Contacts of the helix formed by residues 267 - 271 (chain A) in PDB entry 4J1O
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 LEU 267 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ILE* 4.1 15.0 - - + -
265A MET 4.0 1.4 + - - -
266A LYS* 1.3 71.2 - - - +
268A THR* 1.3 62.9 + - - +
270A ILE* 3.5 2.1 + - - +
271A GLY 3.2 4.9 + - - -
272A GLY* 3.1 59.9 + - - +
273A LEU* 3.6 16.6 - - + +
276A MET* 3.6 31.1 - - + +
292A CYS 6.2 0.2 - - - -
293A ASP 2.9 12.5 + - - +
294A ASP* 3.2 8.9 + - - +
301A ILE* 4.1 1.6 - - + -
304A ALA* 3.6 38.4 - - + +
305A CYS* 4.0 11.7 - - - +
308A ILE* 4.8 1.8 - - + -
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Residues in contact with THR 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLU 4.1 2.2 - - - +
49A THR* 3.6 26.7 + - - +
50A CYS 5.2 0.2 - - - +
98A ASN 3.2 26.9 - - - +
99A TYR* 3.3 18.1 + - - +
102A ALA* 3.6 17.9 - - + -
266A LYS* 4.8 2.3 - - - +
267A LEU* 1.3 73.3 - - - +
269A ARG* 1.3 64.9 + - - +
271A GLY 3.3 3.1 + - - -
294A ASP* 2.6 41.0 + - - +
295A ALA* 4.9 2.9 + - - +
301A ILE* 4.0 14.8 - - + -
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Residues in contact with ARG 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TYR* 4.8 2.2 - - - -
98A ASN* 3.1 24.3 + - - +
242A ASP* 2.8 44.9 + - - -
243A GLU* 3.8 20.6 - - - +
245A GLY 2.9 28.8 + - - +
246A GLU* 3.2 21.7 - - + +
264A GLY 3.0 18.4 + - - -
265A MET* 3.5 8.3 - - - +
266A LYS* 3.2 48.3 + - + +
268A THR* 1.3 82.2 + - - +
270A ILE* 1.3 57.2 + - - +
407A IOD 4.0 31.0 - - + -
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Residues in contact with ILE 270 (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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98A ASN* 3.4 11.5 + - - +
246A GLU 4.3 3.6 - - - -
247A ASP* 4.4 5.0 - - - +
248A LEU* 4.2 23.3 - - + +
251A VAL* 4.7 4.0 - - + -
265A MET* 4.0 24.7 - - + -
266A LYS 3.2 3.2 + - - +
267A LEU 3.6 9.9 - - - +
269A ARG* 1.3 78.7 - - - +
271A GLY* 1.3 60.0 + - - +
272A GLY 3.8 13.2 - - - +
275A GLN* 3.5 26.6 - - + +
276A MET* 3.8 25.6 - - - +
279A PHE* 3.5 37.9 - - + -
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Residues in contact with GLY 271 (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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87A ARG* 5.0 8.4 - - - +
90A MET* 5.7 0.5 - - - +
98A ASN* 3.6 27.6 - - - -
101A LYS* 4.3 5.4 - - - +
102A ALA* 3.7 17.1 + - - -
105A ASP* 4.1 9.0 - - - +
267A LEU 3.2 2.6 + - - -
268A THR 3.8 4.0 - - - -
269A ARG 3.2 3.6 - - - -
270A ILE* 1.3 80.0 - - - +
272A GLY* 1.3 59.2 + - - +
275A GLN* 4.7 8.1 - - - +
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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