Contacts of the strand formed by residues 57 - 67 (chain A) in PDB entry 1QJH
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 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A VAL* 4.8 4.8 - - - +
12A PRO* 3.5 33.7 - - + +
13A ASN* 6.2 0.2 - - - +
45A LEU* 4.1 20.0 - - + +
46A MET 3.3 6.1 - - - +
47A VAL* 3.9 22.9 - - + +
55A ASP* 3.3 10.2 - - - +
56A PRO* 1.3 86.4 - - + +
58A GLY* 1.3 58.4 + - - +
86A ARG* 5.7 2.4 - - - +
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Residues in contact with GLY 58 (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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9A VAL* 3.9 13.2 - - - -
10A LEU 3.3 11.7 - - - -
12A PRO* 3.7 7.2 - - - +
44A GLY 3.7 0.2 - - - +
45A LEU* 3.5 6.7 - - - +
46A MET* 2.8 39.3 + - - +
56A PRO 4.0 0.2 + - - -
57A GLN* 1.3 78.0 - - - +
59A TYR* 1.3 61.7 + - - -
60A PHE* 3.7 0.7 + - - +
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Residues in contact with TYR 59 (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 3.3 1.7 - - - +
9A VAL* 3.2 6.4 - - - -
10A LEU* 2.8 43.4 + - + +
11A ASN 3.4 19.3 - - - -
12A PRO* 3.3 25.7 + - + -
14A LEU* 3.8 20.8 + - + -
15A ASP 5.8 0.2 - - - -
19A LEU* 3.8 42.7 - - + +
42A ILE* 5.0 2.7 - - + -
44A GLY* 3.4 7.4 - - - -
45A LEU* 3.8 39.1 - - + +
58A GLY* 1.3 71.9 - - - -
60A PHE* 1.3 62.3 + - - +
61A LEU* 3.6 2.1 + - + -
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Residues in contact with PHE 60 (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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7A ASN* 3.2 34.8 - - + -
8A ILE 3.5 7.0 - - - -
9A VAL* 4.8 10.3 - - + +
42A ILE* 3.6 2.9 - - - +
43A LEU* 2.7 69.7 + - + +
44A GLY 3.0 11.9 + - - +
46A MET* 3.4 37.7 - - + -
58A GLY 3.7 1.2 + - - +
59A TYR* 1.3 72.9 - - - +
61A LEU* 1.3 76.0 + - - +
62A TRP* 4.3 6.5 - + + -
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Residues in contact with LEU 61 (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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6A VAL 4.5 0.4 - - - -
8A ILE* 2.7 48.2 + - + +
10A LEU* 3.5 34.5 - - + -
19A LEU* 4.3 9.2 - - + -
23A LYS* 4.0 15.7 - - + -
26A ILE* 4.1 10.1 - - + -
40A VAL* 6.5 0.2 - - + -
41A ALA 3.4 1.8 - - - +
42A ILE* 3.3 45.3 - - + -
59A TYR* 4.8 1.6 - - + +
60A PHE* 1.3 80.9 - - - +
62A TRP* 1.3 60.0 + - - +
63A TYR* 3.7 28.0 - - + +
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Residues in contact with TRP 62 (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 GLU* 2.9 51.0 + - + +
6A VAL 3.4 4.7 - - - -
7A ASN* 3.2 27.6 + - - -
39A LYS* 3.7 29.8 - - + -
40A VAL* 3.3 3.0 - - - +
41A ALA* 2.7 59.8 + - + +
43A LEU* 4.1 20.6 - - + -
60A PHE* 4.3 6.3 - + + -
61A LEU* 1.3 75.2 - - - +
63A TYR* 1.3 69.1 + - - +
64A GLN* 3.6 26.5 - - + -
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Residues in contact with TYR 63 (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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4A TYR 3.8 0.2 - - - +
5A GLU* 3.2 4.9 - - - +
6A VAL* 2.7 54.0 + - + +
8A ILE* 4.3 7.2 - - + -
23A LYS* 2.8 33.5 + - + +
26A ILE* 3.4 29.0 - - + +
27A GLN* 3.9 19.5 - - + -
30A LEU* 3.5 26.9 - - + -
37A VAL* 4.5 2.9 - - + -
39A LYS 3.3 5.8 - - - +
40A VAL* 3.3 37.9 - - + -
61A LEU* 3.7 21.9 - - + +
62A TRP* 1.3 81.8 - - - +
64A GLN* 1.3 59.9 + - - +
65A VAL* 4.1 6.5 - - + -
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Residues in contact with GLN 64 (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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3A ARG* 3.4 22.7 - - + +
4A TYR 3.4 9.2 - - - +
5A GLU* 4.4 11.4 - - + +
38A GLU* 2.9 47.8 + - - +
39A LYS* 2.9 56.1 + - + +
62A TRP* 3.6 24.4 - - + -
63A TYR* 1.3 73.2 - - - +
65A VAL* 1.3 66.5 + - - +
93A SER* 5.6 0.4 - - - -
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Residues in contact with VAL 65 (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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3A ARG* 3.1 6.1 - - - +
4A TYR* 2.7 49.8 + - + +
6A VAL* 4.4 8.7 - - + -
30A LEU* 4.2 15.9 - - + -
35A ALA* 4.2 8.5 - - + -
36A ARG 3.3 16.2 - - - +
37A VAL* 3.9 12.6 - - + -
38A GLU* 4.0 7.0 - - - -
63A TYR* 4.2 19.3 - - + -
64A GLN* 1.3 80.6 - - - +
66A GLU* 1.3 60.1 + - - +
67A MET* 4.1 29.6 - - + -
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Residues in contact with GLU 66 (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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1A MET* 3.5 42.7 - - + +
2A ARG* 3.1 13.7 - - - +
3A ARG* 4.6 16.6 + - - +
35A ALA* 3.5 0.2 - - - -
36A ARG* 2.7 45.8 + - + +
38A GLU* 4.2 16.3 + - - +
65A VAL* 1.3 73.1 - - - +
67A MET* 1.3 60.6 + - - +
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Residues in contact with MET 67 (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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1A MET* 3.5 9.0 - - - -
2A ARG 2.8 27.4 + - - +
4A TYR* 3.7 22.1 - - + -
6A VAL* 5.5 2.7 - - - -
30A LEU* 5.2 2.2 - - - -
33A TYR* 3.8 17.5 - - + +
34A GLY 4.0 0.7 - - - -
35A ALA* 3.5 21.5 - - + -
65A VAL* 4.1 15.5 - - + -
66A GLU* 1.3 75.7 - - - +
68A PRO* 1.3 78.4 - - + +
69A GLU 3.5 0.5 + - - -
71A ARG 3.5 34.5 - - - +
72A VAL* 3.8 13.7 - - + +
75A LEU* 4.0 23.3 - - + -
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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