Contacts of the strand formed by residues 117 - 125 (chain D) in PDB entry 2OVI
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 MET 117 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113D LYS* 3.5 0.8 - - - -
114D PHE* 3.0 44.0 + - + +
115D MET 3.4 1.4 + - - +
116D GLY* 1.3 75.2 - - - +
118D ASP* 1.3 73.3 + - - +
119D THR* 3.5 8.0 + - + +
139D ARG* 4.4 18.4 - - - +
143D ARG* 4.4 27.1 - - + -
144D GLN* 4.1 17.5 - - - +
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Residues in contact with ASP 118 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111D GLU* 5.5 9.1 - - - +
112D ARG 3.4 7.5 - - - +
113D LYS* 2.5 37.7 + - - +
117D MET* 1.3 74.2 - - - +
119D THR* 1.3 54.6 + - - +
139D ARG* 2.8 34.3 + - - -
144D GLN* 4.2 18.7 + - - +
145D LEU* 3.8 18.0 - - + +
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Residues in contact with THR 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ILE 5.3 0.2 + - - -
111D GLU* 3.3 6.8 - - - +
112D ARG* 2.8 47.7 + - - +
113D LYS 5.1 0.4 - - - -
114D PHE* 4.4 18.2 - - + +
117D MET* 3.6 10.3 - - + +
118D ASP* 1.3 80.4 - - - +
120D ALA* 1.3 62.9 + - - +
121D SER* 5.7 0.7 + - - -
136D PHE* 5.7 8.5 - - - -
139D ARG* 3.9 15.0 - - - +
145D LEU* 3.9 5.6 - - - +
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Residues in contact with ALA 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ILE 3.3 9.0 - - - +
111D GLU* 4.3 11.2 - - + +
119D THR* 1.3 78.0 - - - +
121D SER* 1.3 62.6 + - - +
136D PHE* 3.6 5.0 - - - +
137D LEU* 3.2 54.0 + - + +
145D LEU* 3.8 14.3 - - + +
150D VAL* 5.3 1.1 - - + -
153D PHE* 4.3 10.3 - - + -
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Residues in contact with SER 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D ALA 3.6 0.9 - - - +
109D LEU* 3.5 3.5 - - - -
110D ILE* 2.8 52.5 + - - +
119D THR* 5.7 1.1 + - - -
120D ALA* 1.3 76.9 - - - +
122D ILE* 1.3 65.1 + - - +
123D LEU* 3.6 12.7 - - - +
135D ILE 3.1 13.2 - - - -
136D PHE* 3.7 26.3 - - - -
137D LEU* 4.9 1.3 - - - -
153D PHE* 3.6 4.5 - - - -
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Residues in contact with ILE 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D VAL* 4.0 9.2 - - + -
54D VAL* 3.3 33.9 - - + -
57D TRP* 4.0 18.8 - - + -
107D ILE* 3.9 19.5 - - + -
108D ALA 3.3 4.0 - - - +
109D LEU* 4.1 17.9 - - + -
121D SER* 1.3 77.2 - - - +
123D LEU* 1.3 65.0 + - - +
124D PHE* 3.7 28.5 - - + -
133D LEU 4.2 0.3 - - - +
134D LYS* 3.3 6.1 - - - -
135D ILE* 2.7 52.3 + - + +
137D LEU* 5.4 1.3 - - + -
153D PHE* 4.3 4.5 - - + -
156D LEU* 4.8 0.9 - - + -
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Residues in contact with LEU 123 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D LEU* 5.6 2.7 - - + -
29D LEU* 4.0 17.7 - - + -
33D VAL* 4.1 15.0 - - + -
107D ILE* 3.0 9.9 - - - +
108D ALA* 2.9 34.3 + - + +
110D ILE* 4.7 8.3 - - + -
121D SER* 3.6 24.2 - - - +
122D ILE* 1.3 81.6 - - - +
124D PHE* 1.3 62.4 + - - +
125D PHE* 3.5 35.9 - - + -
131D ALA* 4.8 3.1 - - + -
133D LEU 3.9 2.0 - - - -
134D LYS* 3.4 32.8 - - + +
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Residues in contact with PHE 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D PHE* 3.9 28.5 - + - -
50D VAL* 4.0 16.4 - - + -
51D TRP* 3.8 21.5 - + - -
54D VAL* 5.8 1.8 - - + -
104D CYS* 4.2 6.3 - - + -
106D HIS 3.6 3.6 - - - -
107D ILE* 3.9 30.1 - - + -
122D ILE* 3.7 24.9 - - + -
123D LEU* 1.3 75.3 - - - +
125D PHE* 1.3 62.6 + - - +
131D ALA* 3.3 4.2 - - - -
132D MET* 2.9 42.0 + - + +
133D LEU* 3.1 30.3 + - + +
135D ILE* 3.7 24.2 - - + -
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Residues in contact with PHE 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D LEU* 3.6 17.3 - - + -
30D LEU* 3.1 58.8 - - + -
33D VAL* 3.8 11.4 - - + -
104D CYS* 3.1 10.7 - - - +
105D THR* 3.0 20.4 + - - +
106D HIS* 2.7 32.2 + - + +
108D ALA* 3.8 18.4 - - + -
123D LEU* 3.5 43.5 - - + -
124D PHE* 1.3 75.3 - - - +
126D ASN* 1.3 67.6 + - - +
129D GLY 3.7 11.0 - - - -
130D SER 3.2 11.2 - - - +
131D ALA 4.3 0.9 - - - -
132D MET* 4.3 2.7 - - - -
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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