Contacts of the helix formed by residues 261 - 267 (chain A) in PDB entry 2JAV
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 SER 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A LYS* 3.8 17.1 - - - +
199A ILE* 5.0 1.1 - - - -
259A ARG 3.6 1.2 + - - -
260A PRO* 1.3 76.3 - - - +
262A VAL* 1.3 64.7 + - - +
263A GLU* 3.5 15.7 + - - +
264A GLU* 2.6 40.0 + - - +
265A ILE* 3.0 22.6 + - - +
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Residues in contact with VAL 262 (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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121A THR* 3.8 29.8 - - + +
124A LEU* 4.4 4.5 - - + -
125A LYS* 3.5 46.7 - - + +
128A HIS* 4.2 16.8 - - + +
199A ILE* 4.2 19.1 - - + +
261A SER* 1.3 71.1 - - - +
263A GLU* 1.3 73.3 + - - +
265A ILE* 3.2 6.2 + - - +
266A LEU* 3.1 27.9 + - + +
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Residues in contact with GLU 263 (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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125A LYS* 4.1 20.8 - - + +
261A SER* 3.2 13.1 + - - +
262A VAL* 1.3 95.4 + - - +
264A GLU* 1.3 61.9 + - + +
266A LEU* 3.4 7.7 + - + +
267A GLU* 3.1 36.3 + - - +
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Residues in contact with GLU 264 (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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196A LYS* 4.9 1.9 + - - -
247A ILE* 5.3 2.0 - - - +
250A ARG* 3.6 23.5 + - - +
259A ARG 4.1 2.6 - - - +
260A PRO* 3.3 13.3 - - + +
261A SER* 2.6 47.0 + - - +
263A GLU* 1.3 76.1 - - + +
265A ILE* 1.3 62.6 + - - +
267A GLU* 3.6 24.5 + - - +
268A ASN* 3.7 9.2 + - - +
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Residues in contact with ILE 265 (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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117A MET* 4.2 14.4 - - + -
121A THR* 3.6 25.4 - - + +
199A ILE* 4.1 20.2 - - + -
202A LEU* 4.1 16.4 - - + -
247A ILE* 4.5 10.3 - - + -
251A MET* 3.8 22.7 - - + -
260A PRO* 3.8 21.5 - - + +
261A SER 3.0 21.1 + - - +
262A VAL 3.2 6.5 + - - +
264A GLU* 1.3 75.6 - - - +
266A LEU* 1.3 57.9 + - - +
268A ASN* 3.1 26.9 + - - +
271A ILE* 3.4 18.2 - - + +
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Residues in contact with LEU 266 (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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118A THR* 3.9 34.1 - - + +
121A THR* 3.9 14.6 - - + -
122A LEU* 3.7 30.7 - - + -
125A LYS* 4.5 9.4 - - + +
262A VAL* 3.1 32.5 + - + +
263A GLU* 4.1 5.6 - - + +
265A ILE* 1.3 71.4 - - - +
267A GLU* 1.3 60.5 + - - +
268A ASN 3.1 10.8 + - - +
271A ILE* 4.0 23.4 - - + +
276A HIS* 5.1 3.1 - - - +
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Residues in contact with GLU 267 (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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263A GLU* 3.1 24.5 + - - +
264A GLU* 3.8 20.7 - - - +
265A ILE 3.3 0.4 - - - -
266A LEU* 1.3 74.3 - - - +
268A ASN* 1.3 63.0 + - - +
269A PRO* 3.4 7.3 - - - +
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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