Contacts of the helix formed by residues 355 - 361 (chain B) in PDB entry 3OFN
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 GLU 355 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B THR* 4.4 2.0 - - - +
353B PHE* 3.8 11.8 + - + -
354B LEU* 1.3 72.0 - - - +
356B ALA* 1.3 61.8 + - - +
357B GLU* 3.4 26.9 - - - +
358B LEU* 3.6 27.8 - - + +
359B PHE* 3.4 5.2 + - - +
366B ALA* 3.2 27.8 + - - +
368B ASN* 3.2 29.9 + - + +
400B ARG* 3.2 27.0 + - - -
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Residues in contact with ALA 356 (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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172B ASP* 4.1 20.5 - - + +
173B ARG 5.5 0.2 - - - +
175B THR* 3.8 23.2 - - + +
354B LEU 3.8 2.8 + - - -
355B GLU* 1.3 71.2 - - - +
357B GLU* 1.3 60.3 + - - +
359B PHE* 3.2 3.2 + - - +
360B TYR* 2.8 35.2 + - + +
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Residues in contact with GLU 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B GLU* 3.4 22.0 - - - +
356B ALA* 1.3 78.6 - - - +
358B LEU* 1.3 66.6 + - + +
360B TYR* 3.7 5.5 + - - +
361B LYS* 3.2 60.3 + - - +
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Residues in contact with LEU 358 (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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355B GLU* 3.6 33.5 + - + +
356B ALA 3.3 0.4 - - - -
357B GLU* 1.3 84.3 - - + +
359B PHE* 1.3 62.9 + - - +
361B LYS* 3.3 14.2 + - + -
362B GLY 3.3 0.2 + - - -
363B ILE* 2.8 56.4 + - + +
366B ALA* 3.4 31.6 - - + +
367B ILE 4.1 11.0 - - - +
400B ARG* 4.4 20.6 - - - +
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Residues in contact with PHE 359 (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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174B GLN* 3.8 25.1 - - + -
175B THR* 3.2 37.2 - - + +
176B GLY* 3.6 9.4 - - - -
355B GLU 3.4 17.1 + - - +
356B ALA* 3.2 8.0 + - - +
358B LEU* 1.3 79.8 - - - +
360B TYR* 1.3 63.7 + - + +
362B GLY 3.2 7.3 + - - -
363B ILE 4.1 3.8 - - - -
364B ARG* 3.0 77.7 + - + -
365B PRO* 6.0 0.4 - - + -
366B ALA* 3.6 11.6 - - + +
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Residues in contact with TYR 360 (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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356B ALA* 2.8 17.1 + - + +
357B GLU* 4.1 5.8 - - - +
359B PHE* 1.3 78.7 - - + +
361B LYS* 1.3 62.6 + - + +
362B GLY 3.2 4.7 + - - -
364B ARG* 4.8 4.0 + - - +
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Residues in contact with LYS 361 (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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357B GLU* 3.2 41.6 + - + +
358B LEU* 3.6 12.6 - - + +
359B PHE 3.2 1.0 - - - -
360B TYR* 1.3 81.9 - - + +
362B GLY* 1.3 58.9 + - - +
363B ILE* 3.4 17.6 + - + +
431B LYS* 5.0 3.3 + - - -
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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