Contacts of the strand formed by residues 95 - 102 (chain O) 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 LEU 95 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93O PRO* 3.5 3.8 - - - +
94O SER* 1.3 80.7 + - - +
96O THR* 1.3 66.7 + - - +
97O VAL* 3.7 24.5 - - + -
110O TYR* 4.8 7.6 - - + -
112O ASP* 3.1 28.7 - - + +
113O TYR* 4.1 20.0 - - + +
144O LEU* 4.3 4.9 - - + -
145O PRO* 4.1 16.4 - - + -
148O MET* 4.6 9.6 - - + -
149O THR 4.0 1.4 + - - -
150O ILE* 3.6 10.8 - - + -
151O ARG* 2.9 25.3 + - - +
219O PHE* 3.8 35.0 - - + -
13U THR* 3.7 3.1 - - - +
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Residues in contact with THR 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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95O LEU* 1.3 76.3 + - - +
97O VAL* 1.3 72.9 + - - +
98O LYS* 4.9 1.8 - - + -
109O GLU 4.4 0.5 - - - +
110O TYR* 4.4 9.5 - - - -
111O THR 4.5 2.4 + - - -
112O ASP* 3.0 20.4 + - - +
151O ARG* 3.0 34.6 + - - +
153O LEU* 4.0 24.5 - - + -
13U THR* 2.7 23.6 + - - +
62U SER* 3.8 22.0 - - - +
63U LEU* 4.5 4.1 - - + +
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Residues in contact with VAL 97 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95O LEU* 3.7 17.7 - - + -
96O THR* 1.3 82.8 - - - +
98O LYS* 1.3 72.4 + - - +
108O TYR* 4.8 6.5 - - + -
109O GLU 3.6 13.2 - - - +
110O TYR* 3.7 29.4 - - + +
142O VAL* 5.2 1.1 - - + -
144O LEU* 3.7 26.5 - - + -
150O ILE* 3.9 5.6 - - + -
151O ARG 2.8 5.9 + - - +
152O MET* 3.2 26.8 - - + +
153O LEU* 2.9 22.3 + - - -
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Residues in contact with LYS 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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96O THR* 4.9 0.9 - - + -
97O VAL* 1.3 80.4 - - - +
99O THR* 1.3 63.2 + - - +
100O MET* 5.3 5.2 - - + -
107O SER 4.7 0.2 - - - -
108O TYR* 3.4 3.3 - - - -
109O GLU* 2.9 71.0 + - + +
111O THR* 3.2 26.1 + - - +
153O LEU* 3.3 26.9 - - + +
179O LEU* 5.3 1.1 - - + -
61U LYS 3.9 0.6 + - - -
62U SER 3.3 18.3 + - - +
63U LEU 3.5 19.3 - - - +
64U CYS 2.7 22.9 + - - +
65U PRO* 3.8 10.8 - - + -
66U ILE* 4.1 2.8 - - - +
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Residues in contact with THR 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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98O LYS* 1.3 76.0 - - - +
100O MET* 1.3 70.0 + - - +
101O GLY 4.2 0.2 - - - -
106O TRP* 3.4 19.7 - - - -
107O SER 3.3 7.7 + - - -
108O TYR* 3.5 26.5 - - - -
152O MET* 3.5 18.6 - - + -
153O LEU 2.9 12.7 + - - +
154O VAL* 3.8 19.5 - - + -
155O SER 3.2 19.9 + - - +
163O TRP* 3.7 12.3 - - + -
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Residues in contact with MET 100 (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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98O LYS* 5.3 3.1 - - + -
99O THR* 1.3 81.3 + - - +
101O GLY* 1.3 61.8 + - - +
102O HIS* 3.0 24.0 - - - +
106O TRP* 3.6 2.9 - - - -
107O SER* 2.9 31.5 + - - +
109O GLU* 3.9 24.0 - - - +
155O SER* 3.4 26.7 - - - +
156O SER 3.8 17.7 - - - +
157O GLU* 3.2 35.0 - - + +
179O LEU* 5.4 0.9 - - - -
65U PRO* 4.0 26.9 - - + -
67U SER* 4.5 1.1 - - - +
68U TRP* 4.6 7.0 - - - +
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Residues in contact with GLY 101 (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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100O MET* 1.3 75.9 - - - +
102O HIS* 1.3 63.2 + - - -
105O TYR 4.1 1.1 - - - -
106O TRP* 3.4 27.7 - - - -
155O SER 3.0 14.4 + - - -
156O SER* 3.6 0.2 + - - -
157O GLU* 3.0 24.6 + - - +
161O HIS* 3.7 18.8 - - - -
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Residues in contact with HIS 102 (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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100O MET* 3.0 27.4 + - - +
101O GLY* 1.3 72.6 + - - -
103O GLN* 1.3 53.5 + - - +
104O TRP 2.5 18.9 + - - -
105O TYR* 3.0 67.0 + + + +
107O SER* 2.8 26.1 + - - -
157O GLU* 3.5 40.0 + - + +
158O ASP* 3.6 9.7 + - - +
161O HIS* 3.4 15.5 + - - -
207O MET* 3.8 0.9 - - - +
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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