Contacts of the strand formed by residues 481 - 489 (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 481 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390A ARG* 3.8 2.7 - - - +
391A LEU 3.0 29.6 + - - +
437A GLN* 4.7 8.7 - - - -
479A PRO 2.8 5.3 + - - -
480A PRO* 1.3 76.3 - - - +
482A GLU* 1.4 56.4 + - - -
483A TYR* 3.2 23.2 - - - -
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Residues in contact with GLU 482 (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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388A LYS* 2.3 45.1 + - - +
389A ILE 3.6 6.5 - - - +
390A ARG* 4.4 28.6 + - + +
437A GLN* 4.0 6.4 - - - +
438A VAL* 2.7 34.6 + - + +
440A ARG 4.2 2.8 - - - +
441A GLU 2.8 22.3 - - - +
442A LEU* 3.3 24.0 - - - +
481A GLY* 1.4 67.1 - - - -
483A TYR* 1.3 61.6 + - - +
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Residues in contact with TYR 483 (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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388A LYS* 3.3 6.9 - - - +
389A ILE* 2.6 48.2 + - + +
391A LEU* 4.1 18.2 - - + -
409A PHE* 6.0 0.2 - - + -
435A VAL* 4.1 12.1 - - + -
436A TYR 3.3 9.6 - - - +
437A GLN* 3.5 39.5 + - + -
438A VAL* 3.9 4.1 - - - +
460A ARG* 4.8 9.2 + - + -
478A LEU* 3.9 29.4 - - + -
479A PRO* 2.3 43.9 + - - +
480A PRO 4.0 0.3 + - - -
481A GLY* 3.2 39.0 + - - -
482A GLU* 1.3 72.7 - - - +
484A ILE* 1.3 57.9 + - - +
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Residues in contact with ILE 484 (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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386A GLN* 3.8 9.9 - - + -
387A PHE 3.5 5.2 - - - +
388A LYS* 4.3 2.2 - - - +
435A VAL* 3.2 5.1 - - - +
436A TYR* 2.5 71.8 + - + +
437A GLN 4.2 3.8 - - - +
438A VAL* 4.4 8.0 - - + +
449A LEU* 3.4 34.8 - - + -
453A PHE* 4.7 2.7 - - + -
454A PHE* 4.4 4.3 - - + -
483A TYR* 1.3 72.6 - - - +
485A VAL* 1.4 61.4 - - - +
486A VAL* 3.0 37.9 - - + -
513A LEU* 3.7 18.6 - - + -
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Residues in contact with VAL 485 (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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386A GLN* 3.9 1.6 - - - -
387A PHE* 2.7 49.1 + - + +
389A ILE* 3.2 28.7 - - + -
411A LEU* 3.4 26.2 - - + -
433A PHE* 4.7 4.9 - - + -
434A ALA 4.5 4.9 - - - +
435A VAL* 4.3 9.4 - - + +
484A ILE* 1.4 73.8 - - - +
486A VAL* 1.3 69.2 + - - +
487A PRO* 4.0 0.7 - - - -
500A LEU* 4.3 9.6 - - + -
502A PHE* 3.7 17.3 - - + -
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Residues in contact with VAL 486 (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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381A PHE* 3.4 36.0 - - + +
384A ASN* 3.9 24.2 - - + +
385A PRO 4.2 4.0 - - - +
386A GLN* 4.3 7.2 - - + +
433A PHE* 3.7 3.6 - - - -
434A ALA* 2.8 36.8 + - - +
436A TYR* 4.6 2.0 - - + -
454A PHE* 4.1 19.5 - - + -
484A ILE* 3.0 36.3 - - + -
485A VAL* 1.3 75.3 - - - +
487A PRO* 1.4 59.4 - - - +
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Residues in contact with PRO 487 (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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365A TRP* 3.5 4.5 + - + +
384A ASN* 3.5 14.2 - - - +
385A PRO* 3.7 8.1 - - + +
387A PHE* 3.5 37.5 - - + -
413A LEU* 3.3 35.0 - - + -
433A PHE* 3.9 5.4 - - + -
485A VAL* 3.7 3.1 - - + +
486A VAL* 1.4 67.7 - - - +
488A SER* 1.3 69.6 + - - +
498A PHE* 4.0 17.7 - - + -
500A LEU* 4.3 9.4 - - + -
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Residues in contact with SER 488 (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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365A TRP* 2.9 24.2 - - - -
373A GLY* 3.6 7.1 + - - -
374A CYS* 3.8 4.2 + - - +
381A PHE* 4.7 4.0 - - - -
384A ASN* 3.2 30.1 - - - -
413A LEU* 4.3 0.2 - - - +
431A ILE* 3.5 3.5 - - - +
432A GLY 3.0 30.3 + - - +
433A PHE* 5.5 0.2 - - - -
466A PHE* 3.9 8.3 - - - -
486A VAL 4.5 0.6 + - - -
487A PRO* 1.3 81.9 - - - +
489A THR* 1.4 74.1 + - - +
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Residues in contact with THR 489 (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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365A TRP* 3.4 32.0 - - + -
371A ALA* 6.4 1.1 - - + -
373A GLY* 3.6 3.9 + - - +
374A CYS 3.3 8.5 + - - -
384A ASN* 5.0 0.2 + - - -
429A GLU* 4.8 8.3 - - + -
430A THR 3.2 16.2 - - - +
431A ILE* 4.1 3.8 - - + +
466A PHE* 3.5 3.8 - - - -
488A SER* 1.4 93.8 + - - +
490A PHE* 1.3 62.1 + - - +
491A GLU 2.3 32.1 + - - -
494A LYS* 3.7 26.9 + - + +
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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