Contacts of the strand formed by residues 257 - 263 (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 GLN 257 (chain t).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249j ILE* 4.2 4.9 - - - +
315j SER* 2.2 42.4 + - - +
318j LEU* 6.1 0.6 - - - +
249t ILE* 4.0 18.1 - - + +
250t GLU 3.4 14.8 - - - +
251t GLU* 4.6 5.7 - - + +
252t ARG* 2.8 30.0 + - - -
255t GLY 4.1 5.1 + - - +
256t ARG* 1.3 74.8 - - - +
258t ARG* 1.3 59.1 + - - +
308t VAL* 3.5 15.9 + - + +
309t ARG 5.8 0.2 + - - -
310t LYS* 5.8 0.2 - - - +
312t ALA 4.3 7.4 - - - +
313t ASN* 5.3 0.3 - - - -
314t ALA* 3.6 25.6 + - + +
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Residues in contact with ARG 258 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246j ARG* 6.1 0.4 - - - +
487j GLU* 4.8 14.3 + - - -
248t VAL 3.9 0.3 - - - +
249t ILE* 3.4 6.1 - - - +
250t GLU* 2.9 71.3 + - + +
251t GLU 5.1 2.6 + - - -
252t ARG* 3.9 26.5 + - + +
257t GLN* 1.3 75.9 - - - +
259t ILE* 1.3 62.0 + - - +
260t VAL* 4.0 8.8 + - + +
293t ARG* 4.4 14.8 - - - +
295t GLU* 5.6 1.0 + - - -
303t ARG* 3.7 17.7 - - - +
305t VAL* 3.6 17.0 - - + +
306t ILE 3.3 15.0 - - - +
307t ASP* 3.6 12.8 - - - +
308t VAL* 4.4 4.0 - - - +
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Residues in contact with ILE 259 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247t ALA* 4.2 9.6 - - + -
248t VAL 3.3 8.3 - - - +
249t ILE* 4.2 16.4 - - + -
258t ARG* 1.3 72.3 - - - +
260t VAL* 1.3 62.6 + - - +
261t VAL* 4.3 10.5 - - + -
304t VAL 3.8 1.2 - - - +
305t VAL* 3.6 3.5 - - - +
306t ILE* 2.9 48.0 + - + +
308t VAL* 4.2 12.8 - - + -
314t ALA* 3.7 21.3 - - + +
317t ILE* 3.9 22.9 - - + -
318t LEU* 3.8 33.2 - - + +
321t LEU* 4.2 7.4 - - + -
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Residues in contact with VAL 260 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246t ARG 4.0 0.9 - - - +
247t ALA* 3.2 2.8 - - - -
248t VAL* 2.8 45.5 + - + +
250t GLU* 3.7 33.4 - - + +
258t ARG* 4.0 16.6 - - + +
259t ILE* 1.3 76.0 - - - +
261t VAL* 1.3 62.2 + - - +
262t THR* 4.1 14.9 + - + +
303t ARG* 3.3 45.1 - - + +
304t VAL 3.5 4.5 - - - +
305t VAL* 4.7 3.8 - - + -
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Residues in contact with VAL 261 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245t SER* 3.9 15.7 - - - +
246t ARG 3.5 4.9 - - - +
247t ALA* 3.9 16.2 - - + -
259t ILE* 4.3 11.4 - - + -
260t VAL* 1.3 73.9 - - - +
262t THR* 1.3 61.3 + - - +
263t GLU 3.7 18.4 - - - +
264t ILE* 4.1 15.0 - - + -
273t MET* 5.1 0.2 - - + -
302t VAL* 4.0 1.6 - - - +
303t ARG* 3.4 5.2 + - - -
304t VAL* 2.9 49.5 + - + +
306t ILE* 4.8 8.5 - - + -
327t LEU* 4.1 23.6 - - + -
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Residues in contact with THR 262 (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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246t ARG* 3.0 26.6 + - - +
248t VAL* 6.2 1.8 - - + -
260t VAL* 4.1 21.1 - - + +
261t VAL* 1.3 76.4 - - - +
263t GLU* 1.3 69.7 + - - +
302t VAL* 3.2 40.5 + - - +
303t ARG* 5.0 5.4 - - + +
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Residues in contact with GLU 263 (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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220t THR 3.8 6.1 - - - +
221t ALA* 3.4 19.6 - - + +
222t GLY* 2.8 36.6 + - - +
245t SER* 3.1 8.7 - - - -
246t ARG* 2.9 64.2 + - + -
261t VAL* 3.7 2.4 - - - +
262t THR* 1.3 87.2 + - - +
264t ILE* 1.3 63.4 + - - +
302t VAL* 4.8 2.0 - - - -
485t ARG 4.5 2.6 - - - +
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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