Contacts of the strand formed by residues 411 - 415 (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 PHE 411 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267D ILE* 3.5 36.8 - - + -
269D SER* 3.2 23.1 - - - -
273D ASP* 3.8 5.6 - - - +
275D HIS* 4.0 4.4 + + - -
301D GLN* 3.6 21.8 - - + -
302D THR* 3.9 18.2 - - + -
306D SER* 3.5 19.9 + - - +
307D THR* 4.2 14.4 - - + -
407D GLY* 3.2 4.0 - - - -
408D ARG 3.0 31.0 + - - +
409D GLY 3.2 0.2 - - - -
410D THR* 1.3 74.3 + - - +
412D CYS* 1.3 59.8 + - - +
446D PHE 4.0 4.9 - - - -
447D ARG* 3.2 40.6 - - - +
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Residues in contact with CYS 412 (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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273D ASP* 3.5 5.3 - - - +
384D GLY 4.2 7.4 - - - -
387D LEU* 4.0 24.2 - - + -
388D LEU* 4.1 15.3 - - - -
391D LEU* 4.2 7.9 - - + -
406D ARG 3.2 7.4 - - - +
407D GLY* 4.0 11.4 - - - -
409D GLY 3.3 24.5 - - - -
410D THR 2.9 12.9 + - - +
411D PHE* 1.3 75.0 - - - +
413D SER* 1.3 65.9 + - - +
445D ARG* 3.5 0.7 - - - -
446D PHE* 2.9 31.9 + - + +
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Residues in contact with SER 413 (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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273D ASP* 3.2 35.4 + - - +
275D HIS* 4.7 0.9 + - - -
391D LEU* 4.9 1.5 - - - +
405D VAL* 3.5 2.6 - - - +
406D ARG* 2.8 54.7 + - - +
412D CYS* 1.3 80.2 - - - +
414D PHE* 1.3 68.2 + - - +
439D CYS* 5.2 1.3 - - - -
443D SER* 5.2 0.2 - - - -
444D ILE 3.2 17.3 - - - -
445D ARG* 4.0 2.0 - - - +
446D PHE* 4.3 4.7 - - - -
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Residues in contact with PHE 414 (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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391D LEU* 4.0 24.9 - - + -
402D ILE* 3.3 28.3 - - + -
403D SER 3.7 9.2 - - - +
404D ARG 4.0 0.9 - - - -
405D VAL* 3.7 17.0 - - + -
406D ARG* 3.6 7.2 - - - +
413D SER* 1.3 80.3 - - - +
415D ASP* 1.3 76.6 + - - +
416D THR* 3.9 6.5 - - + -
443D SER* 3.3 3.3 - - - -
444D ILE* 2.9 68.2 + - + +
446D PHE* 3.7 26.2 - + - -
460D PHE* 4.9 0.4 - + - -
464D PHE* 3.7 22.4 - + - -
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Residues in contact with ASP 415 (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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222D ARG* 5.5 0.7 + - - -
401D PHE 3.4 4.9 - - - +
403D SER* 2.8 46.6 + - - +
404D ARG* 2.8 35.6 + - - -
406D ARG* 3.1 12.9 + - - -
414D PHE* 1.3 80.3 - - - +
416D THR* 1.3 67.7 + - - +
442D LYS* 3.6 19.3 + - - +
443D SER* 2.5 29.2 + - - -
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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