Contacts of the strand formed by residues 31 - 37 (chain O) in PDB entry 2IAN
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 TYR 31 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58K GLY* 4.7 5.8 + - - -
61K ALA* 4.6 6.9 - - + +
62K ASN* 5.0 0.3 + - - -
30M ASN* 3.1 33.7 - - - +
89N LEU* 5.1 5.6 - - + -
94N GLN* 2.6 38.8 + - + +
29O HIS* 4.2 0.7 - - - +
30O ASN* 1.3 77.4 - - - +
32O MET* 1.3 65.1 + - - +
33O TYR* 3.0 28.9 - - + +
49O SER 3.2 5.8 - - - +
50O VAL* 3.5 41.3 - - + -
93O SER* 3.4 3.1 - - - -
94O THR* 3.1 38.4 + - - +
95O TYR* 3.5 29.5 + + - -
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Residues in contact with MET 32 (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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4O VAL* 5.2 0.9 - - + -
23O CYS* 4.2 27.6 - - - +
25O GLN* 3.3 41.3 - - + +
29O HIS 4.4 0.2 - - - +
30O ASN 3.9 0.6 + - - -
31O TYR* 1.3 80.6 - - - +
33O TYR* 1.3 63.3 + - - +
48O TYR* 3.3 4.5 - - - +
49O SER 2.9 32.4 + - - -
68O ARG* 3.6 38.8 - - - +
71O THR 3.9 0.2 - - - +
72O GLU 3.7 13.7 - - - +
74O PHE* 3.4 25.1 - - + -
91O CYS* 4.6 1.8 - - - -
92O ALA 3.5 4.9 - - - +
93O SER* 4.0 9.9 - - - -
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Residues in contact with TYR 33 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89N LEU* 3.9 3.3 - - - +
94N GLN 2.7 29.4 + - - -
95N LYS* 4.8 0.4 - - - -
96N LEU* 3.4 27.8 - - + -
31O TYR* 3.0 37.6 - - + +
32O MET* 1.3 73.9 - - - +
34O TRP* 1.3 61.0 + - - +
35O TYR* 3.6 29.6 - - + +
45O LEU* 4.1 6.1 - - + -
47O TYR 3.8 4.5 - - - -
48O TYR* 3.4 33.2 - + + -
74O PHE* 3.8 3.8 - - - -
90O PHE 3.9 0.3 - - - +
91O CYS* 3.2 8.1 - - - -
92O ALA* 2.8 47.2 + - + +
93O SER* 4.2 0.7 - - - -
94O THR* 3.4 25.9 + - - -
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Residues in contact with TRP 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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6O GLN* 3.4 26.7 - - - -
21O LEU* 3.6 38.8 - - + -
22O GLN 4.2 5.8 - - - -
23O CYS* 3.8 14.6 - - + -
33O TYR* 1.3 70.4 - - - +
35O TYR* 1.3 64.9 + - - +
45O LEU* 3.2 10.2 - - - +
46O ILE* 3.0 31.4 + - + -
47O TYR 3.0 13.5 + - - +
66O VAL* 3.9 11.0 - - + -
74O PHE* 2.9 45.1 + + - -
76O LEU* 3.3 38.7 - - + +
89O TYR* 3.9 15.3 - - + -
90O PHE 3.4 22.9 - - - -
91O CYS* 3.6 15.0 - - + -
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Residues in contact with TYR 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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96N LEU* 3.0 43.5 + - - +
98N PHE* 3.6 17.6 - + - -
33O TYR* 3.6 26.4 - - + +
34O TRP* 1.3 75.1 - - - +
36O ARG* 1.3 58.4 + - - +
43O LEU* 4.1 24.0 - - + -
44O LYS* 3.1 17.5 - - - +
45O LEU* 3.6 32.3 - - + -
46O ILE* 3.6 7.0 - - - -
89O TYR* 3.2 8.1 - - - +
90O PHE* 2.7 45.1 + - + +
92O ALA* 4.0 5.6 - - + -
101O PHE* 3.6 32.8 - + - -
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Residues in contact with ARG 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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35O TYR* 1.3 73.4 - - - +
37O GLN* 1.3 60.6 + - - +
38O ASP* 3.2 21.0 + - - -
42O GLY 4.1 0.2 - - - +
43O LEU* 4.1 1.1 - - - -
44O LYS* 3.0 40.8 + - + +
46O ILE* 3.4 21.9 - - + +
60O VAL* 4.0 24.1 - - + +
64O TYR* 3.1 28.8 + - - -
84O SER* 2.9 31.1 + - - -
85O GLN* 3.8 4.0 - - - +
86O THR 3.5 5.7 + - - -
87O SER* 3.2 28.3 + - - +
88O VAL 3.3 5.8 - - - +
89O TYR* 3.9 11.4 - - + -
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Residues in contact with GLN 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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36N GLN* 2.8 44.2 + - - -
85N PHE* 4.4 8.1 - - - -
36O ARG* 1.3 78.1 - - - +
38O ASP* 1.3 70.0 + - - +
39O PRO* 4.3 0.3 - - - +
40O GLY 5.8 0.8 - - - +
41O MET 2.9 23.6 + - - +
42O GLY* 4.2 8.6 - - - +
43O LEU* 4.0 18.0 - - + +
44O LYS* 6.5 0.2 - - - -
87O SER* 3.3 11.6 + - - -
88O VAL* 2.8 34.8 + - + +
90O PHE* 3.1 16.6 - - + -
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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