Contacts of the strand formed by residues 156 - 164 (chain B) in PDB entry 2X2D
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 ILE 156 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ILE* 3.7 25.1 - - + -
11B ALA 3.5 1.3 - - - -
12B VAL* 3.6 28.5 - - + -
52B CYS* 3.3 5.2 - - - +
53B PHE* 2.9 40.9 + - + +
56B ILE* 4.0 17.9 - - + -
142B MET* 4.0 25.8 - - + -
145B PHE* 3.6 29.2 - - + -
152B THR* 4.6 4.0 + - + -
154B LYS 3.3 15.1 + - - +
155B LYS* 1.3 74.5 - - - +
157B THR* 1.3 60.9 + - - +
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Residues in contact with THR 157 (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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10B ILE* 3.3 7.5 - - - +
11B ALA* 2.8 56.7 + - - +
14B GLY* 4.9 5.1 + - - +
50B GLY* 4.6 9.6 - - - +
51B SER 3.4 11.0 - - - +
52B CYS* 4.2 10.5 - - + -
53B PHE* 5.3 0.2 - - - -
155B LYS* 3.6 18.5 + - + +
156B ILE* 1.3 77.2 - - - +
158B ILE* 1.3 64.9 + - - +
159B ALA* 3.1 6.3 + - - +
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Residues in contact with ILE 158 (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 PHE* 3.3 45.3 - - + -
9B ASP 3.5 4.0 - - - -
10B ILE* 4.2 2.5 - - + -
48B TYR* 4.0 17.9 - - + +
49B LYS* 4.0 0.2 - - - -
50B GLY* 2.8 31.9 + - - -
51B SER* 2.9 21.4 + - - +
52B CYS 5.8 0.9 - - - +
53B PHE* 3.8 24.7 - - + -
65B GLY 5.7 1.1 - - - +
112B PHE* 4.4 7.4 - - + -
157B THR* 1.3 70.8 - - - +
159B ALA* 1.3 58.8 + - - +
160B ASP 3.2 22.9 + - - +
161B CYS* 3.7 24.2 - - + -
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Residues in contact with ALA 159 (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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9B ASP* 3.0 15.5 + - + +
10B ILE 4.9 0.2 - - - -
11B ALA* 3.8 26.7 - - + -
49B LYS* 3.8 17.9 - - - +
50B GLY* 4.7 2.9 + - - +
157B THR* 3.1 7.8 + - - +
158B ILE* 1.3 72.7 - - - +
160B ASP* 1.3 62.5 + - + +
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Residues in contact with ASP 160 (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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7B PHE* 4.1 14.2 - - - -
9B ASP* 2.8 43.2 + - + +
49B LYS* 3.0 30.1 + - - +
158B ILE* 3.2 6.6 - - - +
159B ALA* 1.3 79.7 - - + +
161B CYS* 1.3 81.4 + - - +
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Residues in contact with CYS 161 (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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7B PHE* 3.1 25.7 - - - +
8B PHE* 3.6 17.7 - - + -
39B LEU 4.8 0.2 - - - -
40B SER* 3.2 22.4 - - - +
41B THR* 5.0 1.9 - - - +
48B TYR* 4.0 9.6 - - - -
49B LYS* 3.5 39.4 - - - +
158B ILE* 3.7 8.7 - - + -
160B ASP* 1.3 85.6 + - - +
162B GLY* 1.3 59.9 + - - +
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Residues in contact with GLY 162 (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 VAL* 3.5 8.5 - - - +
7B PHE* 2.9 42.1 + - - +
40B SER* 3.2 14.3 + - - -
41B THR* 4.4 6.7 - - - -
161B CYS* 1.3 78.6 - - - +
163B GLN* 1.3 60.5 + - - -
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Residues in contact with GLN 163 (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 PRO* 3.8 21.0 - - + +
5B THR 3.3 17.7 - - - +
6B VAL* 4.3 7.2 - - + -
7B PHE* 4.1 5.1 - - - -
37B ARG* 2.8 39.7 + - - +
41B THR* 3.9 16.5 - - + +
162B GLY* 1.3 73.1 - - - -
164B LEU* 1.3 65.5 + - - +
165B GLU 3.6 25.8 + - - +
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Residues in contact with LEU 164 (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 THR* 3.0 47.7 + - + +
7B PHE* 3.8 35.7 - - + +
19B ARG* 3.7 25.4 - - - +
21B SER* 4.1 11.7 - - - -
163B GLN* 1.3 71.7 + - - +
165B GLU* 1.3 71.7 + - - +
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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