Contacts of the helix formed by residues 86 - 96 (chain D) in PDB entry 2OV2
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 SER 86 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14D VAL* 6.0 0.2 - - - -
83D SER* 3.2 19.6 + - - +
84D LEU 3.5 0.8 - - - -
85D VAL* 1.3 77.7 - - - +
87D PRO* 1.3 64.6 - - - +
88D ALA* 3.7 8.5 + - - +
89D SER* 2.8 47.9 + - - -
90D PHE* 3.3 4.2 + - - +
129D LEU* 5.1 0.2 - - - -
137D ILE* 5.1 1.3 - - - -
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Residues in contact with PRO 87 (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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107A HIS* 3.6 31.4 - - + +
84D LEU 5.5 0.2 - - - +
85D VAL 3.9 1.3 - - - -
86D SER* 1.3 82.9 - - - +
88D ALA* 1.3 64.3 + - - +
90D PHE* 3.5 2.3 - - + +
91D GLU* 3.0 28.2 + - - +
129D LEU* 3.9 17.9 - - + -
134D LEU* 4.3 24.2 - - + -
135D ALA 3.6 22.7 - - - +
137D ILE* 4.0 16.4 - - + -
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Residues in contact with ALA 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ASP* 5.4 0.7 - - - +
86D SER* 3.2 8.1 + - - +
87D PRO* 1.3 77.5 - - - +
89D SER* 1.3 62.5 + - - +
91D GLU* 3.4 12.4 + - - +
92D ASN* 3.1 33.7 + - - +
134D LEU* 6.0 0.6 - - - +
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Residues in contact with SER 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ASP* 3.3 21.2 + - - +
12D GLY 5.4 0.4 - - - -
14D VAL* 3.7 26.0 - - - -
81D CYS 4.8 1.6 - - - +
82D PHE* 3.6 10.0 - - - +
83D SER* 3.1 22.5 + - - -
86D SER* 2.8 31.4 + - - -
88D ALA* 1.3 78.0 - - - +
90D PHE* 1.3 60.5 + - - +
92D ASN* 3.5 3.6 + - - +
93D VAL* 3.4 16.1 + - - +
97D TRP* 4.9 1.4 - - - -
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Residues in contact with PHE 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PRO* 3.6 34.8 - - + -
107A HIS* 4.2 11.4 - + + -
82D PHE* 3.6 49.1 - + + -
86D SER 3.3 5.8 + - - +
87D PRO 3.5 6.3 - - - +
89D SER* 1.3 78.0 + - - +
91D GLU* 1.3 65.5 + - - +
93D VAL* 3.1 21.4 - - + +
137D ILE* 3.7 29.2 - - + -
141D GLN 3.3 26.5 - - - -
142D GLY* 4.0 5.6 - - - -
145D MET* 3.3 37.8 - - + +
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Residues in contact with GLU 91 (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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106A PRO* 4.6 13.9 - - + -
107A HIS* 3.7 27.6 - - + +
87D PRO 3.0 16.3 + - - +
88D ALA* 3.6 13.5 - - - +
90D PHE* 1.3 75.9 - - - +
92D ASN* 1.3 59.0 + - - +
94D ARG* 3.1 10.4 + - - +
95D ALA* 3.1 23.3 + - + +
145D MET* 4.8 6.5 - - - -
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Residues in contact with ASN 92 (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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11D ASP* 2.9 41.0 + - - +
88D ALA* 3.1 21.4 + - - +
89D SER 3.8 3.1 - - - +
90D PHE 3.2 0.6 - - - -
91D GLU* 1.3 73.2 - - - +
93D VAL* 1.3 60.5 + - - +
94D ARG 3.2 0.2 - - - -
95D ALA* 3.8 17.1 - - - +
96D LYS* 2.8 31.8 + - + +
97D TRP* 2.9 14.7 + - - +
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Residues in contact with VAL 93 (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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80D ILE* 4.1 12.6 - - + -
81D CYS 4.6 1.6 - - - +
82D PHE* 3.9 29.8 - - + -
89D SER 3.4 12.4 + - - +
90D PHE* 3.1 18.4 - - + +
92D ASN* 1.3 77.7 - - - +
94D ARG* 1.3 57.0 + - - +
97D TRP* 3.9 8.3 - - + -
98D TYR* 2.9 31.2 + - - +
112D LEU* 3.7 22.0 - - + -
145D MET* 4.0 16.2 - - + -
149D ILE* 3.9 19.1 - - + -
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Residues in contact with ARG 94 (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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102A ARG 3.6 9.1 + - - -
103A HIS* 2.9 39.4 + - - -
104A HIS 4.7 3.2 + - - -
106A PRO* 3.9 27.3 - - - +
90D PHE 4.2 0.4 + - - -
91D GLU 3.1 8.4 + - - +
93D VAL* 1.3 78.3 - - - +
95D ALA* 1.3 66.1 + - - +
98D TYR* 4.6 9.5 - - + -
99D PRO* 3.2 19.9 - - - +
145D MET* 3.9 22.2 - - + +
148D GLU* 3.2 36.4 + - + +
149D ILE* 4.7 10.1 - - + -
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Residues in contact with ALA 95 (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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91D GLU* 3.1 16.0 + - + +
92D ASN* 3.8 15.7 - - - +
94D ARG* 1.3 80.3 - - - +
96D LYS* 1.3 57.5 + - - +
99D PRO* 3.9 9.9 - - - +
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Residues in contact with LYS 96 (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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11D ASP* 5.3 2.0 - - - +
60D GLY 5.2 1.2 + - - -
62D GLU* 3.8 23.8 + - + +
65D ASP* 2.8 36.8 + - - -
68D ARG* 4.4 1.8 - - - +
92D ASN* 2.8 28.5 + - + +
94D ARG 3.4 0.2 - - - -
95D ALA* 1.3 76.4 - - + +
97D TRP* 1.3 94.7 + - + +
98D TYR 3.5 1.3 - - - -
99D PRO* 3.4 4.3 - - - +
100D GLU* 3.0 46.4 + - + +
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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