Contacts of the strand formed by residues 496 - 504 (chain A) 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 GLY 496 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364A THR* 3.3 1.7 - - - -
365A TRP* 2.9 44.8 + - - +
366A ARG* 3.1 13.6 + - - +
415A GLN* 6.1 1.8 - - - -
495A GLU* 1.3 76.2 - - - +
497A ASP* 1.4 64.7 + - - -
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Residues in contact with ASP 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A GLY 3.2 8.5 - - - +
364A THR* 2.6 25.7 - - + +
365A TRP* 5.1 0.9 - - - -
366A ARG* 3.5 11.4 + - - -
415A GLN* 3.2 9.5 - - - +
416A LYS* 2.8 58.8 + - + +
496A GLY* 1.4 75.5 - - - -
498A PHE* 1.3 62.4 - - - +
779A ASP* 5.4 6.5 - - - +
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Residues in contact with PHE 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A TYR 4.7 1.3 - - - -
362A GLU* 3.4 4.3 - - - +
363A GLY* 2.7 75.6 + - - +
364A THR* 3.4 9.6 - - - -
365A TRP* 3.6 42.8 - + + -
385A PRO* 4.5 4.5 - - + -
387A PHE* 4.3 16.8 - + - -
413A LEU* 3.2 26.0 - - + -
414A MET 3.0 17.9 - - - +
415A GLN* 4.4 0.2 - - - -
416A LYS* 4.3 9.1 - - - -
487A PRO* 4.0 23.1 - - + -
497A ASP* 1.3 77.8 - - - +
499A LEU* 1.3 55.7 + - - +
500A LEU* 4.3 8.5 - - + -
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Residues in contact with LEU 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A TRP* 4.1 10.8 - - + -
146A PHE* 3.5 10.5 - - - +
147A GLY* 3.3 39.3 - - - +
360A PHE* 3.6 27.4 - - + -
361A TYR 3.3 16.6 - - - +
362A GLU* 4.2 9.2 - - + +
412A ALA 3.9 0.7 - - - +
413A LEU* 3.6 0.9 - - - -
414A MET* 3.0 40.2 + - + +
416A LYS* 4.6 5.1 - - + +
498A PHE* 1.3 73.4 - - - +
500A LEU* 1.3 69.6 + - - +
501A ARG* 3.6 17.3 - - - -
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Residues in contact with LEU 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A PHE* 3.4 3.8 - - - -
361A TYR* 2.8 38.9 + - + +
387A PHE* 3.6 35.7 - - + -
411A LEU* 3.5 33.0 - - + -
412A ALA 3.1 7.9 - - - +
413A LEU* 4.1 20.0 - - + +
485A VAL* 4.3 8.5 - - + -
487A PRO* 4.3 10.8 - - + -
498A PHE* 4.3 7.3 - - + -
499A LEU* 1.3 73.9 - - - +
501A ARG* 1.3 64.1 + - - +
502A PHE* 3.3 35.2 - - + -
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Residues in contact with ARG 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A TRP* 3.6 24.3 - - - -
209A GLY 3.5 13.5 + - - -
210A GLY* 2.7 38.2 + - - -
211A VAL* 3.7 13.7 - - - +
358A THR* 6.2 0.7 - - + -
359A THR 3.6 4.5 - - - +
360A PHE* 4.1 10.3 - - + -
410A LEU 3.6 4.0 - - - +
411A LEU* 3.6 2.1 - - - +
412A ALA* 2.5 41.8 + - + +
414A MET* 3.7 1.4 - - - +
471A GLU* 2.8 33.8 + - - -
499A LEU* 3.6 31.2 - - + -
500A LEU* 1.3 80.0 - - - +
502A PHE* 1.3 68.5 + - - +
503A PHE* 4.4 20.7 - - + -
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Residues in contact with PHE 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A ASN 3.6 8.2 - - - +
358A THR* 3.8 10.4 - - - -
359A THR* 2.8 36.1 + - - +
361A TYR* 3.8 19.5 - + - -
387A PHE* 4.3 7.2 - - + -
389A ILE* 3.2 44.6 - - + -
409A PHE* 4.2 16.2 - + + -
410A LEU 3.4 4.5 - - - +
411A LEU* 4.6 6.1 - - + -
485A VAL* 3.7 9.2 - - + -
500A LEU* 3.3 35.4 - - + -
501A ARG* 1.3 80.9 - - - +
503A PHE* 1.3 65.6 + - - +
504A SER* 4.2 2.5 - - - +
508A ALA* 6.4 1.3 - - + -
510A THR* 4.1 12.8 - - + -
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Residues in contact with PHE 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A GLY* 5.2 1.3 - - - -
211A VAL* 4.3 33.0 - - + -
341A CYS* 4.1 14.6 - - + -
342A ASN 3.9 18.4 - - - -
343A LEU* 4.9 6.7 - - + -
356A TRP* 3.9 32.3 - + + -
357A ASN 3.4 4.7 - - - -
358A THR* 3.4 32.3 - - + -
409A PHE* 3.5 1.6 - - - -
410A LEU* 2.7 49.2 + - + +
501A ARG* 4.4 23.6 - - + -
502A PHE* 1.3 75.5 - - - +
504A SER* 1.3 60.3 + - - +
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Residues in contact with SER 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A TRP* 3.1 18.3 - - - -
357A ASN* 3.4 28.1 + - - +
391A LEU* 5.8 1.6 - - - -
408A SER 3.4 17.3 - - - -
409A PHE* 3.8 9.4 - - - +
502A PHE* 5.3 2.0 + - - +
503A PHE* 1.3 77.8 + - - +
505A GLU* 1.3 65.1 + - - +
506A LYS 2.9 23.0 + - - -
508A ALA* 3.6 19.8 - - - +
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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