Contacts of the strand formed by residues 481 - 489 (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 GLY 481 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390B ARG* 3.6 2.0 - - - -
391B LEU* 2.6 37.8 + - - +
437B GLN* 4.8 6.5 - - - -
479B PRO 3.6 0.6 + - - -
480B PRO* 1.3 76.6 - - - +
482B GLU* 1.3 61.8 + - - -
483B TYR* 3.5 16.3 - - - -
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Residues in contact with GLU 482 (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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388B LYS* 2.9 32.4 + - - +
389B ILE 3.2 4.0 - - - -
390B ARG* 3.1 39.6 + - + +
437B GLN* 3.6 8.0 + - - +
438B VAL* 3.0 30.7 + - + +
442B LEU* 3.0 48.2 - - + +
443B ALA 4.6 4.5 - - - +
481B GLY* 1.3 73.8 - - - -
483B TYR* 1.3 65.0 + - - +
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Residues in contact with TYR 483 (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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388B LYS* 3.1 17.7 - - - +
389B ILE* 2.7 37.7 + - + +
391B LEU* 4.0 17.5 - - + -
435B VAL* 3.8 9.2 - - + -
436B TYR 3.5 16.4 - - - +
437B GLN* 4.3 9.9 - - + -
438B VAL* 3.6 1.1 - - - -
460B ARG* 3.2 32.2 + - + -
478B LEU* 3.5 31.2 - - + -
479B PRO* 1.9 49.0 + - - +
480B PRO 3.6 2.4 + - - -
481B GLY* 3.5 26.2 - - - -
482B GLU* 1.3 75.8 - - - +
484B ILE* 1.3 63.5 + - - +
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Residues in contact with ILE 484 (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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386B GLN* 4.6 11.9 - - + +
387B PHE 3.4 6.1 - - - +
388B LYS* 4.3 5.8 - - + -
434B ALA 3.4 1.2 - - - +
435B VAL* 2.9 14.4 - - - -
436B TYR* 2.8 45.4 + - + +
437B GLN 4.6 2.0 - - - -
438B VAL* 2.9 42.8 - - + +
449B LEU* 4.6 11.0 - - + -
453B PHE* 4.9 2.7 - - + -
454B PHE* 4.7 12.6 - - + -
483B TYR* 1.3 72.8 - - - +
485B VAL* 1.3 57.4 + - - +
486B VAL* 4.0 23.3 - - + -
513B LEU* 3.2 34.5 - - + -
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Residues in contact with VAL 485 (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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386B GLN 3.8 0.3 - - - -
387B PHE* 2.7 55.1 + - + +
388B LYS* 4.8 1.3 - - - -
389B ILE* 4.9 2.7 - - + -
411B LEU* 4.4 15.7 - - + -
433B PHE* 4.5 8.7 - - + -
434B ALA 3.5 6.5 - - - +
435B VAL* 4.2 12.1 - - + -
483B TYR 4.1 0.2 - - - -
484B ILE* 1.3 72.9 - - - +
486B VAL* 1.3 73.5 + - - +
487B PRO* 3.4 10.5 - - + +
500B LEU* 4.3 9.9 - - + -
502B PHE* 3.4 34.5 - - + -
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Residues in contact with VAL 486 (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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381B PHE* 3.8 35.6 - - + +
384B ASN* 4.1 26.2 - - + +
385B PRO 4.3 0.7 - - - -
386B GLN* 4.1 16.4 - - + +
433B PHE* 3.4 3.3 - - - -
434B ALA* 3.1 31.1 + - - +
436B TYR* 5.0 0.9 - - + -
454B PHE* 3.9 27.8 - - + -
484B ILE* 4.0 11.4 - - + -
485B VAL* 1.3 81.4 - - - +
487B PRO* 1.3 62.5 - - - +
488B SER* 3.7 2.5 + - - -
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Residues in contact with PRO 487 (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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365B TRP* 3.2 12.4 + - + -
384B ASN* 3.4 6.2 - - - +
385B PRO* 3.2 21.1 - - + +
387B PHE* 4.3 1.3 - - + -
413B LEU* 3.5 29.8 - - + -
432B GLY 3.6 4.7 - - - +
433B PHE* 3.9 4.5 - - + -
485B VAL* 3.4 11.9 - - + +
486B VAL* 1.3 83.7 - - - +
488B SER* 1.3 73.2 + - - +
498B PHE* 3.9 23.1 - - + -
500B LEU* 3.9 19.3 - - + -
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Residues in contact with SER 488 (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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365B TRP* 3.4 14.6 - - - -
373B GLY 2.9 17.5 + - - -
374B CYS* 4.0 9.7 - - - +
381B PHE* 4.5 3.6 - - - -
384B ASN* 3.1 29.1 + - - -
413B LEU* 3.9 0.2 - - - +
431B ILE* 3.3 1.4 - - - -
432B GLY 2.6 46.2 + - - +
433B PHE* 5.5 0.3 - - - -
466B PHE* 3.6 4.0 - - - -
486B VAL* 3.7 5.2 + - - -
487B PRO* 1.3 82.1 - - - +
489B THR* 1.3 64.4 + - - +
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Residues in contact with THR 489 (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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365B TRP* 3.7 34.9 - - + -
371B ALA* 5.7 1.0 - - - -
372B GLY 5.5 0.9 + - - -
373B GLY 3.0 24.9 + - - -
384B ASN* 5.7 0.2 + - - -
429B GLU* 4.6 10.1 - - + +
430B THR 2.7 18.6 - - - +
431B ILE* 4.6 3.4 - - + -
466B PHE* 3.9 1.6 - - - -
488B SER* 1.3 73.0 + - - +
490B PHE* 1.4 65.6 - - - +
491B GLU 2.9 19.5 + - - -
492B PRO* 4.7 0.5 - - - +
494B LYS* 4.2 31.0 + - + +
495B GLU 5.4 0.7 - - - +
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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