Contacts of the helix formed by residues 289 - 295 (chain A) in PDB entry 1C0F
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 289 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A THR* 5.5 0.2 - - + -
166A TYR* 3.5 46.7 - - + +
171A LEU* 3.7 30.7 - - + -
285A CYS* 3.9 8.3 - - + -
286A ASP* 2.8 32.6 + - + +
288A ASP* 1.3 79.0 - - + +
290A ARG* 1.3 65.5 + - - +
291A LYS 3.2 3.4 - - - -
292A ASP* 3.0 23.7 + - + +
293A LEU* 3.2 30.7 + - + +
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Residues in contact with ARG 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A ILE* 3.5 30.4 + - + +
283A MET* 3.4 52.0 + - - +
285A CYS* 2.8 26.7 + - + +
286A ASP* 3.5 9.6 - - - +
287A VAL* 3.3 42.7 + - + +
289A ILE* 1.3 76.7 - - - +
291A LYS* 1.3 64.9 + - - +
293A LEU* 2.9 18.4 + - - +
294A TYR* 2.9 28.0 + - + -
325A MET* 5.3 2.9 - - + -
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Residues in contact with LYS 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A VAL 4.7 1.8 + - - -
288A ASP 5.0 9.4 + - - +
289A ILE 3.2 1.0 - - - -
290A ARG* 1.3 77.3 - - - +
292A ASP* 1.3 67.8 + - - +
294A TYR* 3.7 1.6 + - - +
295A GLY* 3.2 24.3 + - - -
325A MET* 4.0 29.5 - - + +
326A LYS* 4.8 2.2 - - + +
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Residues in contact with ASP 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A THR* 3.9 22.2 - - + +
150A GLY* 4.2 2.8 - - - -
166A TYR* 5.7 3.7 - - + -
288A ASP 5.4 1.4 - - - +
289A ILE* 3.0 16.3 + - + +
291A LYS* 1.3 85.9 - - - +
293A LEU* 1.3 66.2 + - - +
295A GLY 4.0 0.2 - - - -
296A ASN* 2.8 38.0 + - - +
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Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A THR* 4.2 7.0 - - + -
150A GLY* 3.5 34.8 - - - +
151A ILE* 3.6 16.5 - - + +
164A PRO* 4.5 3.8 - - + -
165A ILE 4.0 12.3 - - - +
282A ILE* 4.1 21.5 - - + -
285A CYS* 4.0 21.3 - - + -
289A ILE* 3.2 43.1 + - + +
290A ARG* 2.9 11.9 + - - +
292A ASP* 1.3 76.2 - - - +
294A TYR* 1.3 65.3 + - - +
296A ASN 3.0 22.3 + - - +
297A VAL* 3.6 6.6 + - - +
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Residues in contact with TYR 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A TYR* 3.3 33.0 - + - -
282A ILE* 3.8 34.4 - - + +
283A MET* 4.0 9.1 - - - -
290A ARG* 2.9 29.3 + - + +
291A LYS 3.9 2.9 - - - +
293A LEU* 1.3 76.6 - - - +
295A GLY* 1.3 59.1 + - - +
296A ASN 3.2 0.9 + - - -
297A VAL* 3.7 13.8 - - - +
317A LEU* 4.9 11.0 - - + -
321A ALA* 3.6 25.3 - - + +
322A PRO* 4.6 4.9 - - + +
325A MET* 3.5 33.7 - - + -
326A LYS 3.7 12.1 - - - +
327A ILE* 3.4 22.5 - - + +
328A LYS 3.0 19.2 + - - -
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Residues in contact with GLY 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A LYS 3.2 14.2 + - - -
293A LEU 3.2 0.6 - - - -
294A TYR* 1.3 77.3 - - - +
296A ASN* 1.3 73.3 + - - +
326A LYS* 3.7 17.2 + - - +
328A LYS* 3.4 31.4 - - - +
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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