Contacts of the helix formed by residues 348 - 353 (chain B) in PDB entry 5COX
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 TYR 348 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B PHE* 4.4 15.9 - + - -
201B PHE* 3.4 27.6 - + + -
202B ALA* 3.0 46.4 - - + +
205B PHE* 4.8 7.4 - + - -
206B THR* 4.6 0.9 - - - +
343B ILE 3.4 1.4 + - - +
344B VAL* 3.7 26.5 - - + +
347B ASP* 1.3 77.8 - - - +
349B VAL* 1.3 79.4 + - + +
351B HIS* 3.8 1.7 - - - +
352B LEU* 3.1 44.0 + - + +
385B TYR* 2.7 34.4 + - - -
387B TRP* 3.9 3.7 - + - -
580B PHE* 3.5 17.6 - + + -
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Residues in contact with VAL 349 (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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344B VAL* 2.9 34.3 + - + +
345B ILE* 3.8 8.1 - - + +
348B TYR* 1.3 89.4 - - + +
350B GLN* 1.3 63.9 + - - +
352B LEU* 3.4 5.8 + - + +
353B SER* 2.8 26.8 + - - -
359B LEU* 3.5 22.2 - - + -
530B SER* 4.9 13.2 - - - +
531B LEU* 5.5 12.8 - - + -
534B LEU* 4.9 5.6 - - + -
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Residues in contact with GLN 350 (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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345B ILE 3.3 6.3 + - - +
346B GLU* 3.0 32.2 + - - +
347B ASP 3.1 2.9 + - - +
349B VAL* 1.3 78.0 - - - +
351B HIS* 1.3 61.8 + - - +
353B SER* 2.9 20.6 + - - -
354B GLY* 3.3 4.0 + - - -
355B TYR* 4.2 7.8 + - - +
356B HIS 5.3 1.0 + - - -
357B PHE 3.0 21.5 - - - +
358B LYS* 3.2 23.3 - - - +
359B LEU* 3.1 43.4 + - - +
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Residues in contact with HIS 351 (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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192B GLN* 3.7 18.6 + - + -
194B SER* 2.9 32.9 + - - -
198B PHE* 3.7 12.3 - + - -
347B ASP 2.7 22.2 + - - +
348B TYR 3.8 2.0 - - - +
350B GLN* 1.3 70.0 - - - +
352B LEU* 1.3 72.0 + - + +
353B SER 2.6 15.7 + - - -
354B GLY* 2.9 16.9 + - - -
579B SER* 5.6 0.4 - - - -
580B PHE* 2.9 42.1 + - + -
581B ASN* 3.8 21.7 + - + -
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Residues in contact with LEU 352 (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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192B GLN* 3.9 12.4 - - - +
194B SER* 4.8 2.0 - - - +
198B PHE* 3.4 31.9 - - + -
348B TYR* 3.1 33.7 + - + +
349B VAL* 3.7 6.1 - - + +
351B HIS* 1.3 84.3 + - - +
353B SER* 1.3 59.0 + - - +
387B TRP* 3.5 27.8 - - + -
517B ILE* 3.9 12.3 - - + -
518B PHE* 3.2 36.8 - - + -
523B VAL* 5.8 2.6 - - - +
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Residues in contact with SER 353 (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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90B HIS* 4.8 8.5 + - - -
192B GLN* 4.3 4.8 + - - +
349B VAL* 2.8 17.9 + - - -
350B GLN* 2.9 12.6 + - - -
351B HIS 2.6 7.1 + - - -
352B LEU* 1.3 77.0 - - - +
354B GLY* 1.3 64.9 + - - +
355B TYR* 2.9 51.1 - - - +
359B LEU* 4.8 5.7 - - - +
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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