Contacts of the strand formed by residues 129 - 133 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ILE 3.0 25.1 + - - -
37A ILE 3.1 9.8 - - - +
38A GLN* 3.6 4.3 - - - -
120B LEU* 5.8 0.2 - - - -
127B MET 4.3 0.3 - - - +
128B SER* 1.3 96.6 + - - +
130B LEU* 1.3 63.6 + - - +
337B PHE* 3.3 11.8 - - - +
338B HIS* 3.0 56.6 + - + +
339B LYS 3.7 3.8 - - - +
340B GLU* 3.7 27.0 - - - +
343B ARG* 3.0 38.1 + - + +
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ILE* 2.9 18.2 + - + +
38A GLN* 2.8 29.7 + - - +
115B LEU* 4.1 19.7 - - + -
119B LEU* 3.6 31.6 - - + -
120B LEU* 3.9 23.1 - - + -
129B GLN* 1.3 77.2 - - - +
131B ILE* 1.3 69.8 + - - +
132B THR* 4.7 2.9 - - + -
327B PHE* 3.9 20.0 - - + -
336B PHE 3.6 16.8 - - - +
337B PHE* 3.7 25.4 - - + -
338B HIS* 4.4 0.4 - - - -
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Residues in contact with ILE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLN* 3.9 19.7 - - + +
39A ASN* 5.9 1.8 - - + +
130B LEU* 1.3 82.1 - - - +
132B THR* 1.3 74.5 + - - +
133B MET* 3.8 19.5 - - + -
335B GLY* 3.1 2.8 - - - -
336B PHE* 2.9 47.2 + - + -
338B HIS* 3.8 22.6 + - + +
344B PRO* 4.5 13.9 - - + -
350B ILE* 4.0 28.0 - - + +
355B LEU* 4.5 6.1 - - + -
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Residues in contact with THR 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLN* 4.7 4.6 + - - +
103B LEU* 4.3 1.8 - - - +
111B PHE* 4.2 17.9 - - + -
115B LEU* 4.2 17.0 - - + -
119B LEU* 4.1 25.1 - - + -
130B LEU* 4.7 5.4 - - + -
131B ILE* 1.3 77.1 - - - +
133B MET* 1.3 69.6 + - - +
333B THR* 4.6 6.5 - - - +
334B GLY 3.7 8.1 - - - +
355B LEU* 2.6 48.1 + - - +
356B GLY* 4.8 0.2 - - - -
361B ASN* 4.8 9.2 - - - +
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Residues in contact with MET 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ILE* 3.8 15.0 - - + -
132B THR* 1.3 77.0 - - - +
134B ALA* 1.3 56.4 + - - +
135B CYS 3.4 0.4 - - - -
138B CYS* 3.9 21.5 - - - +
139B SER* 3.4 25.8 - - - +
142B ASN* 3.4 39.9 - - + +
333B THR* 3.1 5.4 + - - -
334B GLY 2.6 35.6 + - - +
335B GLY* 3.9 5.2 - - - +
336B PHE* 4.4 4.9 - - + -
350B ILE* 4.0 5.2 - - + -
351B PHE 5.1 0.9 - - - +
352B ASN* 3.4 23.8 - - - +
355B LEU* 3.4 22.9 - - + -
356B 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