Contacts of the helix formed by residues 293 - 298 (chain F) in PDB entry 2QC8
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 GLY 293 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285F ILE* 3.9 24.5 + - - -
289F ASP* 3.1 19.3 + - - -
291F LYS 3.2 0.6 - - - -
292F GLY* 1.3 76.4 - - - +
294F LEU* 1.3 60.9 + - - +
296F ASN* 3.5 1.3 + - - -
297F ALA* 3.1 23.7 + - - +
309F ILE* 3.6 11.1 - - - +
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Residues in contact with LEU 294 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291F LYS* 3.3 29.9 + - + +
292F GLY 5.6 0.2 - - - -
293F GLY* 1.3 77.1 - - - +
295F ASP* 1.3 66.9 + - - +
297F ALA* 3.5 19.9 - - + +
298F ARG* 4.1 9.5 + - - +
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Residues in contact with ASP 295 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F GLU* 4.9 2.6 - - - +
239F ASP* 4.7 1.1 - - - +
240F PRO* 3.6 23.4 - - + +
289F ASP* 3.5 15.6 + - + -
290F PRO* 4.2 6.6 - - - +
291F LYS* 3.7 28.7 + - - +
293F GLY 3.4 0.2 - - - -
294F LEU* 1.3 77.7 - - - +
296F ASN* 1.3 63.9 + - - +
298F ARG* 3.1 44.0 + - - +
299F ARG 4.0 0.7 + - - -
345F ASN* 2.8 27.2 + - - +
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Residues in contact with ASN 296 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240F PRO* 4.5 0.8 - - - +
285F ILE* 5.1 4.6 + - + +
288F TYR* 3.6 15.4 + - - +
289F ASP* 3.0 16.8 + - - +
293F GLY* 3.5 5.8 + - - +
294F LEU 3.4 0.2 - - - -
295F ASP* 1.3 73.6 - - - +
297F ALA* 1.3 65.9 + - - +
299F ARG* 2.9 33.8 + - - +
300F LEU* 2.8 45.5 + - + +
309F ILE* 3.8 7.4 - - + -
341F ARG 3.3 20.0 + - - -
343F SER* 3.5 26.2 - - - +
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Residues in contact with ALA 297 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293F GLY 3.1 13.6 + - - +
294F LEU* 3.5 20.6 - - + +
295F ASP 3.2 0.6 - - - -
296F ASN* 1.3 77.5 - - - +
298F ARG* 1.3 63.1 + - + +
299F ARG 3.4 0.3 + - - -
300F LEU 4.2 8.5 + - - +
301F THR* 4.3 6.4 - - - +
309F ILE* 3.5 18.7 - - + +
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Residues in contact with ARG 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239F ASP* 2.9 42.8 + - - -
240F PRO* 3.8 3.4 - - - +
241F LYS* 3.3 45.9 + - + +
294F LEU 4.3 6.9 + - - +
295F ASP* 3.1 45.2 + - - +
296F ASN 3.1 1.2 - - - -
297F ALA* 1.3 77.6 - - + +
299F ARG* 1.3 57.5 + - - +
301F THR* 4.1 8.6 - - - +
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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