Contacts of the helix formed by residues 521 - 538 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429A ASP 4.9 1.1 - - - +
431A ASN 4.1 12.3 - - - +
432A THR* 4.2 10.3 - - - +
496A ARG* 3.7 24.9 - - + +
499A GLY* 3.6 29.4 - - - +
500A GLU* 3.3 27.8 - - - +
503A ALA* 5.4 2.5 - - + -
520A LEU* 1.3 85.4 - - + +
522A GLY* 1.3 65.4 + - - +
523A GLY 3.3 0.7 - - - -
524A TYR* 3.2 16.3 + - + +
525A ALA* 3.1 21.0 + - - +
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Residues in contact with GLY 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A PHE* 3.4 24.4 - - - -
427A LEU 4.6 2.9 - - - -
428A PHE* 4.1 7.7 - - - -
429A ASP 4.5 5.4 + - - -
496A ARG* 4.1 12.9 - - - +
520A LEU* 3.3 3.2 - - - +
521A PRO* 1.3 80.3 - - - +
523A GLY* 1.3 56.1 + - - +
525A ALA* 3.2 7.1 + - - +
526A VAL* 3.0 28.1 + - - +
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Residues in contact with GLY 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A PHE* 3.5 9.7 - - - -
351A PHE* 5.6 0.7 - - - -
520A LEU* 4.0 5.6 + - - +
521A PRO 3.3 0.6 - - - -
522A GLY* 1.3 74.3 - - - +
524A TYR* 1.3 63.2 + - - +
526A VAL* 3.2 12.0 - - - +
527A ILE* 3.0 29.6 + - - +
555A HIS* 3.5 34.1 - - - -
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Residues in contact with TYR 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A PHE 4.3 3.8 + - - -
347A GLU* 3.0 49.7 + - + +
350A ALA* 5.2 4.3 - - + -
351A PHE* 3.5 22.6 - + - -
354A ILE* 3.9 2.0 - - + +
495A GLY* 3.4 26.1 - - - +
498A VAL* 4.7 10.1 - - + -
499A GLY* 3.7 15.9 - - - +
502A MET* 4.7 12.7 - - + +
519A ILE* 4.2 24.2 - - + +
520A LEU 3.6 14.4 - - - -
521A PRO* 3.2 23.2 + - + +
523A GLY* 1.3 74.8 - - - +
525A ALA* 1.3 61.9 + - - +
527A ILE* 3.4 10.9 - - + +
528A GLY 3.0 19.2 + - - -
555A HIS* 5.1 2.0 - + - -
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Residues in contact with ALA 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A LEU* 4.1 7.4 - - + +
428A PHE* 3.8 17.7 - - + -
492A ALA* 3.6 14.5 - - + +
495A GLY* 3.7 2.2 - - - -
496A ARG* 3.7 30.5 - - + +
521A PRO 3.1 10.5 + - - +
522A GLY 3.4 9.2 - - - +
524A TYR* 1.3 77.3 - - - +
526A VAL* 1.3 57.6 + - - +
528A GLY* 3.9 0.2 - - - -
529A ALA* 2.9 30.5 + - - +
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Residues in contact with VAL 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A PHE* 5.1 5.2 - - + -
428A PHE* 3.5 27.1 - - + -
488A PHE* 5.9 0.2 - - + -
522A GLY 3.0 13.5 + - - +
523A GLY* 3.2 20.0 - - - +
525A ALA* 1.3 77.3 - - - +
527A ILE* 1.3 64.5 + - + +
529A ALA* 3.4 1.8 + - - -
530A ALA 3.0 22.3 + - - -
546A CYS* 3.3 25.4 - - - +
550A THR* 3.6 35.7 - - + +
555A HIS* 4.9 7.4 - - + -
559A MET* 4.9 7.4 - - + -
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Residues in contact with ILE 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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351A PHE* 3.8 26.0 - - + -
354A ILE* 3.5 32.5 - - + -
523A GLY 3.0 21.1 + - - +
524A TYR* 3.4 11.9 - - - +
526A VAL* 1.3 79.2 - - + +
528A GLY* 1.3 58.9 + - - +
530A ALA* 3.2 4.7 + - - +
531A ALA* 2.9 27.0 + - - +
555A HIS* 3.7 29.8 - - + +
558A PRO* 5.2 2.0 - - + +
559A MET* 3.7 37.1 - - + +
562A ALA* 5.2 6.6 - - + +
563A VAL* 5.3 0.2 - - - +
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Residues in contact with GLY 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A ILE* 4.0 19.5 - - - -
358A CYS* 4.7 3.3 - - - -
491A GLY* 3.5 19.3 - - - -
524A TYR 3.0 16.2 + - - -
525A ALA 3.9 0.7 - - - -
527A ILE* 1.3 77.8 - - - +
529A ALA* 1.3 57.3 + - - +
531A ALA* 3.0 20.6 + - - +
532A LEU* 3.0 15.2 + - - +
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Residues in contact with ALA 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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428A PHE* 4.9 1.6 - - + -
488A PHE* 3.2 37.6 - - + +
491A GLY* 3.5 12.2 + - - -
492A ALA* 3.5 21.1 - - + +
525A ALA 2.9 18.8 + - - +
526A VAL* 3.7 7.6 - - - +
528A GLY* 1.3 72.6 - - - +
530A ALA* 1.3 60.3 + - - +
532A LEU 4.7 0.2 - - - -
533A THR* 3.2 24.2 - - - +
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Residues in contact with ALA 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A VAL 3.0 8.7 + - - +
527A ILE* 3.4 9.6 - - - +
528A GLY 3.2 0.2 - - - -
529A ALA* 1.3 79.6 - - - +
531A ALA* 1.3 65.0 + - - +
532A LEU 3.4 0.2 + - - -
533A THR* 3.6 3.3 - - - +
534A GLY* 3.0 21.0 + - - -
542A THR* 3.9 5.8 - - - +
543A ALA* 4.2 7.4 - - - -
546A CYS* 3.6 30.7 - - + -
559A MET* 4.4 11.0 - - + -
563A VAL* 4.0 18.0 - - + +
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Residues in contact with ALA 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A ILE* 4.1 18.6 - - + +
358A CYS* 4.6 4.9 - - + -
527A ILE 2.9 16.5 + - - +
528A GLY* 3.0 9.7 + - - +
530A ALA* 1.3 75.9 - - - +
532A LEU* 1.3 58.9 + - - +
534A GLY* 3.3 2.1 + - - -
535A ALA* 2.9 27.9 + - - +
562A ALA* 4.5 19.5 - - + +
563A VAL* 3.9 15.3 - - + +
566A ALA* 4.0 7.8 - - + +
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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
----------------------------------------------------------
358A CYS* 3.9 31.9 - - + +
361A LEU* 3.7 33.2 - - + -
362A GLY* 4.5 6.3 - - - -
365A PHE* 5.9 3.6 - - + -
464A PHE* 5.1 1.3 - - + -
468A PHE* 6.2 2.7 - - + -
487A VAL* 3.7 26.7 - - + +
490A LEU* 5.0 9.9 - - + +
491A GLY* 4.2 17.0 - - - +
494A PHE* 5.1 4.5 - - + -
528A GLY 3.0 13.5 + - - +
531A ALA* 1.3 78.1 - - - +
533A THR* 1.3 58.9 + - - +
535A ALA* 3.2 7.2 + - - +
536A VAL* 2.9 39.2 + - + +
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Residues in contact with THR 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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483A GLY 5.0 1.4 + - - -
484A PHE* 3.3 33.5 + - + -
487A VAL* 3.7 26.0 + - - +
488A PHE* 4.1 12.8 - - + -
529A ALA 3.2 26.0 + - - +
530A ALA 3.6 3.1 - - - +
532A LEU* 1.3 74.2 - - - +
534A GLY* 1.3 56.0 + - - +
536A VAL* 4.1 1.4 - - - +
537A SER* 2.4 39.9 + - - -
542A THR* 3.6 13.8 - - + +
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Residues in contact with GLY 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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530A ALA 3.0 17.0 + - - -
531A ALA* 3.7 3.4 - - - -
533A THR* 1.3 76.3 - - - +
535A ALA* 1.3 56.6 + - - +
537A SER* 3.3 6.9 + - - -
538A HIS 3.0 20.8 + - - -
539A THR 3.4 9.8 + - - -
542A THR* 3.8 14.7 - - - +
563A VAL* 5.3 4.9 - - - -
567A ASN* 2.8 19.5 - - - +
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Residues in contact with ALA 535 (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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358A CYS 4.8 0.9 - - - +
359A GLY* 3.9 19.7 - - - +
362A GLY* 5.1 2.9 - - - -
531A ALA 2.9 14.1 + - - +
532A LEU* 3.2 12.3 + - - +
534A GLY* 1.3 75.0 - - - +
536A VAL* 1.3 65.7 + - + +
538A HIS* 3.4 10.0 + - - -
566A ALA* 3.7 25.4 - - + +
567A ASN* 3.8 8.0 - - - -
570A ALA* 3.3 21.8 - - + +
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Residues in contact with VAL 536 (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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362A GLY* 3.8 29.4 - - - +
365A PHE* 4.0 21.1 - - + -
366A VAL* 3.7 23.3 - - + +
483A GLY 5.4 2.5 - - - +
487A VAL* 4.1 21.5 - - + -
532A LEU* 2.9 18.9 + - + +
533A THR 4.1 3.1 - - - +
535A ALA* 1.3 76.8 - - - +
537A SER* 1.3 63.4 + - - +
538A HIS* 3.2 6.1 + - - -
575A PRO 5.2 0.2 - - - +
576A SER* 4.5 0.3 - - - -
577A LEU* 3.8 34.2 + - + +
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Residues in contact with SER 537 (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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288A PHE* 5.4 8.6 - - - -
292A VAL* 4.9 5.5 - - - +
483A GLY 6.1 0.9 - - - -
484A PHE* 5.9 2.2 - - - -
533A THR* 2.4 26.8 + - - -
534A GLY 3.3 2.6 + - - -
535A ALA 3.4 0.2 - - - -
536A VAL* 1.3 77.5 - - - +
538A HIS* 1.3 66.3 + - - +
539A THR* 3.2 24.9 + - - +
542A THR* 3.4 7.6 + - - -
576A SER* 4.5 6.9 + - - -
577A LEU* 5.3 4.9 - - - -
578A TYR* 5.2 15.2 - - - -
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Residues in contact with HIS 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A VAL* 3.9 15.5 - - + +
534A GLY 3.0 6.4 + - - -
535A ALA 3.4 19.1 - - - -
536A VAL 3.2 6.2 + - - -
537A SER* 1.3 80.4 - - - +
539A THR* 1.3 59.4 + - - +
567A ASN* 4.2 8.1 - - - -
570A ALA* 3.6 29.4 + - + +
571A GLN* 3.7 13.4 + - + -
574A GLN 3.4 8.5 + - - -
575A PRO* 3.3 11.7 + - + -
576A SER* 3.3 44.1 + - - +
579A ASP* 5.3 0.2 + - - -
303B TRP* 4.5 13.4 - - + -
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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
------------------------------------------------------------
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