Contacts of the strand formed by residues 32 - 40 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30O LEU* 3.5 9.2 - - - +
31O GLN* 1.3 107.9 + - - +
33O PHE* 1.3 65.8 + - - +
98O TRP 3.4 4.9 - - - -
99O GLU* 3.7 22.5 - - - +
100O SER 3.8 1.7 + - - -
101O SER* 5.1 0.9 + - - -
161O ASP* 3.1 34.1 + - - +
162O SER* 4.0 10.6 - - - +
163O VAL* 4.0 11.7 - - + +
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Residues in contact with PHE 33 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30O LEU* 4.4 7.6 - - + -
32O ASN* 1.3 78.1 - - - +
34O THR* 1.3 73.9 + - - +
35O LEU* 4.1 4.5 - - + -
61O LEU* 3.6 44.0 - - + -
73O LEU* 4.2 6.7 - - + -
75O ILE* 3.6 19.5 - - + -
96O VAL* 3.8 22.9 - - + -
97O SER* 3.1 4.5 - - - -
98O TRP* 2.9 72.4 + + + +
125O VAL* 4.6 8.5 - - + -
159O MET* 4.3 15.0 - - + -
160O TRP 3.2 13.5 - - - +
162O SER 3.4 7.5 + - - +
163O VAL* 4.5 0.9 - - - +
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Residues in contact with THR 34 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33O PHE* 1.3 77.6 + - - +
35O LEU* 1.3 62.7 + - - +
36O CYS* 4.3 6.5 - - - -
96O VAL 3.3 12.3 - - - +
97O SER* 3.5 9.0 - - - -
159O MET* 3.2 5.0 - - - +
160O TRP* 2.8 45.5 + - + +
162O SER 2.7 21.4 + - - -
163O VAL* 3.4 1.9 - - - -
164O LEU* 2.9 25.7 + - + -
169O ILE* 3.7 29.8 - - + -
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Residues in contact with LEU 35 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33O PHE* 4.5 6.7 - - + -
34O THR* 1.3 74.6 - - - +
36O CYS* 1.3 62.1 - - - +
37O PHE* 3.7 20.0 - - + -
50O PHE* 3.5 47.1 - - + -
61O LEU* 5.1 3.4 - - + -
63O VAL* 3.8 16.2 - - + -
94O ILE 3.7 1.0 - - - +
95O CYS* 3.1 2.3 - - - -
96O VAL* 2.8 46.4 + - + +
157O LEU* 3.8 27.8 - - + -
158O TYR 3.4 15.5 - - - +
159O MET* 4.2 13.0 - - + -
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Residues in contact with CYS 36 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34O THR* 4.3 1.3 - - - -
35O LEU* 1.3 74.8 - - - +
37O PHE* 1.3 67.9 + - - +
93O HIS* 4.2 8.1 - - - +
94O ILE 3.1 4.5 - - - -
95O CYS* 2.0 46.2 - - - -
156O ASP 3.8 2.7 - - - +
157O LEU* 3.2 0.9 - - - +
158O TYR* 2.8 35.0 + - + +
160O TRP* 3.5 31.8 - - + -
169O ILE* 4.2 8.7 - - - -
172O ALA* 4.1 9.0 - - + -
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Residues in contact with PHE 37 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35O LEU* 3.7 32.5 - - + -
36O CYS* 1.3 80.9 - - - +
38O ARG* 1.3 68.5 + - - +
39O ALA* 4.5 3.6 - - + -
49O LEU* 3.5 44.4 - - + -
50O PHE* 4.5 5.2 - - + -
63O VAL* 4.2 8.3 - - + -
92O VAL 4.1 0.2 - - - +
93O HIS* 3.6 8.5 + - - -
94O ILE* 2.8 67.6 + - + +
96O VAL* 5.5 0.4 - - + -
154O ILE* 4.6 8.5 - - + -
155O GLY 3.7 7.2 - - - +
156O ASP 3.3 10.5 - - - -
157O LEU* 3.8 24.9 - - + -
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Residues in contact with ARG 38 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37O PHE* 1.3 73.4 - - - +
39O ALA* 1.3 60.3 + - - +
91O PRO* 6.2 0.2 - - - -
92O VAL 3.3 13.7 - - - +
93O HIS* 3.5 27.7 - - + +
153O GLU 3.9 0.2 - - - +
154O ILE* 3.3 8.0 - - - +
155O GLY* 2.8 38.9 + - - +
156O ASP* 3.1 33.5 + - + +
172O ALA 3.4 22.2 + - - -
173O TYR* 3.1 25.9 + - - -
174O GLN 4.8 0.2 - - - -
175O GLY* 4.1 11.5 - - - -
201O LEU* 4.9 1.8 - - + -
203O TRP* 3.6 21.9 - - + -
204O VAL* 3.5 36.4 - - - +
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Residues in contact with ALA 39 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37O PHE* 4.5 9.2 - - + -
38O ARG* 1.3 75.6 - - - +
40O TYR* 1.3 59.5 + - - +
41O SER* 4.2 1.1 - - - +
47O TYR* 6.1 0.4 - - + +
49O LEU* 4.3 19.7 - - + -
90O ALA 4.2 0.9 - - - +
91O PRO* 3.6 1.0 - - - +
92O VAL* 2.8 55.3 + - + +
94O ILE* 4.9 0.4 - - + +
150O PHE* 4.4 5.2 - - + -
153O GLU 3.2 9.2 - - - +
154O ILE* 4.3 11.0 - - + -
203O TRP* 3.8 4.0 - - - -
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Residues in contact with TYR 40 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83K LYS 5.2 2.6 + - - -
112K THR* 4.9 4.0 - - - +
113K PRO 2.7 29.1 + - - -
114K LEU* 3.5 13.7 - - - +
115K VAL* 3.5 38.7 - - + +
39O ALA* 1.3 73.6 - - - +
41O SER* 1.3 63.0 + - - +
89O PRO* 4.7 8.0 + - + +
90O ALA* 3.7 12.1 - - - -
91O PRO* 3.5 35.8 - - + +
152O GLY* 3.4 3.1 - - - -
153O GLU* 2.9 37.9 + - + +
203O TRP* 3.5 54.5 - + + +
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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