Contacts of the strand formed by residues 142 - 150 (chain B) in PDB entry 2Q2L
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 ARG 142 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ASN* 4.7 5.4 - - - +
47B HIS* 3.7 14.8 + - - -
56B CYS* 2.9 49.2 + - + +
57B MET* 3.3 30.5 + - - +
59B THR* 3.1 7.5 + - - -
60B GLY 2.8 33.7 + - - +
61B PRO* 4.3 4.0 - - - +
117B VAL* 3.3 25.8 - - + -
118B VAL 3.7 5.4 - - - -
119B HIS* 3.7 13.4 - - + -
140B GLY 5.1 0.2 - - - +
141B GLY* 1.3 70.4 - - - -
143B ILE* 1.3 60.4 + - - +
144B ALA 3.5 3.0 + - - -
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Residues in contact with ILE 143 (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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91A ASP* 5.4 0.4 - - - +
10B SER* 2.6 31.1 + - - -
11B SER* 4.7 1.2 + - - -
12B GLU* 3.6 46.5 + - + +
13B GLY 5.3 0.2 - - - +
14B VAL* 3.7 11.6 - - + +
36B GLY 5.6 0.9 - - - +
37B LEU* 3.6 30.3 - - + -
38B LYS* 6.1 2.7 - - - +
42B HIS* 5.3 0.4 - - + -
56B CYS* 5.3 0.4 - - - -
118B VAL* 2.8 22.3 + - + +
119B HIS 4.4 2.9 - - - +
120B ALA* 4.2 26.5 - - + +
141B GLY* 3.3 2.4 + - - +
142B ARG* 1.3 73.2 - - - +
144B ALA* 1.3 52.9 + - + +
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Residues in contact with ALA 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 4.1 10.5 - - + -
9B SER 3.3 13.7 - - - +
10B SER* 4.2 0.9 - - - -
14B VAL* 3.4 30.3 - - + -
56B CYS* 3.9 4.9 - - - -
117B VAL* 3.3 4.3 - - - +
118B VAL* 2.9 40.5 + - + +
142B ARG 3.5 1.2 - - - -
143B ILE* 1.3 78.4 - - - +
145B CYS* 1.3 65.0 + - - +
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Residues in contact with CYS 145 (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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8B LEU* 4.0 8.2 - - - +
9B SER* 2.8 37.8 + - - +
52B THR* 4.8 6.1 - - - -
55B GLY 4.5 2.9 - - - -
56B CYS* 2.1 53.4 - - - -
59B THR* 4.6 8.5 - - - -
115B ALA* 4.7 3.6 - - + -
116B VAL 3.0 20.9 - - - +
117B VAL* 3.9 11.7 - - + -
144B ALA* 1.3 76.3 - - - +
146B GLY* 1.3 55.4 + - - +
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Residues in contact with GLY 146 (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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6B ALA* 3.6 8.8 - - - +
7B VAL 3.1 23.6 - - - -
8B LEU* 4.1 4.2 - - - +
9B SER* 5.8 0.2 - - - -
52B THR* 6.0 1.6 - - - -
115B ALA* 3.4 6.4 - - - -
116B VAL 3.2 25.5 + - - -
145B CYS* 1.3 77.0 - - - +
147B ILE* 1.3 65.2 + - - -
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Residues in contact with ILE 147 (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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5B VAL 3.3 8.3 - - - +
6B ALA* 3.3 8.0 - - - -
7B VAL 4.3 2.0 + - - -
50B GLY* 4.4 21.3 - - - +
52B THR* 4.6 17.5 - - + +
113B GLY* 3.3 44.6 - - - +
114B ARG 3.3 6.1 - - - +
115B ALA* 4.3 2.5 - - + +
146B GLY* 1.3 72.2 - - - -
148B ILE* 1.3 65.0 + - - +
149B GLY* 3.1 12.0 + - - +
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Residues in contact with ILE 148 (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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4B GLY* 4.4 1.1 - - - -
5B VAL 3.7 9.2 - - - +
6B ALA* 4.1 6.7 - - + -
20B PHE* 3.8 47.8 - - + -
46B VAL* 4.2 17.5 - - + -
105B LEU* 5.1 0.2 - - + -
111B ILE* 3.6 41.5 - - + +
112B ILE* 3.7 23.0 - - + +
113B GLY* 2.8 27.9 + - - -
114B ARG 2.8 17.4 + - - +
116B VAL* 4.2 11.4 - - + +
147B ILE* 1.3 73.3 - - - +
149B GLY* 1.3 59.8 + - - +
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Residues in contact with GLY 149 (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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4B GLY* 3.1 5.4 - - - -
5B VAL* 2.8 42.5 + - - +
112B ILE* 4.3 1.1 - - - -
147B ILE* 3.1 10.9 + - - -
148B ILE* 1.3 73.5 - - - +
150B LEU* 1.3 65.9 + - - -
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Residues in contact with LEU 150 (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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2B ALA* 6.0 3.4 - - + -
3B LYS 3.4 22.7 - - - +
5B VAL* 4.9 2.3 - - - +
112B ILE* 4.1 26.1 - - + +
148B ILE 4.0 0.8 + - - -
149B GLY* 1.3 72.6 - - - -
151B GLN* 1.3 74.1 + - - +
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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