Contacts of the helix formed by residues 91 - 99 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D ASN* 3.0 31.8 - - + +
52D SER* 3.2 10.7 + - - +
53D TYR 3.5 20.4 - - - +
54D PRO* 4.3 2.0 - - + -
55D GLY 4.4 0.2 - - - +
56D THR* 3.7 4.5 - - - +
57D PHE* 3.6 40.6 - - + +
60D LEU* 4.6 4.7 - - + -
90D GLY* 1.3 80.9 - - - +
92D LEU* 1.3 63.7 + - - +
93D VAL* 3.3 3.1 - - - +
94D GLU* 3.3 20.9 + - - +
95D LEU* 3.0 24.6 + - + +
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Residues in contact with LEU 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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51D ASN* 3.4 5.6 - - - +
79D ILE* 3.6 35.4 - - + -
81D GLN* 3.5 27.8 - - + +
89D SER* 3.1 17.8 + - - +
90D GLY 3.5 0.2 - - - -
91D VAL* 1.3 77.1 - - - +
93D VAL* 1.3 58.0 + - - +
95D LEU* 3.2 5.1 + - + +
96D HIS* 3.0 26.7 + - + +
104D ILE* 4.2 19.7 - - + -
114D LEU* 3.7 34.1 - - + -
118D TYR* 4.9 2.5 - - + -
121D LEU* 3.8 21.1 - - + -
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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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89D SER 4.8 0.4 + - - -
90D GLY 4.9 9.9 - - - +
91D VAL 5.1 0.2 - - - -
92D LEU* 1.3 75.8 - - - +
94D GLU* 1.3 67.6 + - + +
96D HIS* 3.4 4.0 + - + +
97D ARG* 3.0 29.4 + - + +
118D TYR* 5.0 18.8 - - + -
120D SER* 3.4 26.0 - - - +
121D LEU* 4.0 20.9 - - + +
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Residues in contact with GLU 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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55D GLY* 5.1 4.7 + - - -
57D PHE* 3.3 50.5 - - + +
90D GLY 4.5 2.8 - - - +
91D VAL* 3.3 23.5 + - - +
93D VAL* 1.3 83.9 - - + +
95D LEU* 1.3 58.7 + - - +
97D ARG* 3.3 20.6 - - - +
98D ARG* 3.0 27.9 + - - +
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Residues in contact with LEU 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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48D LEU* 3.8 27.1 - - + -
51D ASN* 3.7 36.3 - - + +
57D PHE* 4.1 7.0 - - + -
60D LEU* 4.1 2.9 - - + -
61D MET* 3.5 31.2 - - + -
76D VAL* 5.5 0.4 - - + -
79D ILE* 4.1 23.3 - - + +
91D VAL* 3.0 19.2 + - + +
92D LEU* 3.2 8.3 + - - +
94D GLU* 1.3 73.2 - - - +
96D HIS* 1.3 57.2 + - - +
98D ARG* 3.6 1.5 - - - +
99D PHE* 2.7 52.3 + - + +
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Residues in contact with HIS 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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79D ILE* 4.4 5.5 - - + +
92D LEU 3.0 14.2 + - - +
93D VAL* 3.6 9.0 + - - +
95D LEU* 1.3 76.3 - - - +
97D ARG* 1.3 63.3 + - - +
99D PHE 4.3 5.8 - - - -
100D PRO* 3.4 41.9 + - + +
102D ALA 4.6 10.3 - - - -
104D ILE* 5.1 7.9 - - + -
120D SER 5.0 8.4 + - - -
121D LEU* 3.9 21.8 - - + +
123D GLU* 4.6 3.7 + - + -
124D ALA* 3.5 38.1 - - + +
125D GLU 5.0 1.0 + - - -
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Residues in contact with ARG 97 (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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93D VAL* 3.0 16.4 + - + +
94D GLU* 3.3 25.5 - - - +
96D HIS* 1.3 79.5 + - - +
98D ARG* 1.3 58.5 + - - +
100D PRO* 4.1 10.6 - - - +
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Residues in contact with ARG 98 (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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57D PHE* 4.1 18.4 - - + -
61D MET* 3.6 24.1 - - - +
65D GLU* 2.8 41.4 + - - +
94D GLU 3.0 16.8 + - - +
95D LEU 3.1 3.8 + - - +
97D ARG* 1.3 79.6 - - - +
99D PHE* 1.3 88.3 + - + +
100D PRO* 3.4 7.6 - - - +
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Residues in contact with PHE 99 (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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61D MET* 3.9 27.1 - - + -
64D VAL* 4.5 4.5 - - + -
65D GLU* 6.3 0.4 - - + -
68D LEU* 4.7 6.5 - - + -
74D GLU 5.1 1.1 - - - -
75D ARG* 3.9 17.0 - - + -
76D VAL* 3.5 63.0 - - + +
79D ILE* 4.9 2.0 - - + -
95D LEU* 2.7 31.7 + - + +
96D HIS* 3.5 8.9 - - - +
98D ARG* 1.3 99.4 - - + +
100D PRO* 1.3 66.6 - - - +
101D GLU 3.2 2.9 - - - -
102D ALA* 3.1 23.3 + - + +
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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