Contacts of the strand formed by residues 106 - 114 (chain A) 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 HIS 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A LEU* 4.1 22.4 - - + +
34A ARG* 3.6 13.7 + - - -
41A VAL* 4.1 10.5 - - + -
42A VAL 3.2 9.6 - - - +
44A GLY 3.8 1.1 - - - +
104A CYS* 3.4 2.9 - - - -
105A THR* 1.3 108.9 + - - +
107A ILE* 1.3 69.4 + - - +
125A PHE* 2.8 41.7 + - + +
126A ASN 4.9 1.2 + - - -
127A LYS* 5.8 1.6 - - - -
129A GLY* 6.1 0.6 - - - -
27B THR* 3.9 1.3 - - - -
28B THR* 3.8 22.6 + - + -
31B GLU* 2.9 43.5 + - + +
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Residues in contact with ILE 107 (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 THR 3.7 0.3 - - - +
41A VAL* 3.4 3.3 - - - +
42A VAL* 2.8 42.3 + - + +
43A PRO 4.4 7.4 - - - +
44A GLY* 4.5 1.3 - - - +
46A LYS* 3.7 7.4 - - + +
47A PHE* 3.4 42.4 - - + +
50A VAL* 4.0 17.7 - - + -
104A CYS* 3.6 13.7 - - - -
106A HIS* 1.3 81.9 - - - +
108A ALA* 1.3 66.2 + - - +
109A LEU* 4.4 5.6 - - + +
122A ILE* 4.0 21.5 - - + -
123A LEU 3.3 9.0 - - - +
124A PHE* 3.9 16.4 - - + -
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Residues in contact with ALA 108 (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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33A VAL* 3.7 30.7 - - + -
39A SER* 5.7 0.2 - - - -
40A THR 3.0 10.1 - - - +
41A VAL* 4.4 7.0 - - + -
107A ILE* 1.3 76.3 - - - +
109A LEU* 1.3 67.0 + - - +
110A ILE* 4.0 8.3 - - + -
121A SER 3.7 0.9 - - - +
122A ILE* 3.2 6.1 - - - +
123A LEU* 2.8 39.9 + - + +
125A PHE* 3.8 13.4 - - + -
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Residues in contact with LEU 109 (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 SER 4.8 0.7 - - - +
39A SER* 3.6 0.9 - - - -
40A THR* 2.8 42.7 + - - +
42A VAL* 5.7 0.2 - - + -
50A VAL* 4.9 2.9 - - + -
107A ILE* 4.4 13.5 - - + +
108A ALA* 1.3 79.5 - - - +
110A ILE* 1.3 63.1 + - - +
121A SER 3.5 2.9 - - - -
122A ILE* 3.9 18.2 - - + -
153A PHE* 3.5 47.3 - - + +
156A LEU* 3.9 24.9 - - + -
157A ALA* 4.0 10.8 - - + +
160A LEU* 3.7 22.7 - - + -
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Residues in contact with ILE 110 (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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18A LEU* 3.8 27.1 - - + -
33A VAL* 4.1 15.3 - - + -
36A LEU* 3.8 15.9 - - + -
38A SER 5.8 0.2 - - - -
39A SER* 3.5 26.7 - - - +
108A ALA* 4.5 7.6 - - + -
109A LEU* 1.3 81.1 - - - +
111A GLU* 1.3 66.6 + - - +
112A ARG* 4.3 11.2 - - + -
119A THR* 6.0 1.8 - - + -
120A ALA* 3.3 4.0 - - - -
121A SER* 3.0 52.6 + - - +
123A LEU* 4.1 15.9 - - + -
153A PHE* 3.5 2.0 - - - -
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Residues in contact with GLU 111 (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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36A LEU* 4.5 6.3 - - - +
37A PRO 4.6 10.1 + - - +
38A SER* 5.5 6.6 + - - +
39A SER* 5.6 1.2 - - - +
110A ILE* 1.3 82.5 - - - +
112A ARG* 1.3 65.8 + - - +
119A THR 3.2 7.4 - - - +
120A ALA* 4.0 12.3 - - + +
150A VAL* 4.6 5.2 - - - +
153A PHE* 3.7 18.0 - - + -
154A HIS* 2.6 43.2 + - - -
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Residues in contact with ARG 112 (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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13A GLU* 5.5 1.8 - - - +
14A PRO* 3.8 29.1 + - - +
16A GLY 2.4 32.3 + - - +
17A THR 4.5 0.4 - - - -
18A LEU* 3.2 46.6 - - - +
21A VAL* 5.9 0.2 - - - +
36A LEU* 4.1 23.2 - - + +
110A ILE* 4.3 7.9 - - + -
111A GLU* 1.3 77.6 - - - +
113A LYS* 1.3 66.8 + - - +
114A PHE* 4.0 14.8 - - - +
118A ASP* 4.6 2.2 - - - -
119A THR* 2.8 50.7 + - + +
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Residues in contact with LYS 113 (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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13A GLU* 5.4 20.6 + - + +
14A PRO 4.7 4.9 - - - +
112A ARG* 1.3 90.3 + - - +
114A PHE* 1.3 59.1 + - - +
116A GLY* 2.5 50.3 + - - +
117A MET* 3.4 8.9 - - - +
118A ASP* 4.1 18.9 + - - +
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Residues in contact with PHE 114 (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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14A PRO 6.0 0.2 - - - -
16A GLY* 3.5 39.9 - - - +
17A THR* 4.0 13.2 - - - -
112A ARG* 3.8 12.8 + - - +
113A LYS* 1.3 76.7 - - - +
115A MET* 1.3 104.0 + - + +
117A MET* 3.0 25.5 + - + +
119A THR* 4.5 16.2 - - + -
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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