Contacts of the strand formed by residues 85 - 91 (chain A) in PDB entry 2V7O
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 PHE 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A ILE* 3.7 23.3 - - + -
45A ILE 3.2 12.3 - - - -
46A ASN* 3.8 22.7 - - + -
47A THR* 3.6 5.1 + - - -
48A LYS* 3.2 31.0 - - - -
81A SER* 4.3 0.5 + - - -
82A GLU* 3.0 33.3 + - + +
83A GLU 3.5 0.8 - - - -
84A GLY* 1.3 83.4 - - - +
86A HIS* 1.3 59.2 + - - +
87A TYR* 3.6 30.1 - - + +
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Residues in contact with HIS 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LYS 3.6 0.9 - - - +
44A ILE* 3.5 5.0 - - - +
45A ILE* 2.8 36.5 + - + +
47A THR* 3.7 17.0 - - + +
58A LEU* 4.0 26.3 - - + +
62A ALA* 4.7 4.5 - - + +
79A SER* 2.8 30.1 + - - -
80A ILE 3.3 21.4 + - - -
81A SER* 3.7 19.9 + - - -
85A PHE* 1.3 75.0 - - - +
87A TYR* 1.3 75.7 + - - +
88A LEU* 3.7 22.0 - - + +
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Residues in contact with TYR 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PHE* 3.5 60.5 - + + -
11A THR* 4.8 2.3 + - - -
16A LEU* 4.9 3.8 - - + +
42A ALA* 4.6 1.8 - - + -
43A LYS 3.4 4.9 - - - +
44A ILE* 3.7 36.6 - - + +
78A ASP 3.8 0.7 - - - +
79A SER* 3.4 4.3 - - - -
80A ILE* 2.8 48.3 + - + +
82A GLU* 3.8 31.9 + - + -
85A PHE* 3.6 35.6 - - + +
86A HIS* 1.3 75.1 - - - +
88A LEU* 1.3 63.1 + - - +
89A VAL* 3.8 3.7 + - + -
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ALA 3.5 2.4 - - - +
42A ALA* 3.4 1.4 - - - -
43A LYS* 2.9 41.2 + - + +
45A ILE* 4.2 15.7 - - + -
58A LEU* 4.5 5.8 - - + -
61A GLU* 3.9 36.8 - - + +
62A ALA* 3.9 16.4 - - + +
65A CYS* 5.4 0.7 - - - -
76A LEU* 3.7 9.2 - - + -
78A ASP 3.7 2.2 - - - -
79A SER* 3.3 30.7 - - - +
86A HIS* 3.7 16.4 - - + +
87A TYR* 1.3 69.8 - - - +
89A VAL* 1.3 61.9 + - - +
90A PHE* 3.6 23.3 - - + -
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Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PHE* 3.9 25.6 - - + -
14A TYR* 3.8 19.7 - - + +
31A CYS* 4.3 4.9 - - - -
40A TYR* 3.4 37.7 - - + -
41A ALA 3.7 3.1 - - - +
42A ALA* 4.4 1.6 - - + +
76A LEU* 3.5 3.6 - - - +
77A HIS* 2.6 33.1 + - - +
78A ASP* 2.9 23.0 + - + +
80A ILE* 4.0 22.2 - - + -
87A TYR* 4.5 4.5 - - + +
88A LEU* 1.3 72.5 - - - +
90A PHE* 1.3 54.5 + - - +
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Residues in contact with PHE 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A TYR* 3.2 13.8 - - - +
41A ALA 2.9 32.3 + - - +
43A LYS* 4.4 4.3 - - + -
61A GLU* 4.8 3.1 - - - -
65A CYS* 3.8 28.3 - - + -
74A VAL* 4.0 11.7 - - + -
75A ARG 3.3 19.3 - - - +
76A LEU* 3.6 25.4 - - + -
77A HIS 4.8 0.7 - - - -
88A LEU* 3.6 35.0 - - + -
89A VAL* 1.3 73.9 - - - +
91A ASP* 1.3 73.0 + - - +
158A PHE* 6.3 1.1 - + - -
1303A DRN 3.6 48.5 - + - +
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Residues in contact with ASP 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLN* 5.9 0.5 + - - -
39A GLU 5.2 0.2 - - - -
40A TYR* 4.1 17.9 - - - -
41A ALA* 4.1 0.2 - - - +
74A VAL* 3.6 13.9 - - + +
75A ARG* 3.0 36.1 + - - +
77A HIS* 4.5 6.3 - - - +
90A PHE* 1.3 74.2 - - - +
92A LEU* 1.3 64.9 + - - +
93A VAL* 4.9 3.8 - - + -
154A LYS* 5.1 10.0 + - - -
1303A DRN 2.9 23.6 + - - -
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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