Contacts of the strand formed by residues 488 - 504 (chain B) in PDB entry 4QDQ
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 LEU 488 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440B MET* 5.4 1.8 - - + -
450B ILE* 4.0 8.3 - - + -
451B SER 3.5 15.9 - - - +
452B ALA* 4.2 4.7 - - + -
460B TRP* 3.7 26.2 - - + -
465B ALA* 4.0 19.5 - - + +
474B TRP* 3.8 24.9 - - + -
487B TRP* 1.3 75.4 - - - +
489B GLN* 1.3 61.3 + - - +
490B VAL* 4.3 1.3 + - + -
571B VAL 3.8 0.5 - - - +
572B ARG* 3.1 4.4 - - - -
573B VAL* 2.9 33.7 + - - +
585B MET* 3.9 20.6 - - + +
587B LEU* 3.9 33.1 - - + +
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Residues in contact with GLN 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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449B GLN 3.7 1.1 + - - +
450B ILE* 3.5 7.1 - - - +
451B SER* 2.7 49.6 + - - +
487B TRP* 3.6 18.7 - - + -
488B LEU* 1.3 74.4 - - - +
490B VAL* 1.3 73.7 + - - +
491B ASP* 5.0 4.8 - - - +
535B TRP* 3.5 15.3 - - + -
570B TYR* 3.9 22.1 - - + -
571B VAL 3.3 10.3 - - - +
572B ARG* 2.8 39.9 + - + -
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Residues in contact with VAL 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B MET* 3.8 25.6 - - + -
445B ILE* 3.8 36.8 - - + -
449B GLN 3.7 2.5 - - - -
450B ILE* 5.2 1.8 - - + -
488B LEU* 5.4 1.8 - - + -
489B GLN* 1.3 78.4 - - - +
491B ASP* 1.3 64.4 + - - +
492B LEU* 3.7 15.4 + - + +
569B GLN 3.6 1.2 - - - +
570B TYR* 3.3 4.9 - - - +
571B VAL* 2.8 38.7 + - + +
587B LEU* 4.1 15.3 - - + -
589B VAL* 4.0 22.9 - - + -
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Residues in contact with ASP 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B ILE* 4.4 0.2 - - - +
448B SER 5.7 0.2 - - - +
449B GLN* 2.8 57.1 + - - +
489B GLN* 4.1 5.5 - - - +
490B VAL* 1.3 73.8 - - - +
492B LEU* 1.3 57.4 + - - +
493B GLY* 2.8 25.2 + - - -
569B GLN* 3.1 23.4 + - - +
570B TYR* 3.4 27.9 + - + -
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Residues in contact with LEU 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B LEU* 3.8 28.5 - - + -
445B ILE* 3.8 27.4 - - + +
449B GLN* 3.8 8.1 + - - +
490B VAL* 3.9 13.2 - - + +
491B ASP* 1.3 71.8 - - - +
493B GLY* 1.3 56.0 + - - +
494B THR* 3.1 13.3 + - - +
496B LYS* 2.9 37.2 + - + +
498B VAL* 3.8 23.8 - - + -
568B ALA 3.8 20.6 - - - +
569B GLN 2.7 19.1 + - - +
571B VAL* 4.6 7.0 - - + -
589B VAL* 4.5 6.3 - - + -
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Residues in contact with GLY 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLU* 3.9 15.5 - - - +
449B GLN* 4.2 9.4 - - - -
491B ASP* 2.8 21.6 + - - -
492B LEU* 1.3 75.7 - - - +
494B THR* 1.3 60.5 + - - +
569B GLN* 3.3 14.4 + - - +
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Residues in contact with THR 494 (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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291A GLU* 3.7 40.3 + - + +
492B LEU* 3.1 7.7 + - - +
493B GLY* 1.3 77.2 - - - +
495B PRO* 1.4 89.0 + - - +
496B LYS* 3.4 32.3 + - - +
569B GLN* 3.6 19.0 - - - -
593B ASP* 5.4 1.3 - - - +
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Residues in contact with PRO 495 (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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494B THR* 1.4 95.5 + - - +
496B LYS* 1.3 64.2 + - - +
530B LEU* 3.6 31.6 - - + +
568B ALA 3.7 6.5 - - - +
569B GLN* 3.4 17.7 - - + +
594B TRP* 3.7 42.2 + - + +
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Residues in contact with LYS 496 (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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438B LEU* 4.3 25.8 + - + -
444B LEU* 6.1 3.3 - - - +
445B ILE* 6.0 1.4 - - - +
492B LEU* 2.9 48.9 + - + +
494B THR* 3.6 20.2 - - + +
495B PRO* 1.3 79.3 - - - +
497B THR* 1.3 66.6 + - - +
498B VAL* 3.7 0.6 + - - -
567B PRO* 3.4 4.7 - - - +
568B ALA 2.8 35.2 + - - +
592B CYS 3.7 5.4 - - - +
593B ASP* 3.2 42.2 - - - +
594B TRP* 3.4 12.9 + - - +
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Residues in contact with THR 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B CYS* 3.8 21.3 - - - -
438B LEU* 4.6 0.9 - - - +
496B LYS* 1.3 73.7 - - - +
498B VAL* 1.3 63.2 + - - +
499B LYS* 5.3 0.2 - - + -
565B PRO* 3.7 28.9 - - + -
566B ILE 3.8 7.0 - - - +
567B PRO* 4.8 1.0 - - - +
591B GLY* 3.0 5.2 - - - -
592B CYS* 3.0 37.7 + - - +
593B ASP 5.1 0.2 + - - -
594B TRP* 3.4 19.5 + - - +
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Residues in contact with VAL 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B LEU* 4.6 1.6 - - + -
492B LEU* 3.8 29.4 - - + -
497B THR* 1.3 76.4 - - - +
499B LYS* 1.3 62.0 + - - +
500B GLY 3.9 1.3 - - - +
563B PHE* 3.7 28.5 - - + -
565B PRO* 3.3 3.2 - - - +
566B ILE* 2.9 42.6 + - + +
568B ALA* 4.1 14.1 - - + +
571B VAL* 4.0 18.8 - - + -
589B VAL* 3.7 17.5 - - + -
590B LEU 3.5 12.1 - - - +
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Residues in contact with LYS 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B ALA* 5.8 1.6 - - - +
433B PRO* 3.3 35.1 + - - +
434B CYS* 3.5 36.5 - - + +
435B SER* 5.6 1.6 - - - -
498B VAL* 1.3 73.4 - - - +
500B GLY* 1.3 58.4 + - - +
562B ARG* 3.4 17.9 + - + +
563B PHE* 3.0 41.7 + - - +
565B PRO* 4.0 32.8 - - + -
590B LEU* 2.9 10.3 + - + +
591B GLY* 4.0 1.5 - - - -
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Residues in contact with GLY 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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498B VAL* 3.9 1.4 - - - +
499B LYS* 1.3 80.7 - - - +
501B VAL* 1.3 65.1 + - - +
561B ARG 3.2 13.9 - - - -
562B ARG* 3.9 2.2 - - - -
563B PHE* 3.6 13.6 - - - -
589B VAL* 3.7 4.3 - - - +
590B LEU* 2.7 42.8 + - - +
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Residues in contact with VAL 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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500B GLY* 1.3 78.8 - - - +
502B ILE* 1.3 67.2 + - - +
503B ILE* 5.1 1.1 - - + +
524B PHE* 4.0 32.3 - - + -
526B VAL* 4.8 4.5 - - + -
559B ASP 4.0 0.2 - - - +
560B ILE* 3.5 2.6 - - - +
561B ARG* 2.8 44.1 + - + +
563B PHE* 4.6 13.5 - - + -
571B VAL* 4.7 16.6 - - + -
573B VAL* 4.7 9.2 - - + -
587B LEU* 4.1 17.3 - - + -
588B GLU 3.3 13.0 - - - +
589B VAL* 4.6 7.0 - - + -
590B LEU* 4.3 2.0 - - - +
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Residues in contact with ILE 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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336B LEU* 5.2 0.4 - - + -
403B LEU* 3.7 26.0 - - + -
429B VAL* 4.2 9.0 - - + -
437B MET* 4.0 24.5 - - + -
467B LEU* 3.7 30.9 - - + +
501B VAL* 1.3 78.1 - - - +
503B ILE* 1.3 62.8 + - - +
558B PRO* 3.8 8.1 - - + -
559B ASP 3.4 9.9 - - - +
560B ILE* 4.1 7.2 - - + -
587B LEU* 3.4 7.8 - - - +
588B GLU* 2.8 40.1 + - + +
590B LEU* 3.7 33.8 - - + +
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Residues in contact with ILE 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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467B LEU* 4.3 1.1 - - - -
501B VAL* 4.1 1.7 - - + -
502B ILE* 1.3 73.7 - - - +
504B GLN* 1.3 69.3 + - - +
521B VAL* 3.9 27.1 - - + +
524B PHE* 3.8 44.9 - - + -
550B GLU 4.8 0.9 - - - +
551B GLY* 4.4 6.5 - - - -
552B ASN* 3.1 22.7 + - - +
558B PRO* 3.2 4.3 - - - +
559B ASP* 2.9 42.2 + - + +
561B ARG* 5.2 1.8 - - + -
573B VAL* 4.6 1.3 - - + -
585B MET* 4.0 27.8 - - + -
586B ARG 3.8 2.0 - - - -
587B LEU* 4.4 6.5 - - + -
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Residues in contact with GLN 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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367B THR* 3.5 15.0 + - - +
467B LEU* 3.6 15.9 - - + +
468B VAL* 2.7 30.2 + - - +
503B ILE* 1.3 75.6 - - - +
505B GLY* 1.3 69.7 + - - +
521B VAL 5.5 0.2 + - - -
552B ASN* 3.2 11.5 - - - +
556B ASP* 2.7 45.2 + - - +
558B PRO* 4.2 4.9 - - + +
585B MET* 3.2 10.6 - - - +
586B ARG* 2.9 57.1 + - + +
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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