Contacts of the strand formed by residues 34 - 43 (chain B) in PDB entry 2PS2
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 PHE 34 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B VAL 3.5 0.5 - - - +
15B ASP* 3.7 2.0 - - - -
16B LEU* 2.7 51.5 + - + +
18B TYR* 3.8 37.0 - + + -
23B TYR* 5.4 7.2 - + + -
33B SER* 1.3 82.2 + - - +
35B ASP* 1.3 60.7 + - - +
36B ALA 3.3 4.3 + - - -
54B THR* 3.9 9.0 - - + -
55B PRO 4.2 11.9 - - - +
56B PHE* 3.5 43.1 - + - -
57B GLY* 4.6 6.5 - - - -
299B CYS* 3.5 31.6 - - - -
329B MET* 4.2 8.3 - - + -
330B VAL* 3.9 7.6 - - + -
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Residues in contact with ASP 35 (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 GLN* 3.0 22.3 + - - +
14B VAL 4.0 2.0 - - - -
15B ASP* 4.9 4.7 - - - +
33B SER 4.3 0.8 + - - -
34B PHE* 1.3 69.1 - - - +
36B ALA* 1.3 59.4 + - - +
37B THR* 4.0 1.9 + - - -
54B THR* 3.7 9.7 - - - +
55B PRO* 4.1 8.7 + - - +
65B PRO* 3.3 40.3 - - + +
66B ARG* 5.8 1.4 + - - +
69B ARG* 2.8 38.4 + - - -
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Residues in contact with ALA 36 (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 GLN* 3.4 5.5 - - - -
14B VAL* 2.9 49.8 + - + +
16B LEU* 3.6 22.9 - - + -
34B PHE 3.3 1.0 + - - -
35B ASP* 1.3 75.6 - - - +
37B THR* 1.3 61.0 + - - +
38B ILE* 4.0 5.8 + - + -
52B GLU* 4.0 7.0 - - - +
54B THR* 3.0 22.4 - - + +
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Residues in contact with THR 37 (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 VAL* 3.7 26.7 - - + -
12B PHE 3.5 3.4 - - - +
35B ASP 4.8 1.4 + - - -
36B ALA* 1.3 73.7 - - - +
38B ILE* 1.3 64.4 + - - +
39B VAL* 4.3 2.0 + - + -
52B GLU* 3.5 3.6 - - - +
53B SER* 3.0 43.1 + - - -
65B PRO* 4.2 1.2 + - - +
68B VAL* 3.8 14.3 - - + +
69B ARG* 2.9 39.1 + - + +
72B ILE* 3.9 18.8 - - + -
107B ALA* 4.5 2.2 - - + +
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Residues in contact with ILE 38 (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 VAL* 3.6 2.9 - - - +
12B PHE* 2.8 47.6 + - + +
14B VAL* 4.0 16.4 - - + -
36B ALA* 4.0 3.3 - - + -
37B THR* 1.3 80.0 - - - +
39B VAL* 1.3 65.4 + - - +
50B TRP* 3.6 31.9 - - + -
51B GLY 3.4 6.7 - - - +
52B GLU* 4.0 15.5 - - + -
301B SER* 4.6 4.9 - - - +
303B ILE* 3.6 22.2 - - + -
334B THR* 4.2 13.2 - - + -
363B LEU* 3.4 27.4 - - + -
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Residues in contact with VAL 39 (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 ILE* 3.8 12.1 - - + -
10B ASP 3.4 11.0 - - - +
11B VAL* 4.4 7.2 - - + -
37B THR* 4.6 2.0 - - + -
38B ILE* 1.3 79.6 - - - +
40B ARG* 1.3 67.2 + - - +
41B ILE* 4.1 7.6 - - + -
49B GLY 3.6 0.9 - - - +
50B TRP* 3.2 11.5 - - - -
51B GLY 2.8 32.9 + - - -
72B ILE* 3.8 24.0 - - + -
107B ALA* 3.6 31.0 - - + +
108B ILE* 3.6 25.6 - - + -
111B ALA* 4.1 0.7 - - - +
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Residues in contact with ARG 40 (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 ARG* 3.9 1.7 - - - +
9B ILE* 3.5 2.1 - - - -
10B ASP* 2.9 66.9 + - + +
12B PHE* 3.9 26.4 - - + -
39B VAL* 1.3 75.1 - - - +
41B ILE* 1.3 69.6 + - - +
42B THR* 3.9 9.8 + - - +
48B GLU* 4.0 29.3 + - + -
49B GLY 3.2 6.3 - - - +
50B TRP* 3.3 46.9 - - + +
360B LEU* 5.1 8.5 - - - +
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Residues in contact with ILE 41 (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 ILE* 4.1 25.8 - - + -
8B ARG 3.4 8.5 - - - +
9B ILE* 4.1 14.1 - - + -
39B VAL* 4.1 9.4 - - + -
40B ARG* 1.3 77.9 - - - +
42B THR* 1.3 66.0 + - - +
43B THR* 5.4 0.2 - - + -
47B ILE 3.6 1.0 - - - +
48B GLU* 3.2 4.9 - - - +
49B GLY 2.8 30.8 + - - -
84B PRO* 5.2 0.2 - - + -
108B ILE* 3.6 39.7 - - + +
111B ALA* 3.7 14.4 - - + -
112B CYS* 3.8 15.9 - - - +
115B ILE* 3.4 24.5 - - + +
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Residues in contact with THR 42 (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 ILE* 3.9 1.0 - - - -
7B ALA* 2.9 24.3 + - + +
8B ARG* 3.0 27.1 + - + +
10B ASP* 4.9 3.6 + - - -
40B ARG* 3.9 16.1 + - - -
41B ILE* 1.3 79.0 + - - +
43B THR* 1.3 74.1 + - - +
46B GLY* 4.2 13.9 - - - +
47B ILE 3.3 8.3 - - - +
48B GLU* 3.9 18.0 + - + +
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Residues in contact with THR 43 (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 LEU* 3.5 20.9 - - + -
5B LYS 3.2 9.6 - - - +
6B ILE* 4.6 0.9 - - - +
7B ALA* 3.7 3.5 - - - +
42B THR* 1.3 85.1 - - - +
44B ASP* 1.3 59.2 + - - +
45B THR* 2.7 22.6 + - - -
46B GLY 2.9 15.8 + - - -
47B ILE* 2.9 31.9 + - + +
84B PRO* 4.1 11.4 - - + -
115B ILE* 3.6 37.9 - - + -
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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