Contacts of the strand formed by residues 497 - 504 (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 ASP 497 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363B GLY 3.4 5.4 - - - +
364B THR* 3.9 9.2 - - - +
365B TRP* 4.5 1.1 - - - -
366B ARG* 3.1 28.0 + - - -
415B GLN* 3.5 8.0 - - - +
416B LYS* 3.2 58.4 + - + +
417B HIS 5.7 0.3 - - - -
418B ARG* 5.5 8.3 + - - -
496B GLY* 1.4 74.1 - - - +
498B PHE* 1.4 64.3 + - - +
779B ASP* 5.5 2.4 - - - +
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Residues in contact with PHE 498 (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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361B TYR 4.5 0.4 - - - -
362B GLU* 3.1 9.7 - - - +
363B GLY* 2.7 77.1 + - - +
364B THR 3.9 2.7 - - - -
365B TRP* 3.3 51.6 - + + -
385B PRO* 4.3 10.8 - - + -
387B PHE* 4.3 17.0 - + - -
413B LEU* 3.3 28.9 - - + -
414B MET 3.1 17.7 - - - +
415B GLN* 4.5 0.2 - - - +
416B LYS* 4.7 6.0 - - - +
487B PRO* 3.9 18.6 - - + -
497B ASP* 1.4 74.7 - - - +
499B LEU* 1.4 62.1 + - - +
500B LEU* 3.9 13.7 - - + -
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Residues in contact with LEU 499 (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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144B TRP* 4.0 18.6 - - + -
146B PHE 4.2 2.7 - - - +
147B GLY* 3.9 20.2 - - - +
360B PHE* 3.9 26.2 - - + -
361B TYR 2.7 8.7 - - - +
362B GLU* 3.9 24.2 - - + +
412B ALA 3.3 8.7 - - - +
413B LEU* 4.3 1.1 - - - -
414B MET* 3.4 31.4 + - + +
416B LYS* 5.1 5.6 - - + -
498B PHE* 1.4 62.5 - - - +
500B LEU* 1.4 63.7 + - - +
501B ARG* 3.6 35.5 - - + +
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Residues in contact with LEU 500 (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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360B PHE* 3.3 4.7 - - - +
361B TYR* 2.4 59.0 + - + +
387B PHE* 3.4 45.1 - - + -
411B LEU* 4.3 16.2 - - + -
412B ALA 3.1 17.3 - - - +
413B LEU* 3.7 27.6 - - + -
433B PHE* 5.0 3.1 - - + -
485B VAL* 4.3 13.7 - - + -
487B PRO* 3.9 19.1 - - + -
498B PHE* 3.9 5.7 - - + -
499B LEU* 1.4 71.8 - - - +
501B ARG* 1.3 61.4 + - - +
502B PHE* 4.6 5.8 - - + -
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Residues in contact with ARG 501 (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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144B TRP* 3.1 27.2 - - - -
205B GLU* 3.8 6.5 - - - +
209B GLY 2.7 30.1 + - - -
210B GLY* 2.9 23.0 + - - -
211B VAL* 3.5 13.1 - - - +
343B LEU* 5.4 0.4 - - - +
359B THR 3.4 5.4 - - - +
360B PHE* 4.1 11.9 - - + -
410B LEU 3.5 3.8 - - - +
411B LEU* 3.6 7.4 - - - +
412B ALA* 2.9 37.6 + - + +
471B GLU* 3.0 26.7 + - - -
499B LEU* 3.6 30.7 - - + +
500B LEU* 1.3 76.6 - - - +
502B PHE* 1.3 67.3 + - - +
503B PHE* 4.0 24.2 - - + -
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Residues in contact with PHE 502 (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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357B ASN 3.6 1.3 - - - +
358B THR* 3.4 6.8 - - - -
359B THR* 2.9 41.2 + - - +
361B TYR* 4.2 20.2 - + - -
387B PHE* 4.3 10.5 - - + -
388B LYS 4.9 2.5 - - - -
389B ILE* 3.7 22.4 - - + -
409B PHE* 3.8 21.1 - + - -
410B LEU 3.6 0.9 - - - -
411B LEU* 3.0 28.9 - - + -
485B VAL* 3.4 28.0 - - + -
500B LEU* 4.6 5.8 - - + -
501B ARG* 1.3 76.6 - - - +
503B PHE* 1.3 67.5 - - - +
504B SER* 5.1 4.0 - - - +
510B THR* 3.2 34.3 - - + -
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Residues in contact with PHE 503 (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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210B GLY* 4.7 1.8 - - - -
211B VAL* 4.1 33.7 - - + -
341B CYS* 4.1 14.8 - - + -
342B ASN 3.9 17.3 - - - -
343B LEU* 4.4 11.2 - - + -
356B TRP* 3.9 25.0 - + + -
357B ASN 3.6 2.9 - - - -
358B THR* 3.8 24.7 - - + -
359B THR 5.1 1.1 - - - -
409B PHE* 3.6 2.8 - - - +
410B LEU* 3.0 49.6 + - + +
501B ARG* 4.0 30.5 - - + -
502B PHE* 1.3 83.2 - - - +
504B SER* 1.3 57.5 + - - +
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Residues in contact with SER 504 (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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356B TRP* 3.4 11.9 - - - -
357B ASN* 2.8 47.7 + - - +
389B ILE* 4.8 3.1 - - - +
391B LEU* 4.8 2.2 - - - +
408B SER 3.8 7.2 - - - -
409B PHE* 3.4 19.1 - - - +
502B PHE* 4.1 4.7 - - - +
503B PHE* 1.3 69.7 - - - +
505B GLU* 1.3 64.2 + - - +
506B LYS 3.6 19.7 - - - -
508B ALA* 3.6 20.4 - - - +
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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