Contacts of the strand formed by residues 95 - 102 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B VAL* 4.8 1.6 - - + -
27B GLN 2.9 12.6 + - - +
28B ALA* 3.7 7.3 - - + -
29B MET* 3.0 23.2 + - - +
50B GLU* 2.8 29.7 + - - -
51B PRO* 3.8 31.6 + - + -
84B MET* 4.0 33.6 - - + +
85B PHE 3.4 13.9 - - - +
86B ARG* 4.7 9.0 - - - +
87B ASP* 3.8 13.7 - - - +
92B ASP* 4.7 7.9 + - - -
93B PRO* 3.6 15.7 + - - +
94B ASN* 1.3 84.0 + - - +
96B LEU* 1.3 62.6 + - - +
97B VAL* 4.6 6.3 - - + -
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Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B MET* 3.6 30.1 - - + -
31B ILE* 4.1 16.2 - - + -
83B ALA 3.9 0.2 - - - +
84B MET* 3.4 3.8 - - - +
85B PHE* 2.8 42.3 + - + +
86B ARG 4.2 3.4 - - - +
87B ASP* 3.5 34.5 - - - +
88B PRO* 4.0 18.8 - - + -
89B PHE* 4.6 5.4 - - + -
95B LYS* 1.3 72.7 - - - +
97B VAL* 1.3 60.8 + - - +
98B LEU 4.2 0.7 - - - -
220B VAL* 4.1 15.3 - - + -
223B PHE* 4.3 8.5 - - + -
224B ILE* 4.1 23.1 - - + -
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Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ALA* 4.7 3.1 - - + -
29B MET 2.9 14.2 + - - +
30B TYR* 3.5 17.1 - - + -
31B ILE* 2.8 31.6 + - - +
54B VAL* 4.7 0.2 - - + -
57B LEU* 3.2 43.1 - - + -
81B PRO* 3.7 24.5 - - + -
82B ALA 4.5 0.4 - - - +
83B ALA 3.4 8.1 - - - +
84B MET* 4.6 2.5 - - + -
95B LYS* 4.6 6.5 - - + -
96B LEU* 1.3 78.7 - - - +
98B LEU* 1.3 67.6 + - - +
99B CYS* 3.6 7.1 + - - -
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Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ILE* 3.7 28.4 - - + +
32B TRP* 4.7 3.8 - - - -
33B ILE* 5.1 6.3 - - + -
40B LEU* 4.8 3.4 - - + -
82B ALA* 2.9 25.5 + - + +
83B ALA* 2.8 22.4 + - + +
96B LEU 4.2 0.8 - - - -
97B VAL* 1.3 73.7 - - - +
99B CYS* 1.3 71.8 + - - +
114B ARG* 5.3 3.6 - - - +
215B GLY 4.5 0.4 - - - +
216B ASP* 3.8 44.4 - - + +
219B TRP* 3.9 24.2 - - + -
220B VAL* 3.7 20.0 - - + +
349B PHE* 4.6 8.1 - - + -
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Residues in contact with CYS 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B TYR* 3.4 35.4 - - - -
31B ILE 2.8 20.5 + - - +
32B TRP* 4.1 10.1 - - - +
33B ILE* 5.0 3.1 + - - +
79B LEU* 4.0 22.2 - - + -
80B VAL 3.4 11.4 - - - +
81B PRO* 3.9 18.4 - - - -
82B ALA* 4.2 3.1 - - - +
97B VAL* 3.8 12.1 - - - -
98B LEU* 1.3 84.2 - - - +
100B GLU* 1.3 62.8 + - - +
101B VAL* 4.1 1.2 + - - +
114B ARG* 5.8 1.0 - - - -
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Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B TYR 3.5 3.5 - - - +
79B LEU* 3.6 2.6 - - - -
80B VAL* 3.0 36.5 + - + +
82B ALA* 4.3 4.1 - - + +
99B CYS* 1.3 72.8 - - - +
101B VAL* 1.3 62.3 + - - +
102B PHE* 3.3 16.9 - - + -
112B ASN* 3.0 31.1 + - - +
114B ARG* 2.9 48.9 + - + +
115B HIS* 3.1 32.2 + - - -
118B LYS* 5.2 2.9 - - - +
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Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B TRP* 3.7 42.4 - - + -
33B ILE 3.9 11.0 - - - +
62B PHE* 3.8 27.6 - - + -
69B GLN* 4.2 4.9 - - - +
77B MET* 4.0 11.9 - - + -
78B TYR 3.4 4.3 - - - +
79B LEU* 4.3 1.8 - - + -
99B CYS 4.8 0.4 - - - +
100B GLU* 1.3 73.9 - - - +
102B PHE* 1.3 63.9 + - - +
109B ALA* 3.1 33.3 + - + -
111B THR* 6.0 0.4 - - - +
112B ASN* 2.8 31.2 + - + +
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Residues in contact with PHE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B MET* 3.5 12.1 - - - +
78B TYR* 2.9 44.7 + - + -
80B VAL* 3.7 35.0 - - + -
100B GLU* 3.3 38.8 - - + -
101B VAL* 1.3 77.0 - - - +
103B LYS* 1.3 62.5 + - - +
106B ARG* 3.3 33.0 - - - +
107B ARG 3.4 4.7 - - - +
108B PRO* 3.5 23.6 - - + -
109B ALA 3.9 0.7 - - - +
112B ASN* 4.0 0.9 - - - -
115B HIS* 3.7 25.1 - + - -
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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