Contacts of the strand formed by residues 92 - 99 (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 VAL 92 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O ARG* 3.3 6.7 - - - +
39O ALA* 2.8 53.4 + - + +
65O LYS* 6.2 1.1 - - + +
71O TYR* 3.7 17.9 - - + +
86O GLU* 4.5 4.9 - - + +
90O ALA 4.4 4.9 - - - +
91O PRO* 1.3 76.4 - - - +
93O HIS* 1.3 65.6 + - - +
94O ILE* 3.8 23.6 + - + +
109O ILE* 3.6 31.0 - - + -
110O ASN* 3.7 9.4 - - - +
203O TRP* 4.8 0.4 - - - -
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Residues in contact with HIS 93 (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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36O CYS* 4.2 9.7 - - + +
37O PHE* 3.6 19.1 + - - -
38O ARG* 3.5 35.0 - - - +
92O VAL* 1.3 72.6 - - - +
94O ILE* 1.3 63.3 + - - +
95O CYS* 3.3 33.9 + - - -
108O TRP* 3.6 0.8 + - - +
109O ILE* 3.5 5.2 - - - -
110O ASN* 2.9 34.8 + - - +
111O GLY 5.0 1.6 + - - -
156O ASP* 5.2 3.6 + - + +
169O ILE* 4.5 0.6 - - - +
172O ALA* 3.6 12.9 + - - +
173O TYR* 3.5 50.8 - + + +
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Residues in contact with ILE 94 (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 0.3 - - - +
36O CYS* 3.1 3.3 - - - -
37O PHE* 2.8 77.1 + - + +
39O ALA* 4.9 1.8 - - + -
49O LEU* 3.9 11.9 - - + -
63O VAL* 4.9 2.5 - - + -
71O TYR* 3.6 24.0 - - + -
92O VAL* 3.8 23.6 - - + +
93O HIS* 1.3 78.2 - - - +
95O CYS* 1.3 74.8 + - - +
96O VAL* 4.8 0.9 - - + +
107O PHE* 4.4 15.5 - - + -
108O TRP 3.5 2.5 - - - -
109O ILE* 3.8 22.7 - - + -
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Residues in contact with CYS 95 (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* 4.8 0.2 - - + -
35O LEU 3.1 3.6 - - - -
36O CYS* 2.0 46.4 - - - -
93O HIS* 3.3 22.9 + - - -
94O ILE* 1.3 74.1 - - - +
96O VAL* 1.3 62.0 + - - +
106O GLU 4.3 0.4 - - - -
107O PHE* 3.4 5.5 - - - -
108O TRP* 2.7 46.8 + - + +
169O ILE* 3.8 33.0 - - + -
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Residues in contact with VAL 96 (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* 3.8 10.5 - - + -
34O THR* 3.3 3.2 - - - -
35O LEU* 2.8 55.3 + - + +
63O VAL* 3.8 27.1 - - + -
73O LEU* 3.9 28.7 - - + -
94O ILE* 5.2 2.9 - - + -
95O CYS* 1.3 75.8 - - - +
97O SER* 1.3 64.5 + - - +
105O ALA* 5.3 0.2 - - + -
106O GLU 3.2 12.3 - - - +
107O PHE* 3.7 29.2 - - + -
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Residues in contact with SER 97 (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* 3.1 12.1 - - - -
34O THR* 3.5 17.9 - - - -
96O VAL* 1.3 79.1 - - - +
98O TRP* 1.3 62.2 + - - +
104O ILE 4.4 1.0 + - - -
105O ALA* 3.2 5.7 - - - +
106O GLU* 2.9 61.8 + - - +
108O TRP* 5.2 3.0 + - - -
163O VAL* 3.6 15.5 - - - +
164O LEU 4.9 2.6 + - - -
169O ILE* 5.8 2.0 - - - -
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Residues in contact with TRP 98 (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 4.1 2.0 - - - -
31O GLN 3.6 16.8 - - - -
32O ASN* 3.4 6.2 - - - -
33O PHE* 2.9 64.4 + + + +
73O LEU* 4.2 4.7 - - + -
75O ILE* 3.8 29.3 - - + +
97O SER* 1.3 75.1 - - - +
99O GLU* 1.3 65.4 + - - +
100O SER* 3.7 9.4 - - - -
103O GLY 3.4 16.8 + - - -
104O ILE 3.5 6.1 - - - -
105O ALA* 4.1 4.3 - - + -
119O LEU* 3.1 38.4 + - + +
120O ARG* 3.1 23.3 - - + -
123O TYR* 3.3 29.2 - + - -
125O VAL* 3.7 21.8 - - + -
163O VAL* 3.9 4.3 - - - +
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Residues in contact with GLU 99 (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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199N LYS* 2.8 28.1 + - - -
32O ASN* 3.7 16.4 - - - +
98O TRP* 1.3 77.7 - - - +
100O SER* 1.3 55.8 + - - +
101O SER* 3.4 21.6 + - - +
102O SER* 2.8 26.5 + - - +
103O GLY* 2.7 36.9 + - - -
104O ILE* 3.1 11.5 + - + +
163O VAL* 4.0 20.7 - - + +
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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