Contacts of the strand formed by residues 263 - 267 (chain D) in PDB entry 2JG7
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 ARG 263 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470C GLU* 2.9 34.5 + - - +
471C LYS* 5.1 6.3 - - - +
156D VAL* 3.6 38.6 + - - +
239D ASP* 3.4 38.5 + - - +
240D LEU* 3.3 14.9 - - + -
241D LEU 2.9 22.7 + - - -
257D VAL* 3.8 4.5 - - - +
260D ARG* 5.3 0.9 + - - -
261D PHE 5.6 0.7 - - - +
262D GLY* 1.3 74.9 - - - -
264D LYS* 1.3 60.6 + - - +
486D GLN 4.6 8.5 - - - +
488D MET 4.8 3.7 + - - -
489D ARG* 3.8 23.0 - - - +
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Residues in contact with LYS 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C GLN* 2.9 30.7 - - - +
264C LYS* 4.7 3.7 - - - +
240D LEU* 3.8 5.4 - - - +
241D LEU* 3.3 9.4 - - + +
253D VAL* 6.3 0.4 - - + -
254D ALA* 4.0 29.6 - - + +
257D VAL* 3.9 13.4 - - + +
258D GLN* 2.9 30.9 + - - +
262D GLY 4.0 16.2 + - - -
263D ARG* 1.3 76.4 - - - +
265D LEU* 1.3 60.3 + - - +
266D LEU* 4.1 22.6 + - + -
486D GLN* 5.5 2.1 - - - +
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Residues in contact with LEU 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D ASN* 4.6 1.3 - - - +
240D LEU* 4.2 9.2 - - + -
241D LEU 2.8 9.1 + - - +
242D SER* 3.5 20.8 - - - +
243D PHE 2.8 29.6 + - - +
264D LYS* 1.3 74.5 - - - +
266D LEU* 1.3 62.1 + - - +
267D GLU* 3.7 26.5 - - + -
476D GLY* 3.9 9.9 - - - -
477D ARG 3.4 22.7 - - - +
478D GLU* 4.1 4.9 - - + -
486D GLN* 3.6 30.3 - - + +
487D TYR* 3.6 29.4 - - + +
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Residues in contact with LEU 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C GLN* 4.1 9.2 - - - +
261C PHE* 4.2 15.0 - - + -
241D LEU 5.4 0.4 - - - +
243D PHE* 3.7 17.7 - - + -
250D GLY 4.4 7.9 - - - +
253D VAL* 5.0 2.7 - - + -
254D ALA* 3.7 33.7 - - + +
264D LYS* 4.1 26.2 + - + -
265D LEU* 1.3 80.2 - - - +
267D GLU* 1.3 62.7 - - - +
268D LEU* 4.1 11.0 - - + -
469D GLY 5.6 0.3 + - - -
473D THR 3.3 10.1 - - - +
474D GLY* 3.5 25.0 + - - +
475D GLY 3.9 0.3 + - - -
476D GLY* 3.1 26.1 + - - +
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Residues in contact with GLU 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D SER* 5.7 0.2 - - - +
243D PHE 2.8 8.4 + - - +
244D THR* 3.3 14.8 - - - +
245D GLY 3.2 22.3 + - - -
265D LEU* 3.7 10.8 - - + -
266D LEU* 1.3 74.6 - - - +
268D LEU* 1.3 58.8 + - - +
467D PHE* 2.7 27.0 - - - +
468D GLY* 3.4 15.9 - - - -
469D GLY 4.4 1.2 + - - -
473D THR 3.8 0.9 - - - -
476D GLY 3.3 15.9 - - - +
478D GLU* 3.4 36.9 + - - +
1510D NAD 3.1 36.8 + - - +
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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