Contacts of the strand formed by residues 95 - 102 (chain A) in PDB entry 2QC8
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 LYS 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A VAL* 4.8 1.1 - - + -
27A GLN 3.0 12.0 + - - +
28A ALA* 3.7 8.2 - - + -
29A MET* 2.9 27.9 + - - +
50A GLU* 2.9 27.6 + - - -
51A PRO* 3.5 42.2 + - + -
84A MET* 4.0 21.0 - - + +
85A PHE 3.4 14.4 - - - +
86A ARG* 4.7 13.5 - - - +
87A ASP* 3.7 8.4 - - - +
92A ASP* 4.7 4.0 + - - -
93A PRO 3.4 19.5 + - - +
94A ASN* 1.3 82.2 + - - +
96A LEU* 1.3 66.9 + - - +
97A VAL* 4.6 4.7 - - + -
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Residues in contact with LEU 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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29A MET* 3.5 25.6 - - + -
31A ILE* 3.9 10.1 - - + -
83A ALA 3.9 0.4 - - - +
84A MET* 3.4 4.3 - - - +
85A PHE* 2.8 42.3 + - + +
86A ARG 3.9 5.2 - - - +
87A ASP* 3.3 34.5 - - - +
88A PRO* 3.8 22.2 - - + -
89A PHE* 4.5 7.0 - - + -
95A LYS* 1.3 75.6 - - - +
97A VAL* 1.3 63.2 + - - +
98A LEU 4.2 0.2 - - - -
220A VAL* 4.3 10.5 - - + -
223A PHE* 4.4 13.9 - - + -
224A ILE* 4.0 26.0 - - + -
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Residues in contact with VAL 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ALA* 4.4 7.2 - - + -
29A MET 2.8 15.9 + - - +
30A TYR* 3.4 17.9 - - + -
31A ILE* 2.7 30.7 + - - +
54A VAL* 4.5 2.2 - - + -
57A LEU* 3.4 44.0 - - + -
81A PRO* 3.7 26.5 - - + -
83A ALA 3.6 6.1 - - - +
95A LYS* 4.6 4.0 - - + -
96A LEU* 1.3 80.4 - - - +
98A LEU* 1.3 68.6 + - - +
99A CYS* 3.5 6.4 + - - -
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Residues in contact with LEU 98 (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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31A ILE* 3.6 34.8 - - + +
32A TRP* 4.7 3.8 - - - -
33A ILE* 5.3 6.1 - - + -
40A LEU* 4.9 3.6 - - + -
81A PRO 3.9 0.2 - - - -
82A ALA* 2.8 25.5 + - + +
83A ALA* 2.9 21.0 + - + +
96A LEU 4.2 0.6 - - - -
97A VAL* 1.3 73.5 - - - +
99A CYS* 1.3 68.8 + - - +
114A ARG* 5.0 4.7 - - - +
216A ASP* 3.7 40.6 - - - +
219A TRP* 4.1 26.0 - - + -
220A VAL* 3.7 20.0 - - + +
349A PHE* 4.5 9.4 - - + -
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Residues in contact with CYS 99 (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 TYR* 3.3 37.7 - - - -
31A ILE 2.9 17.6 + - - +
32A TRP* 4.3 7.4 - - + +
33A ILE* 5.1 2.4 + - - +
79A LEU* 3.9 23.3 - - + -
80A VAL 3.2 9.0 - - - +
81A PRO* 3.9 17.9 - - - -
82A ALA* 4.4 2.7 - - - -
97A VAL* 3.7 13.7 - - - -
98A LEU* 1.3 84.8 - - - +
100A GLU* 1.3 61.8 + - - +
101A VAL* 4.2 0.9 + - - +
114A ARG* 5.7 0.9 - - - -
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Residues in contact with GLU 100 (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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78A TYR 3.5 0.7 - - - +
79A LEU* 3.5 6.2 - - - -
80A VAL* 2.8 37.2 + - + +
82A ALA* 4.3 3.7 - - + +
99A CYS* 1.3 73.0 - - - +
101A VAL* 1.3 63.1 + - - +
102A PHE* 3.4 17.2 - - + -
112A ASN* 2.8 32.7 + - - +
114A ARG* 3.1 51.6 + - + +
115A HIS* 3.3 28.1 + - - -
118A LYS* 5.2 2.6 - - - +
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Residues in contact with VAL 101 (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 TRP* 3.6 43.3 - - + -
33A ILE* 4.0 11.7 - - + +
62A PHE* 3.8 23.6 - - + -
69A GLN* 4.3 4.9 - - - +
77A MET* 4.0 11.9 - - + -
78A TYR 3.3 3.1 - - - +
79A LEU* 3.9 5.8 - - + -
99A CYS 4.9 0.7 - - - +
100A GLU* 1.3 72.3 - - - +
102A PHE* 1.3 67.1 - - - +
109A ALA* 3.1 34.2 + - + +
112A ASN* 3.0 25.6 + - + +
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Residues in contact with PHE 102 (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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77A MET* 3.4 12.3 - - - +
78A TYR* 2.9 41.9 + - + -
80A VAL* 3.6 34.8 - - + -
100A GLU* 3.4 40.2 - - + -
101A VAL* 1.3 73.9 - - - +
103A LYS* 1.3 65.1 + - - +
106A ARG* 3.4 32.3 - - - +
107A ARG 3.3 5.8 - - - +
108A PRO* 3.6 24.7 - - + -
109A ALA 3.9 0.9 - - - +
112A ASN* 4.0 0.9 - - - -
115A HIS* 4.1 20.9 - + - -
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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