Contacts of the strand formed by residues 105 - 110 (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 TYR 105 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101O GLY 3.9 0.2 - - - -
102O HIS* 3.0 73.3 + + + +
103O GLN 3.9 11.2 - - - -
104O TRP* 1.3 80.9 - - - +
106O TRP* 1.3 75.4 - - - +
107O SER* 4.3 0.2 - - - -
119O ASP* 3.7 30.1 + - + -
120O SER 3.7 14.6 - - - +
121O TYR* 3.3 46.2 - + + +
207O MET* 3.9 12.8 - - - +
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Residues in contact with TRP 106 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99O THR* 3.4 16.6 - - - -
100O MET 3.6 3.6 - - - -
101O GLY* 3.4 28.7 - - - -
105O TYR* 1.3 78.3 - - - +
107O SER* 1.3 59.9 + - - +
108O TYR* 3.4 24.2 - - + +
120O SER* 2.7 33.5 + - - +
154O VAL* 4.6 2.9 - - + -
161O HIS* 3.5 20.0 - - + -
162O SER 3.5 15.3 - - - -
163O TRP* 3.5 39.0 - + + -
174O ALA* 4.2 7.4 - - + -
196O CYS* 4.2 6.5 - - - -
207O MET* 2.7 53.6 + - + +
208O PRO 3.5 14.6 - - - -
209O ILE* 3.7 12.7 - - + +
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Residues in contact with SER 107 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99O THR* 3.3 5.0 + - - -
100O MET* 2.9 40.7 + - - +
102O HIS* 2.8 29.5 + - - -
106O TRP* 1.3 73.3 - - - +
108O TYR* 1.3 64.5 + - - +
109O GLU* 5.0 4.5 + - - +
117O SER* 5.5 3.1 - - - -
118O PHE 3.2 7.6 - - - -
119O ASP* 3.4 24.5 - - - -
157O GLU* 5.0 0.7 + - - -
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Residues in contact with TYR 108 (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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97O VAL* 4.8 4.7 - - + -
98O LYS 3.4 6.7 - - - +
99O THR* 3.5 22.4 - - - -
106O TRP* 3.4 27.3 - - + +
107O SER* 1.3 74.1 - - - +
109O GLU* 1.3 66.7 + - - +
110O TYR* 4.2 10.8 - - + -
117O SER* 3.3 5.1 + - - -
118O PHE* 2.8 57.7 + + + -
120O SER* 3.5 32.5 + - - -
142O VAL* 3.7 35.2 - - + +
152O MET* 5.0 1.1 - - + -
163O TRP* 3.3 27.8 + + - -
208O PRO 4.8 0.2 + - - -
209O ILE* 3.9 16.1 - - - +
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Residues in contact with GLU 109 (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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97O VAL* 3.6 3.1 - - - -
98O LYS* 2.9 69.4 + - + +
100O MET* 3.9 23.1 - - + +
107O SER* 5.0 4.9 + - - +
108O TYR* 1.3 83.1 - - - +
110O TYR* 1.3 64.5 + - - +
111O THR* 3.8 6.0 + - + -
116O LEU 3.3 6.5 - - - +
117O SER* 4.2 11.6 + - - +
157O GLU* 4.9 1.6 - - - +
65U PRO* 3.7 3.4 - - - +
66U ILE* 3.0 38.8 + - + +
67U SER* 4.5 5.0 + - - -
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Residues in contact with TYR 110 (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* 4.3 7.4 - - + -
96O THR 4.4 6.7 - - - +
97O VAL* 3.7 36.1 - - + -
108O TYR* 4.2 5.6 - - + -
109O GLU* 1.3 78.9 - - - +
111O THR* 1.3 58.4 + - - +
112O ASP 3.8 1.6 - - - +
114O GLU* 3.8 3.2 - - - +
116O LEU* 2.8 48.9 + - + +
118O PHE* 3.6 28.7 - + - -
142O VAL* 3.5 10.9 - - - +
143O VAL 2.6 44.4 + - - -
144O LEU* 3.9 2.7 - - + -
219O PHE* 3.5 27.8 - + + -
222O TRP* 3.6 8.5 - + - -
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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