Contacts of the strand formed by residues 86 - 93 (chain S) in PDB entry 1OCR
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 GLY 86 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27R TRP* 3.6 22.0 - - - -
31R LYS* 5.4 0.2 - - - -
41S GLY 4.2 0.2 - - - +
81S ARG* 2.9 34.7 + - - -
82S CYS 2.8 17.2 + - - -
84S SER 3.7 0.6 - - - -
85S CYS* 1.3 77.3 - - - +
87S THR* 1.3 69.0 + - - +
88S HIS* 3.3 4.0 + - - -
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Residues in contact with THR 87 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514N LYS* 3.9 11.4 - - - +
40S SER 5.3 1.6 + - - -
41S GLY* 3.8 12.7 + - - -
47S ASN* 3.3 27.4 - - - +
60S CYS* 4.6 0.7 - - - -
81S ARG* 3.0 3.5 - - - -
82S CYS 2.8 23.8 + - - +
85S CYS* 3.1 27.6 + - - +
86S GLY* 1.3 75.6 - - - +
88S HIS* 1.3 62.7 + - - +
89S TYR* 3.5 24.3 - - + +
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Residues in contact with HIS 88 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41S GLY* 2.7 30.3 + - - +
42S THR* 3.2 19.7 - - - +
43S LYS* 3.6 35.7 - - + +
46S PRO* 3.6 8.8 - - + +
47S ASN* 2.9 32.3 + - - -
79S ALA* 4.2 18.2 - - + -
80S GLN 3.3 4.0 - - - -
81S ARG* 2.9 53.4 + - + -
86S GLY 3.4 1.2 + - - -
87S THR* 1.3 74.4 - - - +
89S TYR* 1.3 60.3 + - - +
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Residues in contact with TYR 89 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510N TYR* 3.9 5.8 - + - -
512N ASN* 3.4 20.7 + - - +
514N LYS* 3.0 23.6 + - - -
46S PRO* 4.4 0.4 - - - -
47S ASN* 3.2 21.8 - - + -
49S VAL* 3.8 13.5 - - + -
58S VAL* 3.8 20.6 - - + -
59S GLY 4.9 1.0 + - - -
60S CYS* 3.0 24.2 - - - +
72S PHE* 3.7 25.4 - + + -
74S LEU* 3.6 27.1 - - + +
79S ALA* 3.3 3.3 - - - -
80S GLN 2.9 32.4 + - - +
82S CYS* 4.3 1.6 - - + -
87S THR* 3.5 29.5 - - + +
88S HIS* 1.3 74.6 - - - +
90S LYS* 1.3 60.9 + - - +
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Residues in contact with LYS 90 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46S PRO* 4.1 24.0 - - + -
47S ASN 2.7 9.3 + - - -
48S LEU* 3.4 16.5 - - + -
49S VAL 2.8 24.3 + - - -
74S LEU* 3.7 4.7 - - - +
77S GLY 2.8 30.3 + - - +
78S GLU* 4.6 3.1 - - - +
79S ALA* 4.3 15.9 - - + +
89S TYR* 1.3 76.5 - - - +
91S LEU* 1.3 75.9 + - - +
92S VAL* 3.8 2.5 - - + +
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Residues in contact with LEU 91 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49S VAL* 3.2 21.1 - - + +
51S SER* 3.6 24.7 - - - -
53S THR 4.0 5.2 - - - +
54S ASN* 3.5 36.3 - - - +
55S LYS* 3.7 2.7 - - - +
56S ARG* 4.1 12.6 - - + +
74S LEU* 3.4 24.2 - - + +
75S HIS 3.8 16.4 + - - +
76S LYS* 3.8 16.4 - - + +
77S GLY 5.2 2.2 + - - +
90S LYS* 1.3 90.0 + - - +
92S VAL* 1.3 70.7 + - - +
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Residues in contact with VAL 92 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48S LEU* 3.9 30.7 - - + -
49S VAL 2.9 9.4 + - - +
50S PRO* 3.2 9.7 - - + +
51S SER* 2.7 34.8 + - - +
90S LYS* 3.8 11.9 - - + +
91S LEU* 1.3 83.7 - - - +
93S PRO* 1.3 80.8 - - + +
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Residues in contact with PRO 93 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50S PRO* 4.6 2.3 - - - +
51S SER 3.4 6.3 - - - +
92S VAL* 1.3 100.3 - - + +
94S HIS* 1.3 69.6 + - - +
95S GLN* 3.9 2.1 + - - +
97S ALA* 5.6 3.8 - - + -
98S HIS* 4.9 17.9 - - + +
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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