Contacts of the strand formed by residues 411 - 415 (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 PHE 411 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B ILE* 3.5 37.0 - - + -
269B SER* 3.2 23.6 - - - -
273B ASP* 3.8 6.0 - - - +
275B HIS* 4.0 4.2 + - - -
301B GLN* 3.7 22.4 - - + -
302B THR* 3.9 17.3 - - + -
306B SER* 3.5 22.4 + - - +
307B THR* 4.3 13.0 - - + -
407B GLY* 3.2 4.3 - - - -
408B ARG 3.0 30.3 + - - +
409B GLY 3.2 0.2 - - - -
410B THR* 1.3 74.0 + - - +
412B CYS* 1.3 58.2 + - - +
446B PHE 4.0 4.9 - - - -
447B ARG* 3.2 41.5 - - - -
448B PRO* 5.7 0.2 - - - -
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Residues in contact with CYS 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ASP* 3.7 4.7 - - - +
384B GLY 4.2 7.0 - - - -
387B LEU* 4.0 22.9 - - + -
388B LEU* 4.0 15.7 - - - -
391B LEU* 4.2 7.2 - - + -
406B ARG 3.2 8.1 - - - +
407B GLY* 3.9 11.4 - - - -
409B GLY 3.3 25.1 - - - -
410B THR 2.9 13.3 + - - +
411B PHE* 1.3 75.2 - - - +
413B SER* 1.3 66.7 + - - +
445B ARG* 3.5 0.5 - - - -
446B PHE* 2.8 32.7 + - + +
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Residues in contact with SER 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ASP* 3.3 34.2 + - - +
275B HIS* 4.7 0.9 + - - -
391B LEU* 4.8 1.9 - - - +
405B VAL* 3.5 2.4 - - - +
406B ARG* 2.8 55.3 + - - +
412B CYS* 1.3 79.6 - - - +
414B PHE* 1.3 68.5 + - - +
439B CYS* 5.2 1.3 - - - -
443B SER* 5.2 0.2 - - - -
444B ILE 3.1 17.3 - - - -
445B ARG* 4.0 2.2 - - - +
446B PHE* 4.2 4.7 - - - -
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Residues in contact with PHE 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B LEU* 3.9 24.7 - - + -
402B ILE* 3.3 29.8 - - + -
403B SER 3.6 9.6 - - - +
404B ARG 4.0 0.7 - - - -
405B VAL* 3.7 16.8 - - + -
406B ARG* 3.6 7.4 - - - +
413B SER* 1.3 80.0 - - - +
415B ASP* 1.3 74.7 + - - +
416B THR* 3.9 6.1 - - + -
425B LEU* 5.1 0.2 - - + -
436B LEU* 5.7 0.2 - - + -
443B SER* 3.3 2.8 - - - -
444B ILE* 2.9 68.2 + - + +
446B PHE* 3.7 25.6 - + - -
464B PHE* 3.8 22.2 - + - -
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Residues in contact with ASP 415 (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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222B ARG* 4.3 6.8 + - - -
401B PHE 3.4 5.4 - - - +
403B SER* 2.8 47.5 + - - +
404B ARG* 2.8 36.0 + - - -
406B ARG* 3.0 12.9 + - - -
414B PHE* 1.3 78.7 - - - +
416B THR* 1.3 68.1 + - - +
442B LYS* 3.6 18.6 + - - +
443B SER* 2.5 28.6 + - - -
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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