Contacts of the strand formed by residues 44 - 52 (chain B) in PDB entry 2CT8
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 ASP 44 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B MET* 4.8 15.4 - - + +
5B LYS 3.0 19.0 + - - +
6B LYS* 3.2 9.6 - - + +
7B PHE 2.9 21.3 + - - +
42B ASP 4.1 0.6 + - - -
43B TYR* 1.3 67.9 - - - +
45B VAL* 1.3 63.1 + - - +
247B ILE* 2.9 23.7 - - - +
248B TYR* 2.6 33.0 + - - -
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Residues in contact with VAL 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PHE* 3.3 16.2 - - + +
9B VAL* 5.0 0.9 - - + -
35B ALA* 4.2 18.8 - - + +
38B TYR* 3.8 8.7 - - + -
39B ARG* 3.5 65.1 + - + +
43B TYR* 3.0 25.2 + - + +
44B ASP* 1.3 79.8 + - - +
46B PHE* 1.3 72.3 + - - +
47B PHE* 4.3 0.9 - - + +
92B THR* 3.6 5.0 + - - +
248B TYR* 4.5 3.3 + - - -
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Residues in contact with PHE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PHE 3.1 4.9 + - - +
8B TYR* 3.2 26.1 - + + -
9B VAL* 3.2 25.1 + - - +
44B ASP 4.0 0.6 + - - -
45B VAL* 1.3 75.5 - - - +
47B PHE* 1.3 67.2 + - - +
48B LEU* 3.9 25.4 - - + -
92B THR* 3.4 22.2 - - + -
93B LYS* 4.0 27.4 - - + -
240B ALA 4.4 5.2 - - - -
241B LEU* 3.6 24.7 - - + -
244B LYS* 4.7 11.2 - - + -
248B TYR* 3.7 43.5 - + + -
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Residues in contact with PHE 47 (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 VAL* 3.6 13.7 - - + -
11B THR* 3.7 5.4 - - + -
28B THR* 3.9 11.4 - - + -
31B ALA* 3.6 16.4 - - + -
32B ASP* 3.2 40.4 - - + -
35B ALA* 3.7 24.9 - - + -
39B ARG* 3.9 8.3 - - - +
45B VAL* 4.6 0.2 - - + -
46B PHE* 1.3 73.8 - - - +
48B LEU* 1.3 80.3 + - - +
49B THR* 4.4 2.0 - - - -
89B ILE* 3.8 19.3 - - + -
90B GLU 3.6 15.9 - - - -
91B TYR* 3.6 9.3 - - + +
92B THR* 2.8 41.3 + - - +
93B LYS 3.4 4.2 + - - -
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Residues in contact with LEU 48 (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 TYR* 3.8 32.3 - - + +
9B VAL 3.1 7.3 + - - +
10B THR* 3.5 3.5 - - + -
11B THR 3.1 25.8 + - - +
13B ILE* 5.6 0.2 - - + -
46B PHE* 3.9 14.1 - - + -
47B PHE* 1.3 84.6 - - - +
49B THR* 1.3 72.7 + - - +
93B LYS* 4.1 18.6 - - + +
95B ILE* 4.5 5.8 - - + -
236B ASN* 3.3 34.5 - - - +
237B TYR* 4.1 10.8 - - + -
240B ALA* 3.4 24.9 - - + -
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Residues in contact with THR 49 (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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11B THR* 3.1 25.0 + - - -
13B ILE* 4.8 0.9 - - - -
14B TYR* 4.0 8.7 - - - -
28B THR* 4.2 4.8 + - + -
47B PHE* 4.4 4.9 - - + -
48B LEU* 1.3 83.1 - - - +
50B GLY* 1.3 60.9 + - - +
84B TRP* 3.7 18.6 + - + -
91B TYR* 3.8 35.7 - - + -
93B LYS 3.3 4.7 + - - +
94B PHE* 3.2 18.4 - - + -
95B ILE* 3.1 19.3 + - - +
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Residues in contact with GLY 50 (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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11B THR* 4.3 2.0 + - - -
12B PRO 4.4 0.4 + - - -
13B ILE* 3.6 11.8 - - - +
14B TYR* 3.2 24.8 + - - -
49B THR* 1.3 79.6 + - - +
51B THR* 1.3 68.7 + - - +
80B PHE* 5.5 0.2 - - - -
84B TRP* 5.5 0.5 + - - -
94B PHE* 4.2 12.0 - - - -
95B ILE* 3.2 20.4 - - - -
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Residues in contact with THR 51 (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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13B ILE* 3.7 6.3 - - - +
14B TYR 3.3 9.4 - - - +
16B VAL* 3.4 29.6 - - + -
50B GLY* 1.3 78.6 - - - +
52B ASP* 1.3 60.9 + - - +
53B GLU* 2.6 25.5 + - - +
77B ALA* 4.2 4.8 - - - +
80B PHE* 3.7 24.2 - - + -
94B PHE* 3.8 12.1 - - + -
95B ILE* 2.8 12.6 + - - +
96B ARG* 3.8 4.5 - - - +
97B THR* 3.4 25.3 + - - +
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Residues in contact with ASP 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ILE* 3.5 12.7 - - + +
14B TYR 2.9 10.2 + - - +
15B TYR* 3.7 22.2 + - + -
16B VAL* 3.6 17.2 + - - +
51B THR* 1.3 69.8 - - - +
53B GLU* 1.3 61.7 + - - +
54B HIS 3.9 5.3 + - - +
58B ILE* 4.7 1.0 - - - +
97B THR* 3.8 7.0 + - - +
229B VAL* 4.5 10.2 - - - +
230B TRP* 5.4 1.2 - - - -
232B ASP* 4.6 2.4 - - - +
233B ALA* 3.0 38.1 + - - +
1501B MSP 2.9 35.0 + - - +
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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