Contacts of the strand formed by residues 32 - 40 (chain B) in PDB entry 2A3W
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 ASN 32 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LEU* 3.5 10.2 - - - +
31B GLN* 1.3 119.9 + - + +
33B PHE* 1.3 66.8 + - - +
98B TRP* 3.5 4.9 - - - -
99B GLU* 3.6 24.4 - - - +
100B SER* 3.7 1.7 + - - -
101B SER* 5.0 1.2 + - - -
161B ASP* 3.1 25.6 + - - +
162B SER* 3.9 17.6 - - - +
163B VAL* 4.2 11.2 - - + +
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Residues in contact with PHE 33 (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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30B LEU* 4.0 12.8 - - + -
32B ASN* 1.3 77.7 - - - +
34B THR* 1.3 67.0 + - - +
35B LEU* 4.0 9.6 - - + -
61B LEU* 3.5 41.1 - - + -
73B LEU* 4.3 7.9 - - + -
75B ILE* 3.7 15.3 - - + -
96B VAL* 3.9 19.3 - - + -
97B SER* 3.1 4.7 - - - -
98B TRP* 3.0 69.9 + + + +
125B VAL* 4.8 3.1 - - + -
159B MET* 3.8 23.6 - - + -
160B TRP 3.2 14.1 - - - +
162B SER 3.3 10.1 + - - +
163B VAL* 4.3 1.0 - - - +
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Residues in contact with THR 34 (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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33B PHE* 1.3 76.0 + - - +
35B LEU* 1.3 62.6 + - - +
36B CYS* 4.1 7.0 - - - -
95B CYS* 4.9 0.2 - - + -
96B VAL 3.3 10.3 - - - +
97B SER* 3.4 8.4 - - - -
159B MET* 3.2 5.7 - - - +
160B TRP* 2.8 44.1 + - + -
162B SER 2.8 20.4 + - - -
163B VAL* 3.4 0.2 - - - -
164B LEU* 2.9 31.5 + - + -
169B ILE* 3.8 28.0 - - + -
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Residues in contact with LEU 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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33B PHE* 4.0 6.7 - - + -
34B THR* 1.3 74.3 - - - +
36B CYS* 1.3 61.5 + - - +
37B PHE* 4.0 13.4 - - + -
50B PHE* 3.4 54.7 - - + -
61B LEU* 5.3 3.4 - - + -
63B VAL* 3.9 17.0 - - + -
94B ILE 3.8 1.0 - - - +
95B CYS* 3.2 1.9 - - - -
96B VAL* 2.7 47.2 + - + +
157B LEU* 3.6 26.0 - - + -
158B TYR 3.4 14.6 - - - +
159B MET* 4.0 13.9 - - + -
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Residues in contact with CYS 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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34B THR* 4.1 7.2 - - - -
35B LEU* 1.3 74.5 - - - +
37B PHE* 1.3 65.5 + - - +
93B HIS* 4.1 7.9 - - - +
94B ILE 3.1 4.7 - - - -
95B CYS* 2.0 46.2 - - - -
156B ASP 3.9 2.9 - - - +
157B LEU* 3.2 1.7 - - - +
158B TYR* 2.8 35.7 + - + +
160B TRP* 3.6 31.6 - - + -
164B LEU* 4.7 0.4 - - - -
169B ILE* 4.3 3.1 - - - -
172B ALA* 4.1 8.7 - - + -
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Residues in contact with PHE 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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35B LEU* 4.0 29.6 - - + -
36B CYS* 1.3 80.8 - - - +
38B ARG* 1.3 68.4 + - - +
39B ALA* 4.2 3.8 + - + -
49B LEU* 3.6 46.4 - - + -
50B PHE* 4.7 6.1 - - + -
63B VAL* 4.4 6.7 - - + -
93B HIS* 3.6 9.5 + - - -
94B ILE* 2.8 71.6 + - + +
96B VAL* 5.7 0.7 - - + -
154B ILE* 4.6 9.4 - - + -
155B GLY 3.7 7.6 - - - +
156B ASP 3.3 10.3 - - - -
157B LEU* 3.8 24.0 - - + -
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Residues in contact with ARG 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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37B PHE* 1.3 73.7 - - - +
39B ALA* 1.3 62.7 + - - +
92B VAL 3.3 10.5 - - - +
93B HIS* 3.8 25.9 - - + +
154B ILE* 3.3 8.3 - - - +
155B GLY* 2.8 38.3 + - - +
156B ASP* 2.6 32.4 + - + +
172B ALA 3.3 15.2 + - - -
173B TYR* 3.0 33.5 + - - -
174B GLN 4.5 0.4 - - - -
175B GLY* 3.9 11.5 - - - +
201B LEU* 4.7 2.9 - - - -
203B TRP* 3.6 17.0 - - + -
204B VAL* 3.4 39.4 - - - +
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Residues in contact with ALA 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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37B PHE* 4.2 18.8 - - + -
38B ARG* 1.3 76.9 - - - +
40B TYR* 1.3 61.1 + - - +
41B SER* 4.3 1.1 - - - +
47B TYR* 6.2 0.2 - - - +
49B LEU* 4.3 16.6 - - + -
90B ALA 4.3 0.5 - - - +
91B PRO* 3.5 1.4 - - - +
92B VAL* 2.9 46.6 + - + +
94B ILE* 4.8 0.7 - - + -
150B PHE* 4.3 7.9 - - + -
153B GLU 3.1 9.9 - - - +
154B ILE* 4.3 2.7 - - + -
203B TRP* 3.8 3.7 - - - -
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Residues in contact with TYR 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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39B ALA* 1.3 75.9 - - - +
41B SER* 1.3 63.5 + - - +
89B PRO* 4.8 8.1 + - + +
90B ALA* 3.8 12.1 - - - -
91B PRO* 3.5 36.2 - - + +
150B PHE* 4.5 0.2 - - - -
152B GLY* 3.3 3.6 - - - -
153B GLU* 2.8 38.0 + - + +
203B TRP* 3.5 51.6 - + + +
83C LYS 5.2 2.4 + - - -
112C THR* 5.0 3.5 - - - +
113C PRO* 2.8 28.8 + - + -
114C LEU* 3.4 24.9 - - - +
115C VAL* 3.6 27.3 + - + +
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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