Contacts of the strand formed by residues 277 - 285 (chain B) in PDB entry 1QXP
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 277 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273B THR* 4.1 8.6 - - - +
274B TYR 2.9 33.6 + - - +
275B GLN 3.5 1.6 + - - -
276B GLY* 1.4 79.0 + - - +
278B ARG* 1.4 66.6 + - - +
279B VAL* 4.0 4.7 + - - +
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Residues in contact with ARG 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B GLN* 3.2 48.6 + - + +
272B VAL* 3.0 10.8 - - - +
273B THR* 3.4 13.7 + - - +
277B GLN* 1.4 89.3 - - - +
279B VAL* 1.3 63.6 + - - +
280B ASN* 4.3 0.4 + - - -
311B GLU* 2.9 28.7 + - - -
329B ARG* 5.3 3.8 + - - -
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Residues in contact with VAL 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B GLN* 3.3 5.4 - - - -
272B VAL* 3.1 28.9 + - + -
274B TYR* 4.5 20.4 - - + +
277B GLN 4.3 10.1 - - - +
278B ARG* 1.3 78.6 - - - +
280B ASN* 1.3 63.0 - - - +
281B LEU* 3.2 31.0 + - + +
297B TRP* 3.5 20.0 - - + +
327B SER* 5.7 3.6 - - - +
329B ARG* 5.2 3.8 - - - +
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Residues in contact with ASN 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B TYR* 2.7 44.3 - - + +
271B GLN* 3.2 23.0 - - - +
278B ARG 4.3 0.6 + - - -
279B VAL* 1.3 72.4 - - - +
281B LEU* 1.3 60.3 + - - +
327B SER* 3.4 3.6 + - - -
328B PHE* 2.5 46.9 + - + -
329B ARG* 3.7 30.5 + - - +
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B TYR* 2.7 31.9 + - - -
269B ALA* 3.4 2.4 - - - -
270B LYS 2.8 29.4 + - - +
272B VAL* 4.1 18.2 - - + -
279B VAL* 3.2 32.3 + - + +
280B ASN* 1.3 78.6 - - - +
282B ILE* 1.4 60.7 + - - +
297B TRP* 3.6 46.2 - - + +
304B TRP* 6.2 1.8 - - + -
325B TRP* 3.5 28.7 - - + -
326B MET 3.3 10.8 - - - +
327B SER* 4.1 2.9 - - - -
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Residues in contact with ILE 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B TYR* 5.1 2.5 - - + -
228B ILE* 4.4 16.6 - - + -
266B VAL* 4.1 28.5 - - + -
268B ASP 4.2 2.9 - - - +
269B ALA* 4.6 5.6 - - + -
281B LEU* 1.4 62.7 - - - +
283B ARG* 1.4 62.4 + - - +
284B MET* 4.3 7.6 - - - -
325B TRP* 3.6 5.6 - - - -
326B MET* 2.7 56.4 + - + +
327B SER 4.5 0.2 - - - +
328B PHE* 4.3 24.5 - - + -
330B ASP* 3.2 30.1 - - - +
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Residues in contact with ARG 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B VAL* 3.7 1.6 - - - +
267B THR* 3.2 53.7 + - - +
268B ASP* 3.2 20.4 + - - +
270B LYS* 5.6 1.6 - - - +
282B ILE* 1.4 75.5 - - - +
284B MET* 1.3 74.5 + - - +
314B GLN 5.0 0.2 - - - -
315B LEU* 3.2 25.1 + - - +
317B VAL* 4.0 16.0 + - - +
318B LYS 4.6 2.0 + - - -
319B MET* 3.6 28.3 - - - +
323B GLU* 3.5 19.5 + - + +
324B PHE 3.4 8.7 - - - +
325B TRP* 3.0 49.4 - - + +
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Residues in contact with MET 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B CYS* 3.4 42.8 - - + -
264B TYR* 4.0 16.6 - - + +
265B SER 3.6 4.7 - - - +
266B VAL* 3.5 23.6 - - + -
267B THR* 4.4 0.4 - - - -
282B ILE* 4.3 8.3 - - + -
283B ARG* 1.3 80.7 - - - +
285B ARG* 1.4 55.1 - - - +
323B GLU* 2.1 24.3 - - - +
324B PHE* 2.8 64.9 + - + -
326B MET* 3.8 18.8 - - + +
330B ASP* 5.0 2.9 - - - +
334B GLU* 3.5 17.7 - - - +
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Residues in contact with ARG 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B THR* 2.9 38.6 + - - +
115B THR* 5.3 1.8 + - - +
116B LEU* 4.0 48.2 + - + +
264B TYR* 3.3 11.3 - - - -
265B SER* 2.9 34.1 + - - +
267B THR* 4.3 9.2 + - + +
284B MET* 1.4 72.4 - - - +
286B ASN* 1.4 70.2 + - - +
287B PRO* 3.7 6.1 - - - +
320B GLU* 3.3 36.9 + - - +
321B ASP 3.3 19.8 + - - +
322B GLY 3.0 11.9 - - - +
323B GLU* 3.0 22.1 + - - +
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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