Contacts of the helix formed by residues 359 - 363 (chain X) in PDB entry 2EXC
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 ILE 359 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167X SER 3.3 21.8 - - - +
170X LEU* 3.8 15.0 - - + -
171X TYR* 3.6 40.6 - - + +
174X LEU* 4.2 6.7 - - + -
335X LEU* 4.0 16.4 - - + -
353X ALA 3.4 26.2 - - - +
354X LEU* 3.9 16.4 - - + +
356X HIS* 3.0 3.1 + - + +
358X TYR* 1.3 92.2 - - + +
360X ASN* 1.3 56.7 + - - +
361X VAL 2.8 12.1 + - - -
362X TRP* 3.0 24.8 + - - +
363X TYR 4.1 0.6 + - - +
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Residues in contact with ASN 360 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354X LEU 3.3 22.0 - - - +
355X GLN* 4.0 17.7 - - - +
356X HIS 2.7 14.4 + - - +
357X PRO* 3.1 29.3 - - - +
358X TYR 3.7 0.8 - - - -
359X ILE* 1.3 67.3 - - - +
361X VAL* 1.3 63.9 + - - +
362X TRP 2.9 6.9 + - - -
363X TYR* 3.1 22.8 + - + +
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Residues in contact with VAL 361 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164X GLU* 5.8 2.2 - - + -
167X SER* 5.1 1.1 - - - +
328X LYS* 3.7 17.5 - - - +
357X PRO 3.6 21.3 - - - +
358X TYR 4.2 6.7 - - - +
359X ILE 2.8 0.6 + - - -
360X ASN* 1.3 80.7 - - - +
362X TRP* 1.3 93.0 + - + +
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Residues in contact with TRP 362 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164X GLU* 3.2 55.6 - - + -
167X SER* 2.6 41.0 + - - -
168X TYR* 3.5 34.4 - + + +
171X TYR* 3.3 30.9 + - + -
359X ILE 3.0 20.2 + - - +
360X ASN 2.9 0.6 - - - -
361X VAL* 1.3 97.8 - - + +
363X TYR* 1.3 67.0 + - - +
364X ASP* 3.1 7.3 + - - +
367X GLU* 4.1 0.9 - - - +
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Residues in contact with TYR 363 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171X TYR* 3.9 9.3 - + - -
354X LEU* 3.7 26.5 - - + -
355X GLN* 3.4 24.2 + - - -
359X ILE 4.1 0.8 + - - -
360X ASN* 3.1 25.0 + - + +
361X VAL 3.6 0.4 - - - -
362X TRP* 1.3 78.3 - - - +
364X ASP* 1.3 60.4 + - - +
365X PRO* 3.8 32.2 - - + +
368X VAL* 3.4 32.7 - - + +
369X GLU* 2.8 22.3 + - - -
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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