Contacts of the helix formed by residues 93 - 99 (chain D) in PDB entry 1OHV
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 ASN 93 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88C VAL* 5.6 0.2 - - - -
87D LEU* 2.9 39.0 + - - +
88D VAL 5.3 0.7 - - - +
90D GLN* 3.0 22.0 + - - +
92D GLN* 1.3 85.4 + - - +
94D VAL* 1.3 65.9 + - - +
95D SER 3.3 2.0 - - - -
96D THR* 3.2 19.9 + - - -
97D PHE* 3.2 18.9 - - + -
362D LEU* 3.6 36.2 - - + +
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Residues in contact with VAL 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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85C VAL* 4.1 27.4 - - + -
88C VAL* 4.2 26.7 - - + -
89C GLN* 4.8 16.4 - - + +
88D VAL 5.7 1.6 - - - +
90D GLN 3.9 2.6 + - - +
91D PRO* 3.2 28.8 + - + +
92D GLN 3.4 0.4 - - - -
93D ASN* 1.3 76.2 - - - +
95D SER* 1.3 64.9 + - - +
97D PHE* 3.0 16.3 + - - +
98D ILE* 3.3 30.0 + - + +
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Residues in contact with SER 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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49C TYR* 3.4 22.1 - - - +
50C GLU* 3.5 32.5 + - - -
80C SER* 5.0 1.3 - - - -
92D GLN 4.6 1.7 + - - -
93D ASN 3.3 0.4 - - - -
94D VAL* 1.3 80.2 - - - +
96D THR* 1.3 57.1 + - - +
97D PHE 3.1 0.2 + - - -
98D ILE* 4.0 5.6 - - - -
99D ASN* 2.8 61.3 + - - +
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Residues in contact with THR 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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50C GLU* 4.3 9.8 + - - -
92D GLN 4.9 0.7 + - - -
93D ASN* 3.2 19.5 + - - -
95D SER* 1.3 78.0 - - - +
97D PHE* 1.3 60.5 + - + +
98D ILE 3.8 0.2 + - - -
99D ASN 4.4 9.4 + - - +
100D ARG* 5.2 1.7 + - - -
110D ASN* 5.2 5.7 + - - -
357D ASP* 4.4 4.0 - - - +
358D PRO* 3.7 19.1 - - + +
359D SER* 3.6 39.8 + - - +
362D LEU* 4.2 18.5 - - + +
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Residues in contact with PHE 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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88C VAL* 4.1 25.4 - - + -
97C PHE* 3.5 41.6 - + + -
360C LYS* 4.6 8.7 + - - +
363C LEU* 3.4 20.3 - - - +
88D VAL* 3.9 38.4 - - + -
93D ASN* 3.2 28.3 - - + -
94D VAL 3.0 7.3 + - - +
96D THR* 1.3 79.7 - - - +
98D ILE* 1.3 58.2 + - - +
99D ASN 3.7 0.4 - - - -
100D ARG* 6.1 1.1 - - - +
359D SER* 3.7 26.5 - - - -
362D LEU* 4.1 24.0 - - + -
363D LEU* 4.5 10.3 - - + -
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Residues in contact with ILE 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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75C ILE* 5.2 3.8 - - - +
80C SER* 3.8 22.2 - - - +
81C HIS 4.2 1.8 - - - +
84C LEU* 3.7 33.1 - - + +
85C VAL* 3.6 35.2 - - + +
88C VAL* 3.4 33.0 - - + -
332C MET* 5.0 7.4 - - - +
363C LEU* 4.2 11.9 - - + -
94D VAL* 3.6 16.8 - - + +
95D SER* 3.9 7.9 - - - +
97D PHE* 1.3 79.0 - - - +
99D ASN* 1.3 71.5 + - - +
100D ARG* 3.7 3.6 + - - -
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Residues in contact with ASN 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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49C TYR* 3.5 27.5 + - + +
75C ILE* 4.7 6.3 - - - +
78C GLY 4.6 0.9 - - - +
79C TYR* 3.4 17.7 - - + -
80C SER* 2.8 45.8 + - - +
95D SER* 2.8 43.0 + - - +
96D THR* 4.4 6.9 - - - +
97D PHE 3.7 0.2 - - - -
98D ILE* 1.3 85.0 - - - +
100D ARG* 1.3 62.5 + - - +
101D PRO* 3.3 12.0 - - - +
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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