Contacts of the helix formed by residues 91 - 99 (chain I) in PDB entry 2OHI
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 VAL 91 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51I ASN* 3.0 30.6 - - + +
52I SER* 3.4 6.9 + - - +
53I TYR 3.8 17.5 - - - +
54I PRO* 4.1 1.8 - - + -
56I THR* 3.9 4.9 - - - +
57I PHE* 3.8 37.0 - - + +
60I LEU* 3.8 19.5 - - + -
90I GLY* 1.3 80.5 - - - +
92I LEU* 1.3 59.8 + - - +
93I VAL* 3.3 3.4 - - - +
94I GLU* 3.2 18.2 + - - +
95I LEU* 2.9 26.6 + - + +
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Residues in contact with LEU 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I ASN* 3.2 5.8 - - - +
79I ILE* 3.8 28.9 - - + -
81I GLN* 3.2 31.6 - - - +
89I SER 3.3 12.3 + - - +
90I GLY 3.7 0.4 - - - -
91I VAL* 1.3 76.5 - - - +
93I VAL* 1.3 53.6 + - - +
95I LEU* 3.0 9.1 + - + +
96I HIS* 2.8 34.5 + - + +
104I ILE* 4.0 21.8 - - + -
114I LEU* 3.7 28.7 - - + -
118I TYR* 4.8 4.2 - - + -
121I LEU* 3.6 26.7 - - + -
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Residues in contact with VAL 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89I SER 5.1 0.2 + - - -
90I GLY 5.0 7.2 - - - +
91I VAL 4.8 2.7 - - - -
92I LEU* 1.3 79.2 - - - +
94I GLU* 1.3 75.4 + - + +
96I HIS* 3.6 3.6 + - - +
97I ARG* 3.2 21.1 + - - +
118I TYR* 4.9 23.3 - - + -
120I SER* 3.5 24.9 - - - +
121I LEU* 4.5 16.9 - - + +
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Residues in contact with GLU 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55I GLY* 4.5 10.7 + - - -
57I PHE* 3.4 48.7 - - + +
90I GLY 4.8 2.0 - - - +
91I VAL* 3.2 22.3 + - - +
93I VAL* 1.3 86.2 - - + +
95I LEU* 1.3 60.1 - - - +
97I ARG* 3.3 8.2 + - - +
98I ARG* 2.9 29.3 + - - +
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Residues in contact with LEU 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I LEU* 3.5 36.1 - - + -
51I ASN* 3.8 31.0 - - + +
57I PHE* 3.8 6.3 - - + -
60I LEU* 4.1 7.0 - - + -
61I MET* 3.7 26.5 - - + -
79I ILE* 4.0 25.5 - - + +
91I VAL 2.9 12.1 + - - +
92I LEU* 3.0 11.0 + - - +
94I GLU* 1.3 76.3 - - - +
96I HIS* 1.3 52.2 + - - +
98I ARG* 3.2 4.1 + - - +
99I PHE* 2.7 51.0 + - + +
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Residues in contact with HIS 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I ILE* 4.4 7.4 - - + +
92I LEU 2.8 15.4 + - - +
93I VAL 3.9 5.3 + - - +
95I LEU* 1.3 76.9 - - - +
97I ARG* 1.3 61.7 + - - +
99I PHE 4.1 11.2 - - - -
100I PRO* 3.2 39.8 + - + +
102I ALA 4.2 14.9 + - - -
104I ILE* 4.8 9.9 - - + -
120I SER 5.7 1.5 + - - -
121I LEU* 3.8 22.7 - - + +
123I GLU 4.8 3.1 - - - -
124I ALA* 3.8 33.4 - - + +
125I GLU 4.5 2.6 + - - -
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Residues in contact with ARG 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93I VAL 3.2 14.6 + - - +
94I GLU* 3.6 10.5 - - - +
95I LEU 3.2 0.8 - - - -
96I HIS* 1.3 77.7 + - - +
98I ARG* 1.3 62.8 + - - +
100I PRO* 3.9 9.1 - - - +
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Residues in contact with ARG 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57I PHE* 3.9 15.3 - - + -
61I MET* 4.1 21.6 - - + +
65I GLU* 2.8 31.1 + - - -
74I GLU 5.7 3.2 + - - -
75I ARG* 5.8 1.8 - - - +
94I GLU 2.9 16.3 + - - +
95I LEU* 3.5 5.4 - - - +
97I ARG* 1.3 79.4 - - - +
99I PHE* 1.3 98.1 + - + +
100I PRO* 3.4 6.8 - - - +
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Residues in contact with PHE 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61I MET* 3.7 30.5 - - + -
64I VAL* 4.6 2.7 - - + -
65I GLU* 5.5 0.7 - - - -
68I LEU* 5.4 3.1 - - + -
74I GLU 5.8 0.2 - - - -
75I ARG* 4.2 14.8 - - + -
76I VAL* 3.5 65.1 - - + +
79I ILE* 4.9 2.7 - - + -
95I LEU* 2.7 31.3 + - + +
96I HIS* 3.2 13.5 - - - +
98I ARG* 1.3 115.7 - - + +
100I PRO* 1.4 65.0 - - - +
101I GLU 3.2 4.2 + - - +
102I ALA* 3.2 20.4 + - + +
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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