Contacts of the strand formed by residues 304 - 308 (chain T) 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 T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259T ILE 3.7 1.7 - - - +
260T VAL* 3.5 3.3 - - - -
261T VAL* 2.9 50.6 + - + +
264T ILE* 5.5 0.9 - - + -
270T LYS* 4.1 15.3 - - + -
273T MET* 4.8 12.8 - - + -
274T ILE* 3.9 31.4 - - + -
277T ILE* 5.5 1.6 - - + -
292T LEU* 4.4 14.4 - - + -
293T ARG 3.6 11.4 - - - +
294T ASP* 3.9 14.1 - - - +
302T VAL* 4.5 6.1 - - + -
303T ARG* 1.3 72.3 - - - +
305T VAL* 1.3 61.6 + - - +
306T ILE* 4.2 7.5 + - + +
327T LEU* 6.4 0.2 - - + -
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Residues in contact with VAL 305 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258T ARG* 3.6 21.8 - - + -
259T ILE 3.6 4.0 - - - +
260T VAL* 4.9 2.7 - - + -
291T ASP 4.6 0.2 - - - -
292T LEU* 3.4 4.9 - - - +
293T ARG* 2.8 66.8 + - - +
295T GLU* 3.4 34.8 - - + +
303T ARG* 3.9 22.7 - - + +
304T VAL* 1.3 74.6 - - - +
306T ILE* 1.3 65.1 + - - +
307T ASP* 3.4 14.3 + - - +
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Residues in contact with ILE 306 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258T ARG* 3.3 1.6 - - - -
259T ILE* 2.9 58.1 + - + +
261T VAL* 4.8 11.2 - - + -
277T ILE* 4.3 15.3 - - + -
289T ILE* 3.6 43.3 - - + -
291T ASP 3.5 3.8 - - - +
292T LEU* 3.7 20.4 - - + -
304T VAL* 4.8 7.2 - - + +
305T VAL* 1.3 74.2 - - - +
307T ASP* 1.3 63.9 + - - +
308T VAL* 3.8 3.0 + - + +
321T LEU* 3.6 27.6 - - + -
327T LEU* 5.4 1.6 - - + -
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Residues in contact with ASP 307 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252T ARG* 3.7 31.1 + - - +
258T ARG* 3.6 11.5 - - - +
289T ILE* 3.5 6.8 - - - +
290T THR* 2.9 43.4 + - - +
291T ASP* 3.0 19.8 + - + +
293T ARG* 3.0 28.9 + - - -
305T VAL* 3.4 20.6 - - - +
306T ILE* 1.3 71.3 - - - +
308T VAL* 1.3 56.5 + - - +
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Residues in contact with VAL 308 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252T ARG* 2.7 25.0 + - - -
256T ARG* 4.5 0.5 - - - +
257T GLN* 3.5 23.9 + - + +
258T ARG* 4.6 2.9 - - - -
259T ILE* 4.2 21.1 - - + -
288T GLY 3.4 4.0 - - - +
289T ILE* 5.4 0.2 - - + -
290T THR* 3.9 0.9 - - - -
306T ILE* 4.0 11.9 - - + +
307T ASP* 1.3 76.9 - - - +
309T ARG* 1.3 74.0 + - - +
310T LYS 3.7 0.3 + - - -
312T ALA* 3.7 16.4 - - + +
314T ALA* 4.2 17.3 - - + -
317T ILE* 3.5 33.4 - - + -
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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