Contacts of the helix formed by residues 521 - 538 (chain B) in PDB entry 6QVC
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 PRO 521 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429B ASP 4.9 1.3 - - - +
431B ASN 4.1 12.3 - - - +
432B THR* 4.2 10.8 - - - +
496B ARG* 3.7 24.1 - - + +
499B GLY* 3.6 28.9 - - - +
500B GLU* 3.3 28.7 - - - +
503B ALA* 5.4 2.2 - - + -
520B LEU* 1.3 84.9 - - + +
522B GLY* 1.3 63.2 + - - +
523B GLY 3.3 1.1 - - - -
524B TYR* 3.2 16.0 + - + +
525B ALA* 3.1 22.0 + - - +
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Residues in contact with GLY 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B PHE* 3.4 24.5 - - - -
427B LEU 4.6 2.7 - - - -
428B PHE* 4.1 7.7 - - - -
429B ASP 4.5 6.0 + - - -
496B ARG* 4.1 12.2 - - - +
520B LEU* 3.3 3.2 - - - +
521B PRO* 1.3 80.0 - - - +
523B GLY* 1.3 57.9 + - - +
525B ALA* 3.2 7.5 + - - +
526B VAL* 3.0 28.8 + - - +
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Residues in contact with GLY 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B PHE* 3.5 10.1 - - - -
351B PHE* 5.6 0.9 - - - -
520B LEU* 4.0 4.9 + - - +
521B PRO 3.3 0.6 - - - -
522B GLY* 1.3 73.5 - - - +
524B TYR* 1.3 63.8 + - - +
526B VAL* 3.2 11.4 - - - +
527B ILE* 3.0 28.7 + - - +
555B HIS* 3.5 34.5 - - - -
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Residues in contact with TYR 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B PHE 4.3 3.9 + - - -
347B GLU* 3.0 49.3 + - + +
350B ALA* 5.2 4.5 - - + -
351B PHE* 3.5 21.5 - + - -
354B ILE* 3.9 2.5 - - + +
495B GLY* 3.4 26.1 - - - +
498B VAL* 4.7 9.4 - - + -
499B GLY* 3.7 16.6 - - - -
502B MET* 4.7 13.1 - - + +
519B ILE* 4.2 24.6 - - + +
520B LEU 3.6 14.6 - - - -
521B PRO* 3.2 23.8 + - + +
523B GLY* 1.3 75.0 - - - +
525B ALA* 1.3 64.7 + - - +
527B ILE* 3.4 9.9 - - + +
528B GLY* 3.0 19.4 + - - -
555B HIS* 6.4 1.3 - + - -
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Residues in contact with ALA 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B LEU 4.1 7.0 - - - +
428B PHE* 3.8 19.1 - - + -
492B ALA* 3.6 14.0 - - + +
495B GLY* 3.7 2.2 - - - -
496B ARG* 3.7 29.6 - - + +
521B PRO 3.1 11.0 + - - +
522B GLY 3.2 8.7 + - - +
524B TYR* 1.3 77.1 - - - +
526B VAL* 1.3 58.7 + - - +
528B GLY* 3.9 0.3 - - - -
529B ALA* 2.9 30.0 + - - +
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Residues in contact with VAL 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B PHE* 5.1 5.6 - - + -
428B PHE* 3.5 26.2 - - + -
488B PHE* 5.9 0.4 - - + -
522B GLY 3.0 14.4 + - - +
523B GLY* 3.2 20.0 - - - +
525B ALA* 1.3 77.0 - - - +
527B ILE* 1.3 63.3 + - + +
529B ALA* 3.4 1.4 + - + -
530B ALA 3.0 22.0 + - - -
546B CYS* 3.3 25.3 - - - +
550B THR* 3.6 36.1 - - + +
555B HIS* 4.9 7.4 - - + -
559B MET* 4.9 7.2 - - + -
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Residues in contact with ILE 527 (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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351B PHE* 3.8 26.2 - - + -
354B ILE* 3.5 33.4 - - + -
523B GLY 3.0 21.1 + - - +
524B TYR* 3.4 11.4 - - - +
526B VAL* 1.3 78.0 - - + +
528B GLY* 1.3 59.6 + - - +
530B ALA* 3.2 5.5 + - - +
531B ALA* 2.9 26.6 + - - +
555B HIS* 3.7 30.1 - - + +
558B PRO* 5.2 2.2 - - + +
559B MET* 3.7 34.5 - - + +
562B ALA* 5.2 6.4 - - + +
563B VAL* 5.3 0.3 - - - +
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Residues in contact with GLY 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B ILE* 4.0 18.8 - - - -
358B CYS* 4.7 3.6 - - - -
491B GLY* 3.5 19.2 - - - -
495B GLY 5.1 0.2 - - - -
524B TYR 3.0 16.9 + - - -
525B ALA 3.9 0.7 - - - -
527B ILE* 1.3 77.8 - - - +
529B ALA* 1.3 56.3 + - - +
531B ALA* 3.0 21.0 + - - +
532B LEU* 3.0 15.4 + - - +
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Residues in contact with ALA 529 (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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428B PHE* 4.9 1.8 - - + -
488B PHE* 3.2 36.4 - - + +
491B GLY* 3.5 11.7 + - - -
492B ALA* 3.5 20.9 - - + +
525B ALA 2.9 17.9 + - - +
526B VAL* 3.8 7.6 - - - +
528B GLY* 1.3 73.8 - - - +
530B ALA* 1.3 59.4 + - - +
533B THR* 3.2 23.8 - - - +
546B CYS* 4.9 0.2 - - - -
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Residues in contact with ALA 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B VAL 3.0 8.9 + - - +
527B ILE* 3.4 9.6 - - - +
528B GLY 3.2 0.2 - - - -
529B ALA* 1.3 78.5 - - - +
531B ALA* 1.3 62.5 + - - +
532B LEU 3.4 0.2 + - - -
533B THR* 3.6 3.0 - - - +
534B GLY* 3.0 21.7 + - - -
542B THR* 3.9 5.8 - - - +
543B ALA* 4.2 7.2 - - - -
546B CYS* 3.6 31.1 - - + -
559B MET* 4.4 10.8 - - + -
563B VAL* 4.0 19.1 - - + +
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Residues in contact with ALA 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B ILE* 4.1 18.2 - - + +
358B CYS* 4.6 5.4 - - + -
527B ILE 2.9 16.5 + - - +
528B GLY* 3.0 9.8 + - - +
530B ALA* 1.3 76.8 - - - +
532B LEU* 1.3 58.1 + - - +
534B GLY* 3.3 2.3 + - - -
535B ALA* 2.9 29.0 + - - +
562B ALA* 4.5 20.2 - - + +
563B VAL* 3.9 14.7 - - + +
566B ALA* 4.0 6.9 - - + +
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Residues in contact with LEU 532 (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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358B CYS* 3.9 31.6 - - + +
361B LEU* 3.6 32.8 - - + -
362B GLY* 4.5 7.0 - - - -
365B PHE* 5.9 3.1 - - + -
464B PHE* 5.1 1.3 - - + -
468B PHE* 6.2 2.9 - - + -
487B VAL* 3.7 26.5 - - + +
490B LEU* 5.0 10.1 - - + +
491B GLY* 4.2 17.7 - - - +
494B PHE* 5.1 4.0 - - + -
528B GLY 3.0 13.9 + - - +
531B ALA* 1.3 79.2 - - - +
533B THR* 1.3 58.9 + - - +
535B ALA* 3.2 7.4 + - - +
536B VAL* 2.9 39.4 + - + +
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Residues in contact with THR 533 (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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483B GLY 5.0 1.0 + - - -
484B PHE* 3.3 33.7 + - + -
487B VAL* 3.7 26.9 + - - +
488B PHE* 4.1 12.3 - - + -
491B GLY* 5.7 0.2 - - - -
529B ALA* 3.2 25.3 + - - +
530B ALA 3.6 3.4 - - - +
532B LEU* 1.3 75.5 - - - +
534B GLY* 1.3 56.8 + - - +
536B VAL* 4.0 2.0 - - - +
537B SER* 2.4 38.9 + - - -
542B THR* 3.6 13.5 - - + +
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Residues in contact with GLY 534 (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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530B ALA 3.0 16.6 + - - -
531B ALA 3.7 3.6 - - - -
533B THR* 1.3 76.9 - - - +
535B ALA* 1.3 55.5 + - - +
537B SER* 3.3 6.8 + - - -
538B HIS 3.0 21.0 + - - -
539B THR 3.4 10.3 + - - -
542B THR* 3.8 14.1 - - - +
563B VAL* 5.3 5.2 - - - -
567B ASN* 2.8 19.7 - - - +
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Residues in contact with ALA 535 (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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358B CYS 4.8 1.6 - - - +
359B GLY* 3.9 18.8 - - - +
362B GLY* 5.1 2.6 - - - -
531B ALA 2.9 13.8 + - - +
532B LEU* 3.2 12.1 + - - +
534B GLY* 1.3 74.8 - - - +
536B VAL* 1.3 65.5 + - + +
538B HIS* 3.4 10.9 - - - -
566B ALA* 3.7 26.7 - - + +
567B ASN* 3.8 8.3 + - - -
570B ALA* 3.3 20.8 - - + +
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Residues in contact with VAL 536 (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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362B GLY* 3.8 30.3 - - - +
365B PHE* 4.0 22.0 - - + -
366B VAL* 3.7 23.0 - - + +
483B GLY 5.4 1.6 - - - +
487B VAL* 4.1 21.3 - - + -
532B LEU* 2.9 17.9 + - + +
533B THR* 4.1 3.1 - - - +
534B GLY 3.4 0.2 - - - -
535B ALA* 1.3 77.6 - - - +
537B SER* 1.3 64.6 + - - +
538B HIS* 3.2 5.7 + - - -
575B PRO 5.2 0.2 - - - +
576B SER* 4.5 0.3 - - - -
577B LEU* 3.8 34.8 + - + -
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Residues in contact with SER 537 (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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288B PHE* 5.4 8.2 - - - -
292B VAL* 4.9 5.4 - - - +
483B GLY 6.1 1.3 - - - -
484B PHE* 5.9 3.1 - - - -
533B THR* 2.4 27.6 + - - -
534B GLY 3.3 2.8 + - - -
536B VAL* 1.3 78.6 - - - +
538B HIS* 1.3 67.0 + - - +
539B THR* 3.2 25.0 + - - +
542B THR* 3.4 7.0 + - - -
576B SER* 4.5 6.5 + - - -
577B LEU* 5.3 4.9 - - - -
578B TYR* 5.3 16.1 - - - -
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Residues in contact with HIS 538 (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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303A TRP* 4.6 13.1 - - + -
292B VAL* 3.9 15.2 - - + +
534B GLY 3.0 7.6 + - - -
535B ALA 3.4 18.6 + - - -
536B VAL 3.2 6.5 - - - -
537B SER* 1.3 79.9 - - - +
539B THR* 1.3 61.1 + - - +
567B ASN* 4.2 7.9 - - - -
570B ALA* 3.6 30.2 + - + +
571B GLN* 4.3 13.4 - - + +
574B GLN 3.4 8.1 + - - -
575B PRO* 3.3 11.3 + - + -
576B SER* 3.3 43.6 - - - +
579B ASP* 5.3 0.2 + - - -
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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