Contacts of the helix formed by residues 513 - 534 (chain A) in PDB entry 3W6R
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 ASP 513 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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511A ASN 3.7 1.4 + - - -
512A PRO* 1.3 72.9 - - - +
514A PRO* 1.4 69.7 - - + +
515A VAL* 3.3 13.5 + - - +
516A THR* 2.8 45.2 + - - -
517A MET* 2.8 24.8 + - - +
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Residues in contact with PRO 514 (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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512A PRO 3.8 2.2 - - - +
513A ASP* 1.4 88.7 - - + +
515A VAL* 1.3 64.3 + - + +
517A MET* 3.7 18.5 - - + +
518A LEU* 3.2 31.1 + - + +
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Residues in contact with VAL 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A ASP* 3.2 10.3 + - - +
514A PRO* 1.3 82.0 - - + +
516A THR* 1.3 64.5 + - - +
518A LEU* 4.0 2.2 - - - +
519A GLN* 3.1 49.0 + - + +
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Residues in contact with THR 516 (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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440A ARG* 3.5 28.0 - - - +
509A VAL* 6.0 2.5 - - + -
512A PRO* 4.3 10.8 - - + -
513A ASP* 2.8 33.4 + - - +
515A VAL* 1.3 73.3 - - - +
517A MET* 1.3 57.5 + - - +
519A GLN* 3.2 14.2 + - + +
520A ASP* 2.8 48.5 + - - +
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Residues in contact with MET 517 (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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507A HIS* 3.6 25.9 - - + +
512A PRO* 4.0 17.4 - - + +
513A ASP 2.8 21.6 + - - +
514A PRO* 3.7 18.4 - - + +
515A VAL 3.3 0.2 - - - -
516A THR* 1.3 74.9 - - - +
518A LEU* 1.3 81.7 + - + +
520A ASP* 3.4 3.3 + - - +
521A ILE* 3.3 25.8 + - + +
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Residues in contact with LEU 518 (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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514A PRO* 3.2 17.9 + - + +
515A VAL 4.2 2.2 - - - +
517A MET* 1.3 95.9 - - + +
519A GLN* 1.3 64.2 + - - +
521A ILE* 3.4 35.5 - - + +
522A LYS* 3.7 24.3 + - - +
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Residues in contact with GLN 519 (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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515A VAL* 3.1 39.8 + - + +
516A THR* 3.2 15.6 + - + +
518A LEU* 1.3 76.8 - - - +
520A ASP* 1.3 65.8 + - - +
522A LYS* 3.4 20.1 + - - +
523A ARG* 3.4 22.3 - - - +
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Residues in contact with ASP 520 (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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440A ARG* 3.0 35.6 + - - -
443A MET* 3.9 13.6 - - + +
506A ALA 4.6 0.2 - - - +
507A HIS* 2.7 41.9 + - + +
516A THR* 2.8 34.0 + - - +
517A MET 3.6 2.0 - - - +
519A GLN* 1.3 75.4 - - - +
521A ILE* 1.3 57.7 + - - +
523A ARG* 2.8 25.8 + - - +
524A GLN* 3.1 18.4 + - - +
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Residues in contact with ILE 521 (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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502A PRO* 5.1 9.2 - - + -
507A HIS* 4.3 8.1 - - + +
517A MET* 3.3 15.7 + - + +
518A LEU* 3.4 40.2 - - + +
520A ASP* 1.3 75.8 - - - +
522A LYS* 1.3 62.6 + - + +
524A GLN* 3.6 27.5 - - - +
525A PRO* 3.3 19.8 - - - +
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Residues in contact with LYS 522 (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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518A LEU* 3.7 24.2 + - - +
519A GLN* 3.4 14.1 + - + +
520A ASP 3.1 0.2 - - - -
521A ILE* 1.3 80.9 - - + +
523A ARG* 1.3 62.5 + - + +
524A GLN 3.5 0.2 - - - -
525A PRO* 3.7 9.1 - - - +
526A LYS* 5.5 1.2 + - - +
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Residues in contact with ARG 523 (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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440A ARG* 4.1 21.0 + - - +
443A MET* 3.8 40.0 - - - +
444A GLU* 4.1 16.4 + - - +
446A ALA* 5.6 0.3 - - - +
447A GLU* 2.8 45.7 + - - +
519A GLN* 3.4 24.6 - - - +
520A ASP* 2.8 9.7 + - - +
522A LYS* 1.3 82.3 - - + +
524A GLN* 1.3 64.0 + - - +
525A PRO 3.6 0.8 - - - -
526A LYS* 3.9 11.2 + - - +
527A VAL* 3.7 15.2 + - - +
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Residues in contact with GLN 524 (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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443A MET* 4.1 2.2 - - + -
501A GLY* 3.6 22.4 - - - +
502A PRO* 3.2 27.4 - - - +
505A VAL* 3.8 24.3 - - + +
506A ALA* 2.7 35.8 + - - +
507A HIS* 4.1 8.9 + - - -
520A ASP 3.1 10.4 + - - +
521A ILE* 3.6 29.3 - - - +
523A ARG* 1.3 75.9 - - - +
525A PRO* 1.4 71.5 - - + +
527A VAL* 3.0 20.4 + - - +
528A VAL* 3.4 8.1 + - - +
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Residues in contact with PRO 525 (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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497A ALA* 3.3 36.8 - - + +
498A LYS* 4.3 22.2 - - + +
501A GLY* 5.3 1.1 - - - -
502A PRO* 6.2 0.7 - - + -
521A ILE 3.3 19.7 - - - +
522A LYS 3.7 7.9 - - - +
523A ARG 3.6 2.9 - - - -
524A GLN* 1.4 90.8 - - + +
526A LYS* 1.3 57.4 + - - +
528A VAL 3.1 2.6 + - - +
529A GLU* 2.8 30.2 + - - +
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Residues in contact with LYS 526 (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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446A ALA* 3.4 33.0 - - + +
447A GLU* 5.3 6.3 - - + -
522A LYS 5.5 1.3 + - - +
523A ARG* 3.9 8.5 + - - +
524A GLN 3.3 0.8 - - - -
525A PRO* 1.3 79.8 - - - +
527A VAL* 1.3 61.7 + - - +
529A GLU* 3.6 27.4 + - + +
530A ARG* 3.0 52.5 + - + +
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Residues in contact with VAL 527 (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 LEU* 3.8 22.2 - - + -
442A PHE* 3.6 45.1 - - + +
443A MET* 3.7 22.0 - - + +
446A ALA* 3.7 9.2 - - + -
458A MET* 4.1 1.9 - - + +
505A VAL* 4.1 9.0 - - + -
523A ARG 3.7 13.5 - - - +
524A GLN 3.0 8.4 + - - +
526A LYS* 1.3 77.8 - - - +
528A VAL* 1.3 57.9 + - - +
530A ARG* 3.3 4.7 + - - +
531A LEU* 3.0 32.9 + - + +
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Residues in contact with VAL 528 (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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477A MET* 4.9 5.6 - - + -
480A LEU* 5.6 0.9 - - + -
497A ALA* 3.7 21.8 - - - -
500A PHE* 4.0 18.2 - - + +
501A GLY* 3.9 18.4 - - - +
504A ILE* 4.1 14.8 - - + -
505A VAL* 3.8 25.6 - - + -
524A GLN 3.8 5.8 - - - +
525A PRO 3.1 5.9 + - - +
527A VAL* 1.3 72.4 - - + +
529A GLU* 1.3 59.3 + - - +
531A LEU* 3.2 7.2 + - - +
532A LEU* 2.9 47.3 + - + +
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Residues in contact with GLU 529 (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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493A VAL* 3.9 26.4 - - + +
494A ALA* 3.7 25.1 - - - +
497A ALA* 3.7 8.7 - - + +
525A PRO* 2.8 18.6 + - - +
526A LYS* 3.6 37.6 + - + +
528A VAL* 1.3 77.0 - - - +
530A ARG* 1.3 55.0 + - + +
532A LEU 3.6 0.7 + - - -
533A SER* 2.7 35.1 + - - +
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Residues in contact with ARG 530 (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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446A ALA* 3.4 24.7 + - + +
448A ILE 3.0 24.4 + - - -
449A THR* 4.5 8.3 + - - +
451A GLU* 2.8 39.6 + - - -
454A SER* 2.9 25.8 + - - +
455A ILE* 4.6 12.3 - - + +
458A MET* 4.0 18.6 - - + -
526A LYS* 3.0 43.4 + - + +
527A VAL 3.6 4.0 - - - +
529A GLU* 1.3 72.2 - - - +
531A LEU* 1.3 66.5 + - - +
533A SER* 3.1 17.5 + - - -
534A LEU* 3.1 19.1 + - - +
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Residues in contact with LEU 531 (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 LEU* 4.0 16.6 - - + -
442A PHE* 4.2 2.7 - - + -
458A MET* 3.6 19.5 - - + -
462A VAL* 3.9 14.1 - - + -
473A LEU* 4.0 19.3 - - + -
477A MET* 3.7 13.2 - - - -
504A ILE* 4.3 9.6 - - + -
527A VAL* 3.0 37.2 + - + +
528A VAL* 3.6 5.4 - - - +
530A ARG* 1.3 76.3 - - - +
532A LEU* 1.3 59.7 + - - +
534A LEU* 3.2 10.9 + - + +
539A TRP* 2.9 54.6 + - + -
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Residues in contact with LEU 532 (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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477A MET* 3.7 31.0 - - + +
480A LEU* 3.6 31.2 - - + -
481A GLN* 2.9 37.3 + - + +
484A ALA* 6.3 0.2 - - + -
493A VAL* 3.8 46.0 - - + +
496A LEU* 4.3 15.7 - - + -
528A VAL* 2.9 35.5 + - + +
531A LEU* 1.3 77.3 - - - +
533A SER* 1.3 58.1 + - - +
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Residues in contact with SER 533 (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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451A GLU* 5.8 2.9 - - - -
455A ILE* 5.6 6.5 - - - +
493A VAL* 4.4 8.8 - - - +
529A GLU* 2.7 23.4 + - - +
530A ARG* 3.1 11.7 + - - -
532A LEU* 1.3 75.3 - - - +
534A LEU* 1.3 62.2 + - - +
535A PRO* 3.5 6.9 - - - +
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Residues in contact with LEU 534 (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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455A ILE* 3.8 33.0 - - + -
458A MET* 4.6 14.1 - - + -
459A TYR* 3.6 26.5 - - + +
462A VAL* 4.8 2.7 - - + -
481A GLN* 2.8 29.6 + - - -
530A ARG 3.1 10.1 + - - +
531A LEU* 3.2 16.3 + - + +
533A SER* 1.3 76.3 - - - +
535A PRO* 1.3 65.4 - - + +
538A TYR* 3.7 23.6 - - + -
539A TRP* 3.3 34.5 + - + +
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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