Contacts of the strand formed by residues 488 - 504 (chain A) in PDB entry 4QDR
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440A MET* 4.7 5.4 - - + -
450A ILE* 4.3 7.9 - - + -
451A SER 3.6 13.5 - - - +
452A ALA* 4.3 4.7 - - + -
460A TRP* 4.6 2.7 - - + -
465A ALA* 3.8 32.1 - - + -
474A TRP* 4.0 31.6 - - + -
487A TRP* 1.3 73.9 - - - +
489A GLN* 1.3 64.4 + - - +
490A VAL* 4.8 1.1 - - + -
571A VAL 3.9 0.7 - - - +
572A ARG* 3.3 3.3 - - - +
573A VAL* 2.9 35.7 + - + +
585A MET* 4.5 14.1 - - + -
587A LEU* 3.5 41.4 - - + +
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Residues in contact with GLN 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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449A GLN 3.9 1.0 - - - +
450A ILE* 3.7 5.2 - - - +
451A SER* 2.8 54.7 + - - +
487A TRP* 3.8 10.8 - - + -
488A LEU* 1.3 74.8 - - - +
490A VAL* 1.3 72.4 + - - +
491A ASP* 5.5 2.2 - - - +
532A GLY 5.6 1.4 + - - -
535A TRP* 3.5 15.8 - - + -
570A TYR* 3.8 23.1 - - + -
571A VAL 3.3 8.7 - - - +
572A ARG* 2.9 45.4 + - + -
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Residues in contact with VAL 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A MET* 3.9 26.5 - - + -
445A ILE* 3.9 32.8 - - + -
449A GLN 3.8 3.4 - - - +
450A ILE* 5.1 2.7 - - + -
488A LEU* 4.8 3.8 - - + -
489A GLN* 1.3 80.5 - - - +
491A ASP* 1.3 70.3 + - - +
492A LEU* 3.9 10.7 - - + +
569A GLN 3.5 1.4 - - - +
570A TYR* 3.3 4.3 - - - -
571A VAL* 2.8 37.9 + - + +
587A LEU* 4.1 21.3 - - + -
589A VAL* 4.4 13.2 - - + -
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Residues in contact with ASP 491 (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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445A ILE* 3.8 6.8 - - - +
449A GLN* 2.9 55.6 + - + +
489A GLN* 4.2 3.4 - - - +
490A VAL* 1.3 71.0 - - - +
492A LEU* 1.3 62.2 + - - +
493A GLY* 3.1 7.8 + - - -
569A GLN* 3.0 33.6 + - - +
570A TYR* 3.4 29.1 + - + -
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Residues in contact with LEU 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A LEU* 4.1 20.2 - - + -
445A ILE* 3.8 29.4 - - + +
449A GLN* 3.7 6.2 + - - +
490A VAL* 3.9 14.1 - - + +
491A ASP* 1.3 72.3 + - - +
493A GLY* 1.3 54.6 + - - +
494A THR* 3.2 16.5 + - - +
496A LYS* 3.8 29.6 + - + -
498A VAL* 3.7 24.0 - - + -
568A ALA 3.7 21.1 - - - +
569A GLN 2.6 21.0 + - - +
571A VAL* 4.4 6.3 - - + -
589A VAL* 4.1 10.5 - - + -
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Residues in contact with GLY 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A GLN* 3.9 12.1 - - - -
491A ASP* 3.1 14.7 + - - -
492A LEU* 1.3 76.2 - - - +
494A THR* 1.3 67.1 + - - +
569A GLN* 3.1 17.1 + - - +
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Residues in contact with THR 494 (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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492A LEU* 3.2 5.7 + - - +
493A GLY* 1.3 80.8 - - - +
495A PRO* 1.3 78.7 - - + +
496A LYS* 3.3 31.0 + - - +
569A GLN* 3.5 14.3 - - - +
593A ASP* 4.1 8.7 + - - -
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Residues in contact with PRO 495 (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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494A THR* 1.3 89.4 + - + +
496A LYS* 1.3 58.8 + - - +
530A LEU* 3.9 25.1 - - + +
568A ALA 3.7 10.3 - - - +
569A GLN* 3.5 14.8 - - + +
593A ASP* 3.3 17.3 - - - +
594A TRP* 3.8 34.2 - - + +
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Residues in contact with LYS 496 (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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438A LEU* 4.5 24.0 + - + +
492A LEU* 3.8 35.8 + - + -
494A THR* 3.3 26.4 + - - +
495A PRO* 1.3 73.8 - - - +
497A THR* 1.3 66.7 + - - +
498A VAL 3.9 0.4 - - - -
567A PRO* 3.5 5.5 - - - +
568A ALA 2.8 35.0 + - - +
592A CYS 3.4 15.5 - - - +
593A ASP* 3.6 23.9 + - - +
594A TRP* 4.0 8.9 + - - -
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Residues in contact with THR 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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434A CYS* 3.9 20.6 - - - -
438A LEU* 4.6 0.3 - - - +
496A LYS* 1.3 74.0 - - - +
498A VAL* 1.3 63.2 + - - +
499A LYS* 5.2 0.2 - - + -
565A PRO* 3.6 29.8 - - + -
566A ILE 3.5 7.8 - - - +
567A PRO* 5.5 0.9 - - - +
591A GLY* 3.1 24.6 - - - -
592A CYS* 2.9 21.6 + - - +
593A ASP 4.7 0.3 - - - -
594A TRP* 4.1 20.7 - - - -
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Residues in contact with VAL 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A LEU* 4.9 0.7 - - + -
492A LEU* 3.7 30.3 - - + -
496A LYS 4.7 0.2 - - - +
497A THR* 1.3 74.4 - - - +
499A LYS* 1.3 62.4 + - - +
500A GLY 4.1 1.6 - - - +
501A VAL* 5.6 0.4 - - + -
563A PHE* 3.7 23.9 - - + -
565A PRO* 3.2 3.3 - - - +
566A ILE* 2.8 49.9 + - + +
568A ALA* 4.0 21.5 - - + +
571A VAL* 4.0 12.3 - - + -
589A VAL* 3.9 15.7 - - + -
590A LEU 3.5 9.6 - - - +
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Residues in contact with LYS 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A PRO* 3.4 30.0 + - - +
434A CYS* 3.3 39.3 - - + +
435A SER* 5.5 0.2 - - - -
497A THR 4.0 0.2 + - - -
498A VAL* 1.3 74.2 - - - +
500A GLY* 1.3 58.2 + - - +
562A ARG* 3.4 19.5 + - + +
563A PHE* 2.9 43.6 + - - +
565A PRO* 4.3 28.5 - - + +
590A LEU* 2.8 11.4 + - + +
591A GLY* 4.6 1.3 - - - -
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Residues in contact with GLY 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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499A LYS* 1.3 82.0 - - - +
501A VAL* 1.3 65.6 + - - +
561A ARG 3.2 13.2 - - - -
562A ARG* 4.0 1.8 - - - -
563A PHE* 3.4 14.6 - - - -
589A VAL* 3.6 3.8 - - - +
590A LEU* 2.6 42.7 + - - +
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Residues in contact with VAL 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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500A GLY* 1.3 79.7 - - - +
502A ILE* 1.3 65.0 + - - +
503A ILE 4.8 0.7 - - - +
524A PHE* 4.0 32.8 - - + -
526A VAL* 4.8 2.9 - - + -
560A ILE* 3.4 4.5 - - - +
561A ARG* 2.8 45.6 + - + +
563A PHE* 4.4 14.4 - - + -
571A VAL* 4.8 13.5 - - + -
573A VAL* 4.6 10.8 - - + -
587A LEU* 4.1 18.2 - - + -
588A GLU 3.3 12.6 - - - +
589A VAL* 4.6 7.9 - - + -
590A LEU* 4.3 2.5 - - - +
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Residues in contact with ILE 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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336A LEU* 5.0 1.3 - - + -
403A LEU* 3.6 29.6 - - + -
429A VAL* 4.6 10.5 - - + -
437A MET* 4.4 13.7 - - + -
467A LEU* 3.7 40.8 - - + +
501A VAL* 1.3 77.2 - - - +
503A ILE* 1.3 61.6 + - - +
558A PRO* 3.8 6.1 - - + -
559A ASP 3.3 10.5 - - - +
560A ILE* 4.3 8.7 - - + -
587A LEU* 3.4 7.6 - - - +
588A GLU* 2.9 35.2 + - + +
590A LEU* 3.9 32.5 - - + -
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Residues in contact with ILE 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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501A VAL* 4.1 1.9 - - + -
502A ILE* 1.3 73.6 - - - +
504A GLN* 1.3 67.1 + - - +
521A VAL* 3.9 16.2 - - + +
524A PHE* 3.6 47.3 - - + -
550A GLU 4.7 1.1 - - - +
551A GLY* 4.3 6.5 - - - -
552A ASN* 2.8 36.7 + - - +
558A PRO* 3.3 2.9 - - - +
559A ASP* 2.8 31.3 + - + +
561A ARG* 5.0 2.5 - - + -
573A VAL* 4.8 2.2 - - + -
585A MET* 3.7 30.7 - - + -
586A ARG 3.7 7.2 - - - +
587A LEU* 4.4 7.4 - - + -
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Residues in contact with GLN 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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367A THR* 3.6 21.4 + - - +
467A LEU* 3.6 17.0 - - + -
468A VAL* 2.8 30.6 + - - +
503A ILE* 1.3 76.2 - - - +
505A GLY* 1.3 67.5 + - - +
552A ASN* 3.2 11.3 - - - +
556A ASP* 2.9 30.4 + - - +
558A PRO* 3.9 3.8 - - + -
585A MET* 3.0 9.2 - - - +
586A ARG* 2.6 73.4 + - + +
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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
------------------------------------------------------------
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