Contacts of the strand formed by residues 74 - 82 (chain A) in PDB entry 6QPA
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 MET 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A LYS* 3.3 3.4 - - - -
15A ILE* 2.9 48.1 + - + +
16A ALA 4.6 2.7 - - - +
17A ASN* 3.6 31.0 - - - +
22A TYR* 3.4 29.6 - - - +
25A MET* 6.0 0.4 - - - -
49A LEU* 4.0 24.0 - - + -
50A GLN* 3.4 22.0 - - - +
68A ARG* 4.8 9.4 - - + +
71A LEU* 3.9 22.9 - - + +
72A ASN* 4.1 0.6 - - - +
73A PRO* 1.3 75.0 - - - +
75A GLY* 1.3 64.9 + - - +
76A MET 3.6 0.2 + - - -
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Residues in contact with GLY 75 (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 ALA 3.5 7.0 - - - -
14A LYS* 4.3 13.2 - - - +
49A LEU* 3.6 5.0 - - - +
50A GLN* 2.8 51.3 + - - +
73A PRO 4.4 0.2 + - - -
74A MET* 1.3 76.2 - - - +
76A MET* 1.3 60.1 + - - +
77A PHE* 4.2 4.5 - - - -
297A MET* 4.6 6.7 - - - -
299A PHE* 4.4 3.1 - - - -
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Residues in contact with MET 76 (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 ASN 3.4 3.6 - - - +
13A ALA* 2.8 42.0 + - + +
15A ILE* 4.0 22.9 - - + -
25A MET* 4.2 12.8 - - + +
47A GLN* 4.2 17.3 - - + +
48A LEU 3.4 9.6 - - - +
49A LEU* 3.8 20.0 - - + -
75A GLY* 1.3 71.2 - - - +
77A PHE* 1.3 63.1 + - - +
78A GLN* 3.9 35.2 - - - +
109A MET* 4.3 23.1 - - + -
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Residues in contact with PHE 77 (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 ILE* 3.9 21.1 - - + -
11A ASN 3.3 3.4 - - - -
12A MET* 3.8 41.5 - - + -
13A ALA 4.6 4.0 - - - -
14A LYS* 5.9 2.0 - - + -
46A GLU 3.5 1.7 - - - +
47A GLN* 3.8 0.2 - - - -
48A LEU* 2.8 55.5 + - + +
75A GLY* 4.8 1.6 - - - -
76A MET* 1.3 88.0 - - - +
78A GLN* 1.3 60.4 + - - +
79A TYR* 4.0 1.1 - - + -
162A ILE* 3.6 31.4 - - + -
254A LEU* 5.0 1.6 - - + -
297A MET* 4.4 20.2 - - + -
299A PHE* 3.8 22.4 - + + -
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Residues in contact with GLN 78 (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 ALA 3.4 2.4 - - - +
10A ILE* 3.5 0.4 - - - -
11A ASN* 2.9 53.7 + - + +
29A GLY* 5.1 10.3 + - - -
32A VAL* 5.4 11.2 - - - +
33A CSS 5.5 11.5 - - - -
45A PHE* 6.4 0.7 - - + -
46A GLU 3.2 5.2 - - - +
47A GLN* 3.4 34.2 - - + +
76A MET* 3.9 25.3 - - - +
77A PHE* 1.3 76.8 - - - +
79A TYR* 1.3 65.3 + - - +
80A THR* 3.6 8.1 + - + +
116A GLU* 5.3 0.2 - - - +
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Residues in contact with TYR 79 (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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8A ILE* 3.8 24.5 - - + -
9A ALA 3.4 4.9 - - - -
10A ILE* 3.8 27.4 - - + -
45A PHE* 3.0 11.0 - - - +
46A GLU* 2.7 57.2 + - + +
48A LEU* 3.5 23.5 - - + +
77A PHE* 4.5 2.5 - - + -
78A GLN* 1.3 75.1 - - - +
80A THR* 1.3 60.6 + - - +
81A VAL* 4.6 3.8 - - + -
162A ILE* 3.3 23.2 - - + +
197A MET* 4.0 13.5 - - + -
199A MET* 3.5 17.7 - - + +
256A HIS* 2.8 39.6 + + - -
308A TRP* 5.0 2.7 - + - -
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Residues in contact with THR 80 (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* 3.5 1.9 - - - -
9A ALA* 2.9 46.7 + - - +
33A CSS 4.3 20.0 - - - -
36A THR* 4.4 7.9 - - + +
42A PHE* 4.1 14.4 - - + -
44A GLY 3.5 3.1 - - - -
78A GLN* 3.6 8.0 + - + +
79A TYR* 1.3 79.5 - - - +
81A VAL* 1.3 60.5 + - - +
82A TRP* 2.8 32.7 + - + -
88A HIS* 3.9 6.3 + - - +
116A GLU* 4.2 4.7 + - - +
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Residues in contact with VAL 81 (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 PRO* 3.7 24.2 - - + -
7A ILE 3.5 6.1 - - - +
8A ILE* 4.2 20.9 - - + -
42A PHE* 3.7 4.0 - - - -
43A LEU* 2.7 32.6 + - + -
44A GLY 2.8 18.8 + - - +
45A PHE* 4.6 0.9 - - - +
79A TYR* 4.6 5.8 - - + -
80A THR* 1.3 78.6 - - - +
82A TRP* 1.3 62.6 + - - +
308A TRP* 3.7 56.3 - - + -
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Residues in contact with TRP 82 (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 PRO* 3.3 5.9 - - - +
7A ILE* 2.8 40.5 + - + +
9A ALA* 4.3 6.3 - - + +
36A THR* 3.5 34.1 - - + -
39A HIS* 4.1 5.4 - - + -
41A GLY 3.4 19.7 - - - -
42A PHE* 3.6 25.1 - + + -
43A LEU* 3.7 5.6 - - - -
80A THR* 2.8 44.6 + - - -
81A VAL* 1.3 75.0 - - - +
83A LYS* 1.3 62.3 + - - +
84A ASP 3.4 18.4 - - - +
87A SER* 3.8 15.5 - - - -
88A HIS* 3.2 48.0 - + + -
91A MET* 3.8 23.8 - - + -
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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