Contacts of the strand formed by residues 304 - 308 (chain j) in PDB entry 6QX2
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 VAL 304 (chain j).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259j ILE 3.8 1.7 - - - +
260j VAL* 3.5 3.0 - - - -
261j VAL* 2.9 52.4 + - + +
264j ILE* 5.5 0.9 - - + -
270j LYS* 4.2 14.6 - - + -
273j MET* 4.8 13.0 - - + -
274j ILE* 3.9 32.1 - - + -
277j ILE* 5.6 1.3 - - + -
292j LEU* 4.4 14.4 - - + -
293j ARG 3.6 11.2 - - - +
294j ASP* 3.9 14.1 - - - +
302j VAL* 4.5 6.1 - - + -
303j ARG* 1.3 74.0 - - - +
305j VAL* 1.3 61.1 + - - +
306j ILE* 4.7 7.1 - - + +
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Residues in contact with VAL 305 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258j ARG* 3.6 23.8 - - + +
259j ILE 3.6 2.9 - - - +
260j VAL* 4.7 15.7 - - + -
291j ASP 4.2 0.5 - - - +
292j LEU* 3.4 4.7 - - - +
293j ARG* 2.8 66.8 + - - +
295j GLU* 3.4 35.2 - - + +
303j ARG* 4.6 2.9 - - + +
304j VAL* 1.3 74.8 - - - +
306j ILE* 1.3 64.5 + - - +
307j ASP* 3.4 15.0 - - - +
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Residues in contact with ILE 306 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258j ARG* 3.3 2.2 - - - -
259j ILE* 2.9 59.3 + - + +
261j VAL* 4.5 12.6 - - + -
277j ILE* 4.6 12.1 - - + -
289j ILE* 3.6 43.7 - - + -
291j ASP 3.5 3.8 - - - +
292j LEU* 3.7 20.0 - - + -
304j VAL* 4.7 6.3 - - + +
305j VAL* 1.3 75.4 - - - +
307j ASP* 1.3 62.8 + - - +
308j VAL* 3.8 2.8 + - + +
321j LEU* 3.6 27.6 - - + -
327j LEU* 5.3 1.6 - - + -
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Residues in contact with ASP 307 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252j ARG* 3.7 29.5 + - - +
258j ARG* 3.6 12.3 - - - +
289j ILE* 3.5 6.9 - - - +
290j THR* 2.9 43.3 + - - +
291j ASP* 3.0 19.6 + - + +
293j ARG* 3.0 29.1 + - - -
305j VAL* 3.4 21.0 - - - +
306j ILE* 1.3 72.0 - - - +
308j VAL* 1.3 56.6 + - - +
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Residues in contact with VAL 308 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252j ARG* 2.6 25.0 + - - -
257j GLN* 3.5 23.2 + - + +
258j ARG* 4.5 3.8 - - - -
259j ILE* 4.2 16.4 - - + -
288j GLY 3.4 3.6 - - - +
289j ILE* 5.5 0.2 - - + -
290j THR* 3.9 1.1 - - - -
306j ILE* 4.0 11.0 - - + +
307j ASP* 1.3 75.7 - - - +
309j ARG* 1.3 74.2 + - - +
310j LYS* 3.7 0.5 + - - -
312j ALA* 3.6 17.0 - - + +
314j ALA* 4.1 22.2 - - + -
317j ILE* 3.5 33.7 - - + -
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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