Contacts of the strand formed by residues 74 - 82 (chain A) in PDB entry 6B0B
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 TYR 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A LEU* 3.7 22.0 - - + -
35A THR 4.2 4.5 - - - +
36A PRO* 3.5 45.1 - - + -
37A GLN* 5.0 0.2 - - - -
38A ASN* 4.0 1.6 - - - -
68A LEU* 4.6 12.6 - - + -
69A ASP* 3.1 39.4 + - - +
72A GLN* 2.6 39.6 + - - -
73A CYS* 1.3 76.9 - - - +
75A GLN* 1.3 59.0 + - - +
76A VAL 3.5 1.4 + - - -
101A HIS* 2.9 21.4 + + - -
102A LEU* 3.6 26.9 - - + +
103A ASN* 2.9 30.1 + - - +
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Residues in contact with GLN 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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35A THR* 2.2 39.7 + - - +
37A GLN* 3.8 21.6 + - - +
74A TYR* 1.3 69.4 - - - +
76A VAL* 1.3 58.7 + - - +
77A THR* 3.8 3.9 + - + +
103A ASN* 2.9 38.7 - - + +
104A LEU 5.4 0.6 - - - -
105A ARG* 3.2 40.8 + - - +
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Residues in contact with VAL 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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32A TYR* 4.9 8.5 - - + -
33A GLN 3.5 17.7 - - - +
34A LEU* 3.8 21.8 - - + +
59A PHE* 5.0 10.5 - - + -
75A GLN* 1.3 74.4 - - - +
77A THR* 1.3 71.4 + - - +
78A CYS* 5.2 0.4 - - + -
96A ILE* 5.8 0.9 - - + -
102A LEU* 4.1 21.3 - - + -
103A ASN 2.9 13.0 + - - +
104A LEU* 3.2 26.2 - - + +
105A ARG* 2.9 25.1 + - - +
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Residues in contact with THR 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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33A GLN* 2.8 58.9 + - + +
35A THR* 4.8 3.8 - - + -
75A GLN* 4.7 5.4 - - + +
76A VAL* 1.3 76.1 - - - +
78A CYS* 1.3 64.3 + - - +
79A TYR* 3.2 32.6 - - + +
105A ARG* 3.5 32.1 - - - +
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Residues in contact with CYS 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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30A LEU* 3.5 41.1 - - - -
31A CYS 3.2 11.9 - - - -
32A TYR* 4.5 4.7 - - - -
59A PHE* 5.5 5.4 - - + -
76A VAL* 5.2 1.1 - - + -
77A THR* 1.3 77.2 + - - +
79A TYR* 1.3 63.4 + - - +
80A LEU* 3.7 8.4 + - - +
104A LEU* 3.9 9.2 - - + -
105A ARG 2.9 8.7 + - - +
106A ILE* 3.6 27.0 - - + -
107A PHE 2.9 27.0 + - - +
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Residues in contact with TYR 79 (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 PHE* 3.7 8.7 - - + -
31A CYS* 3.1 36.3 + - + +
33A GLN* 6.5 0.2 - - + -
77A THR* 3.2 21.5 + - + +
78A CYS* 1.3 71.5 - - - +
80A LEU* 1.3 59.7 + - - +
105A ARG* 3.2 20.8 + - - -
107A PHE* 3.2 39.9 - + + +
136A MET* 6.3 0.7 - - + -
140A GLU* 3.3 39.5 - - + +
141A PHE* 6.5 0.2 - - + -
143A ASP* 3.5 29.6 + - + -
144A CYS* 3.5 26.9 - - + -
147A ASN* 5.7 1.1 - - - -
148A PHE* 4.8 8.5 - + - -
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Residues in contact with LEU 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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13A PHE* 3.8 4.2 - - - -
29A LEU 3.4 14.6 - - - +
30A LEU* 4.0 18.2 - - + +
56A GLU* 3.5 26.5 - - + +
78A CYS* 3.9 6.1 - - - +
79A TYR* 1.3 74.3 - - - +
81A THR* 1.3 61.6 - - - +
82A TRP 3.5 17.5 - - - +
84A PRO* 3.6 17.0 - - + -
106A ILE* 3.7 26.9 - - + -
107A PHE 2.9 29.0 + - - +
108A ALA* 3.1 15.0 - - + -
109A SER* 2.9 24.6 + - - -
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Residues in contact with THR 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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12A GLN* 3.5 24.7 - - + +
13A PHE* 3.5 43.5 - - + -
15A ASN* 4.4 0.6 - - - +
27A LYS 4.0 0.4 + - - -
29A LEU* 2.7 47.2 + - + -
80A LEU* 1.3 70.3 - - - +
82A TRP* 1.3 77.9 + - - +
109A SER* 3.1 10.7 + - - -
110A ARG* 2.9 29.1 + - - +
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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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12A GLN 3.8 9.8 + - - -
14A ASN 5.8 0.2 - - - -
15A ASN* 3.7 26.9 - - + -
26A ARG* 3.4 48.9 - - + +
27A LYS 2.7 33.3 + - - +
28A ALA* 3.3 19.5 - - + +
29A LEU 4.3 1.8 + - - +
56A GLU* 4.5 2.4 - - - +
80A LEU* 3.5 17.1 - - - +
81A THR* 1.3 96.9 + - - +
83A SER* 1.3 67.5 + - - +
84A PRO* 4.4 0.5 - - - +
110A ARG* 3.4 33.2 - - + -
112A TYR* 3.4 37.9 - + + -
0C U 3.5 21.3 - + - -
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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