Contacts of the strand formed by residues 91 - 96 (chain A) in PDB entry 3Q3G
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 VAL 91 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A TYR 3.8 0.5 - - - +
43A GLN* 3.6 1.9 - - - -
44A GLN* 2.7 46.1 + - + +
90A ALA* 1.4 74.2 - - - +
92A TYR* 1.3 63.2 + - - +
93A TYR* 3.6 37.0 + - + +
106A ALA 5.1 0.9 - - - +
107A GLY* 4.0 3.6 - - - -
108A THR 3.4 21.3 - - - +
109A LYS* 3.7 33.7 - - + +
618A EDO 6.5 1.3 - - - -
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Residues in contact with TYR 92 (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 GLN* 2.7 24.8 + - - -
21A MET* 3.7 29.4 - - + -
41A TRP* 4.6 4.3 - - + -
42A TYR 3.3 5.4 - - - +
43A GLN* 2.9 34.7 + - + -
53A LEU* 3.7 26.0 - - + -
68A PHE* 3.6 18.2 - + - -
79A LEU* 3.7 20.9 - - + -
81A ILE* 4.0 3.9 - - + +
88A ASP* 2.5 33.4 + - - +
90A ALA* 3.8 11.2 - - + -
91A VAL* 1.3 74.5 - - - +
93A TYR* 1.3 56.6 + - - +
107A GLY* 3.2 1.6 - - - -
108A THR 2.9 29.2 + - - +
110A LEU* 3.7 16.4 - - + -
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Residues in contact with TYR 93 (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 GLN* 3.6 3.1 - - - -
41A TRP* 3.3 6.6 - - - -
42A TYR* 2.7 45.5 + - + +
44A GLN* 3.4 30.6 + - + -
91A VAL* 3.6 29.7 - - + +
92A TYR* 1.3 75.7 - - - +
94A CYS* 1.3 62.7 + - - +
104A PHE* 4.6 5.2 - - + -
105A GLY 3.3 21.5 - - - -
106A ALA 3.6 20.5 + - - -
107A GLY* 3.7 6.7 - - - -
41B GLN* 3.4 16.1 + - - -
45B GLN 3.7 12.6 + - - -
46B GLY* 3.7 13.0 - - - -
47B LEU* 3.8 30.1 - - + -
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Residues in contact with CYS 94 (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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4A MET* 4.0 13.4 - - - +
6A GLN* 3.2 22.6 + - - -
23A CYS* 2.1 52.9 - - + -
39A LEU* 4.5 2.7 - - + -
40A ALA 3.2 9.9 - - - +
41A TRP* 3.9 16.2 - - + -
93A TYR* 1.3 74.8 - - - +
95A GLN* 1.3 62.0 + - - +
104A PHE* 3.4 5.5 - - - +
105A GLY 2.9 25.1 + - - -
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Residues in contact with GLN 95 (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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4A MET* 4.1 6.5 - - - -
39A LEU* 3.4 4.3 - - - +
40A ALA* 2.9 39.7 + - - +
42A TYR* 2.6 45.2 + - + -
94A CYS* 1.3 76.4 - - - +
96A GLN* 1.3 77.4 + - - +
97A TYR* 3.8 18.9 + - - +
102A LEU* 3.9 7.1 - - - +
103A THR 3.3 16.6 - - - +
104A PHE* 3.6 20.0 - - + -
111B MET* 3.4 28.4 - - - +
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Residues in contact with GLN 96 (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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2A ILE* 3.7 24.2 - - + +
4A MET* 3.8 14.4 - - + +
29A LEU* 3.6 27.6 - - + -
38A TYR 3.3 4.7 - - - -
95A GLN* 1.3 85.8 - - - +
97A TYR* 1.3 59.9 + - - +
98A TYR* 2.9 28.6 + - - +
99A SER 3.0 17.9 + - - -
101A PRO 2.9 28.1 + - - -
102A LEU* 3.9 2.4 - - - -
103A THR* 3.0 39.7 + - - +
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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