Contacts of the strand formed by residues 129 - 133 (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 GLN 129 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C ILE 2.9 25.5 + - - -
37C ILE 3.0 15.3 - - - +
38C GLN* 3.6 4.3 - - - -
127D MET 4.3 0.2 - - - +
128D SER* 1.3 96.9 + - - +
130D LEU* 1.3 61.6 + - - +
337D PHE* 3.2 11.1 - - - +
338D HIS* 3.0 57.7 + - + +
339D LYS 3.8 3.1 - - - +
340D GLU* 3.7 27.7 - - - +
343D ARG* 3.0 36.8 + - + +
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Residues in contact with LEU 130 (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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37C ILE* 2.9 19.0 + - + +
38C GLN* 2.8 27.8 + - - +
115D LEU* 4.1 21.3 - - + -
119D LEU* 3.6 32.1 - - + -
120D LEU* 4.0 22.2 - - + -
129D GLN* 1.3 75.7 - - - +
131D ILE* 1.3 75.5 + - - +
132D THR* 4.7 2.5 - - + -
327D PHE* 3.9 23.6 - - + -
336D PHE 3.7 12.6 - - - +
337D PHE* 3.8 21.8 - - + -
338D HIS* 4.5 0.4 - - - -
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Residues in contact with ILE 131 (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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38C GLN* 3.8 21.5 - - + +
39C ASN 5.9 0.9 - - - +
130D LEU* 1.3 81.9 - - - +
132D THR* 1.3 74.5 + - - +
133D MET* 3.8 19.3 - - + -
146D THR* 5.2 0.2 - - - +
335D GLY* 3.1 2.4 - - - -
336D PHE* 2.9 47.9 + - + +
338D HIS* 3.7 22.0 - - + +
344D PRO* 4.6 13.7 - - + -
350D ILE* 4.0 28.0 - - + +
355D LEU* 4.6 6.3 - - + -
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Residues in contact with THR 132 (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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38C GLN* 4.7 5.0 + - - +
103D LEU* 4.3 2.5 - - - +
111D PHE* 4.2 17.9 - - + -
115D LEU* 4.2 17.7 - - + -
119D LEU* 4.1 25.4 - - + -
130D LEU* 4.7 6.3 - - + -
131D ILE* 1.3 77.5 - - - +
133D MET* 1.3 68.7 + - - +
333D THR* 4.4 7.6 - - - +
334D GLY 3.7 7.9 - - - +
355D LEU* 2.6 49.1 + - - +
356D GLY* 4.8 0.9 - - - -
361D ASN* 4.8 8.1 - - - +
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Residues in contact with MET 133 (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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131D ILE* 3.8 14.1 - - + -
132D THR* 1.3 75.6 - - - +
134D ALA* 1.3 55.8 + - - +
135D CYS 3.4 0.4 - - - -
138D CYS* 3.8 21.8 - - - +
139D SER* 3.5 25.6 - - - +
142D ASN* 3.3 43.7 - - + +
333D THR* 3.0 6.1 + - - -
334D GLY 2.7 33.0 + - - +
335D GLY* 3.7 5.4 - - - +
336D PHE* 4.4 5.6 - - + -
350D ILE* 4.0 5.4 - - + -
351D PHE 5.1 0.7 - - - +
352D ASN* 3.4 18.8 - - - +
355D LEU* 3.4 23.8 - - + -
356D GLY 3.7 9.6 - - - +
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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