Contacts of the helix formed by residues 27 - 40 (chain B) in PDB entry 2W3B
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 LEU 27 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B TRP* 3.9 23.4 - - + +
25B PRO 3.4 11.2 + - - +
26B PRO* 1.3 75.9 - - - +
28B ARG* 1.3 66.1 + - - +
29B ASN 3.4 2.5 - - - -
30B GLU* 3.1 14.4 + - + -
31B PHE* 3.0 29.3 + - - -
138B ILE* 4.2 16.4 - - + -
172B GLU* 3.7 44.4 - - + +
173B LYS* 4.6 4.5 - - + -
175B ILE* 4.1 23.8 - - + -
177B TYR* 4.2 19.1 - - + -
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Residues in contact with ARG 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PRO* 3.8 4.8 + - - +
27B LEU* 1.3 71.1 - - - +
29B ASN* 1.3 67.3 + - - +
31B PHE* 3.3 12.5 + - - +
32B ARG* 2.9 39.3 + - + +
172B GLU* 3.4 9.0 + - - +
173B LYS* 5.8 1.4 - - - +
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Residues in contact with ASN 29 (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 ARG* 1.3 74.3 - - - +
30B GLU* 1.3 60.4 + - - +
32B ARG* 3.6 22.1 - - - +
33B TYR* 3.0 27.7 + - - +
172B GLU* 2.8 33.6 + - - +
177B TYR* 4.0 6.3 - - - +
179B PHE* 5.0 2.1 - - + -
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Residues in contact with GLU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ALA* 3.9 8.9 - - + +
24B TRP* 5.5 3.3 + - - -
27B LEU* 3.1 29.5 + - + +
29B ASN* 1.3 73.8 - - - +
31B PHE* 1.3 66.5 + - - +
33B TYR* 3.2 12.0 + - - +
34B PHE* 3.0 19.1 + - - +
136B THR* 2.7 43.0 + - + +
138B ILE* 5.7 0.4 - - + -
172B GLU* 3.2 5.1 + - - -
177B TYR* 3.6 19.0 + - + +
179B PHE* 4.3 2.0 - - + -
301B VG9 2.9 38.6 + - - -
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Residues in contact with PHE 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 3.9 15.9 - - + -
26B PRO* 4.0 28.9 - - + -
27B LEU 3.0 22.8 + - - -
28B ARG* 3.4 10.5 - - - +
30B GLU* 1.3 78.0 + - - +
32B ARG* 1.3 57.1 + - + +
34B PHE* 3.2 10.3 + - + +
35B GLN* 2.9 28.8 + - - +
301B VG9 3.4 90.4 - + + +
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Residues in contact with ARG 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ARG* 2.9 27.5 + - + +
29B ASN* 3.6 26.5 - - - +
30B GLU 3.3 0.2 - - - -
31B PHE* 1.3 76.5 - - + +
33B TYR* 1.3 57.3 + - - +
35B GLN* 3.5 17.7 + - - +
36B ARG* 2.8 30.2 + - - +
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Residues in contact with TYR 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 4.1 15.9 - - + -
29B ASN 3.0 13.8 + - - +
30B GLU* 3.3 16.4 - - - +
32B ARG* 1.3 72.0 - - - +
34B PHE* 1.3 68.2 + - - +
36B ARG* 3.2 31.7 + - - +
37B MET* 2.9 50.9 + - + +
134B PHE* 3.4 29.2 - - + +
135B VAL 6.2 0.2 - - - -
136B THR* 4.2 5.2 - - - -
165B VAL* 3.6 23.6 - - + +
166B LEU 5.6 0.2 - - - -
179B PHE* 3.4 52.8 - + + +
180B GLU 5.0 1.6 + - - -
181B VAL* 4.9 0.5 - - - +
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Residues in contact with PHE 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 3.8 20.0 - - + -
30B GLU 3.0 12.6 + - - +
31B PHE* 3.4 9.9 - + - +
33B TYR* 1.3 77.9 - - - +
35B GLN* 1.3 58.4 + - - +
37B MET* 4.1 0.5 - - - +
38B THR* 2.8 38.5 + - + +
67B LEU* 4.1 14.1 - - + -
70B ARG* 3.9 7.2 - - - -
115B VAL* 3.7 24.5 - - + -
301B VG9 3.2 116.4 - + + +
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Residues in contact with GLN 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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31B PHE 2.9 11.9 + - - +
32B ARG* 3.5 22.0 + - - +
34B PHE* 1.3 76.8 - - - +
36B ARG* 1.3 57.3 + - - +
38B THR* 4.0 2.5 - - - -
39B THR* 2.7 46.8 + - + +
68B LYS* 4.6 15.2 - - - +
70B ARG* 4.0 7.6 + - - +
301B VG9 3.8 26.6 - - + +
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Residues in contact with ARG 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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32B ARG 2.8 19.6 + - - +
33B TYR* 3.2 33.0 + - - +
35B GLN* 1.3 72.8 - - - +
37B MET* 1.3 79.0 + - - +
39B THR* 4.9 1.6 - - - -
40B THR* 2.7 41.6 + - - +
164B GLY* 3.0 33.1 + - - -
165B VAL* 4.8 1.2 - - - +
166B LEU* 5.4 4.9 - - - +
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Residues in contact with MET 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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7B ILE* 3.9 16.8 - - + -
33B TYR* 2.9 49.6 + - + +
34B PHE 4.1 0.2 - - - +
36B ARG* 1.3 103.6 - - - +
38B THR* 1.3 62.7 + - - +
39B THR 3.5 0.2 + - - -
40B THR* 3.9 9.3 + - - +
48B ASN* 4.1 1.4 + - - -
111B MET* 4.9 0.5 - - - +
113B TRP* 3.2 32.8 + - + -
134B PHE* 3.4 36.6 - - + -
162B TYR* 5.8 2.2 - - + -
164B GLY 4.9 0.7 - - - +
165B VAL* 4.7 7.0 - - + -
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Residues in contact with THR 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 3.8 19.5 - - + -
34B PHE* 2.8 46.9 + - + +
35B GLN 3.5 0.2 + - - -
37B MET* 1.3 77.5 - - - +
39B THR* 1.3 57.2 + - - +
48B ASN* 2.9 27.1 + - - +
50B VAL* 4.0 8.1 - - - +
70B ARG* 2.9 38.3 + - - +
113B TRP* 3.9 24.7 - - + +
115B VAL* 4.1 3.4 - - + -
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Residues in contact with THR 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLN* 2.7 28.3 + - + +
36B ARG* 4.4 1.8 - - - -
38B THR* 1.3 78.2 - - - +
40B THR* 1.3 65.4 + - - +
41B SER* 3.2 7.4 + - - -
47B GLN* 5.9 0.3 - - - -
48B ASN* 3.6 6.2 + - - +
68B LYS 4.4 7.4 - - - +
69B GLY* 4.0 23.3 - - - +
70B ARG* 3.2 27.5 + - - +
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Residues in contact with THR 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ARG* 2.7 34.8 + - - +
37B MET* 3.9 4.4 + - - +
38B THR 3.6 0.8 - - - -
39B THR* 1.3 75.9 - - - +
41B SER* 1.3 67.5 + - - +
48B ASN* 3.0 13.0 + - - -
111B MET* 3.6 13.2 - - - +
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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
------------------------------------------------------------
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