Contacts of the strand formed by residues 56 - 61 (chain A) in PDB entry 1QA7
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 GLU 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A VAL* 3.6 4.9 - - - -
19A GLY 2.9 32.8 + - - +
21A LYS* 3.5 51.8 + - + +
54A MET 5.0 1.8 - - - +
55A MET* 1.3 80.4 - - - +
57A PHE* 1.3 62.0 + - - +
58A TYR* 3.8 15.0 - - + +
67A SER* 3.2 21.6 + - - -
68A ILE* 3.6 4.0 + - - -
69A SER* 3.7 32.1 + - - -
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Residues in contact with PHE 57 (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 PHE* 3.4 17.7 - + + -
17A GLY 3.6 1.1 - - - -
18A VAL* 3.6 10.1 - - + -
46A TYR* 3.4 42.4 - + + -
52A TYR* 5.2 0.9 - + - -
55A MET* 3.6 21.1 - - + -
56A GLU* 1.3 76.3 - - - +
58A TYR* 1.3 61.0 + - - +
59A PHE* 3.5 18.5 - - + -
67A SER* 3.2 23.2 - - - -
68A ILE* 2.9 17.3 + - + +
70A ALA* 4.0 15.3 - - + -
73A VAL* 4.0 27.1 - - + -
75A ILE* 5.0 3.4 - - + -
88A MET* 3.5 32.1 - - + -
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Residues in contact with TYR 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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16A PHE* 3.3 8.1 - - - -
17A GLY 2.6 35.2 + - - +
18A VAL 4.0 0.7 - - - -
19A GLY 3.5 36.6 - - - -
20A GLU 3.1 17.6 + - - -
21A LYS* 3.2 23.8 + - - +
23A GLY 5.1 0.5 + - - -
25A VAL* 3.3 48.2 - - + -
27A TRP* 3.9 10.1 - - + -
56A GLU* 3.8 12.2 + - + +
57A PHE* 1.3 72.1 - - - +
59A PHE* 1.3 66.3 + - - +
65A TYR* 4.3 15.7 - + + -
66A TYR 3.5 4.9 - - - -
67A SER* 3.6 22.7 - - - -
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Residues in contact with PHE 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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14A VAL* 4.1 12.1 - - + -
15A GLN 3.4 5.4 - - - -
16A PHE* 3.4 27.4 - + - -
27A TRP* 4.4 0.9 - - - -
31A ALA* 4.4 0.9 - - + -
39A LEU* 3.9 26.0 - - + -
41A VAL* 4.5 6.5 - - + -
57A PHE* 3.5 25.1 - - + -
58A TYR* 1.3 76.2 - - - +
60A ASN* 1.3 57.4 + - - +
61A ARG 3.4 2.4 + - - -
64A THR 3.4 2.4 - - - +
65A TYR* 4.3 2.5 - - - -
66A TYR* 2.8 44.4 + - - +
68A ILE* 4.1 7.2 - - + -
88A MET* 3.7 24.2 - - - -
90A VAL* 3.7 35.2 - - + -
93A ILE* 3.8 20.0 - - + -
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Residues in contact with ASN 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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13A LEU 4.9 0.2 - - - +
14A VAL* 3.1 22.3 - - - +
15A GLN* 3.0 38.2 + - + +
27A TRP* 3.7 21.4 - - + -
59A PHE* 1.3 69.7 - - - +
61A ARG* 1.3 58.5 + - - +
62A GLY 3.9 1.3 + - - -
63A GLY* 3.0 32.1 + - - +
64A THR 3.3 7.1 + - - +
65A TYR* 3.6 17.8 + - + -
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Residues in contact with ARG 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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11A LYS 3.0 26.7 + - - -
12A ASN* 4.3 2.2 + - - +
14A VAL* 3.8 13.8 - - + +
59A PHE 3.4 0.6 + - - -
60A ASN* 1.3 72.9 - - - +
62A GLY* 1.3 63.4 + - - +
64A THR* 3.0 10.7 + - - -
66A TYR* 3.5 27.8 + - + -
93A ILE* 3.7 17.9 - - + -
94A PRO* 2.4 57.3 + - + +
95A LYS 2.8 22.0 + - - -
96A PHE* 3.1 32.0 - - - +
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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