* 3.0 24.0 + - - +
23A LEU* 4.6 0.2 - - - +
28A THR* 3.0 21.2 + - - +
29A THR* 1.3 78.7 + - - +
31A THR* 1.3 62.8 + - - +
54A ASN* 3.0 28.1 + - - -
56A ILE* 4.0 14.1 - - + +
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Residues in contact with THR 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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8A PHE* 4.7 0.4 - - - +
9A VAL* 3.0 13.9 - - + +
11A VAL* 5.3 2.7 - - + -
19A ILE* 4.6 7.0 - - + -
23A LEU* 3.6 21.1 - - + -
29A THR 3.3 10.3 - - - +
30A ASN* 1.3 81.6 - - - +
32A ILE* 1.3 64.8 + - - +
33A ILE* 3.9 14.7 - - - +
53A SER* 2.8 30.1 + - - +
54A ASN 3.2 4.6 + - - -
55A PRO* 3.1 14.4 - - - +
56A ILE* 2.8 29.7 + - - +
57A GLY 3.7 0.2 + - - -
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Residues in contact with ILE 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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8A PHE* 3.6 23.8 - - + -
9A VAL 2.9 5.5 + - - -
10A ASP* 3.0 32.5 - - + +
11A VAL 3.1 5.4 + - - +
31A THR* 1.3 76.0 - - - +
33A ILE* 1.3 61.9 + - - +
56A ILE* 3.6 17.0 - - + -
57A GLY* 3.2 21.8 - - - +
58A PHE 3.9 13.2 - - - +
59A TYR* 4.1 9.3 - - + +
90A VAL* 4.3 4.5 - - + -
149A TRP* 4.0 19.7 - - + -
173A TRP* 3.4 37.7 - - + -
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Residues in contact with ILE 33 (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 VAL* 3.6 15.7 - - + -
31A THR* 3.9 18.6 - - - +
32A ILE* 1.3 77.0 - - - +
34A LYS* 1.3 76.1 + - - +
35A ILE 3.4 0.9 + - - -
43A ASN* 3.8 2.7 - - - +
46A LEU* 3.9 11.0 - - + -
49A GLN* 3.2 60.3 - - + +
50A VAL* 3.6 18.8 - - + +
53A SER* 4.2 0.2 - - - +
55A PRO* 4.5 4.3 - - + -
57A GLY 3.3 6.5 + - - -
58A PHE* 3.2 21.5 - - + +
59A TYR* 3.0 21.5 + - - -
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Residues in contact with LYS 34 (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 VAL 2.9 13.9 + - - +
12A SER* 3.8 18.7 - - - -
13A SER 5.3 0.4 - - - +
33A ILE* 1.3 74.4 - - - +
35A ILE* 1.3 61.9 + - - +
36A SER 3.9 18.8 - - - +
37A GLU* 2.9 28.0 + - - -
41A TYR* 3.7 22.0 + - + -
43A ASN* 2.8 35.6 + - + +
46A LEU* 4.2 1.9 - - - +
59A TYR* 3.3 47.0 - - + +
61A PHE* 4.0 15.8 - - - +
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Residues in contact with ILE 35 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A LYS* 1.3 75.6 - - - +
36A SER* 1.3 70.9 + - - +
42A LEU* 3.4 8.6 - - + +
43A ASN* 2.8 28.6 + - - +
46A LEU* 4.0 17.7 - - + +
58A PHE* 3.4 45.3 - - + -
59A TYR 3.1 6.5 + - - -
78A PHE* 3.7 18.8 - - + -
81A ASN* 3.7 29.2 - - + +
82A VAL* 3.6 13.5 - - + -
83A PRO* 3.5 21.3 - - + -
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Residues in contact with SER 36 (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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34A LYS* 3.9 8.6 - - - +
35A ILE* 1.3 86.2 - - - +
37A GLU* 1.3 61.8 + - - +
41A TYR* 3.2 14.1 - - - -
42A LEU* 4.0 2.7 - - - -
59A TYR 4.0 2.0 + - - +
60A HIS* 2.9 25.7 + - - -
61A PHE 2.9 23.0 + - - -
77A PHE* 3.5 20.4 - - - -
78A PHE* 3.4 24.6 - - - -
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Residues in contact with GLU 37 (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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34A LYS* 2.9 25.7 + - - -
36A SER* 1.3 76.3 - - - +
38A SER* 1.3 78.2 + - - +
39A THR* 4.1 0.2 - - - -
40A THR 3.6 0.3 + - - -
41A TYR* 3.1 46.1 + - + +
60A HIS* 3.8 0.7 - - - -
61A PHE* 3.4 27.0 - - + +
63A ARG* 3.2 38.1 + - + +
77A PHE* 4.2 0.3 - - - -
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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