Contacts of the helix formed by residues 508 - 528 (chain A) in PDB entry 4CCZ
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 GLU 508 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507A THR* 1.3 93.2 + - - +
509A THR* 1.3 65.7 + - - +
510A ASP* 4.4 5.1 - - + +
511A THR* 2.6 43.3 + - + +
512A LYS* 2.8 15.4 + - - +
553A TYR* 6.2 0.9 - - + -
556A ASN* 3.5 7.0 - - - +
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Residues in contact with THR 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A GLU* 1.3 72.5 - - - +
510A ASP* 1.3 66.5 + - - +
512A LYS* 3.5 4.4 + - - +
513A ILE* 3.1 38.0 + - + +
556A ASN* 2.8 40.0 + - - +
559A HIS* 3.5 32.1 - - + +
560A ALA* 3.7 13.4 - - - +
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Residues in contact with ASP 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A GLU* 3.2 5.3 - - + +
509A THR* 1.3 78.5 - - - +
511A THR* 1.3 64.0 + - + +
513A ILE* 3.2 14.3 + - - +
514A ARG* 2.8 30.1 + - - +
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Residues in contact with THR 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A ALA* 3.6 11.6 - - - +
507A THR 3.5 7.3 + - - +
508A GLU* 2.6 55.9 + - + +
510A ASP* 1.3 78.0 - - + +
512A LYS* 1.3 62.5 + - - +
514A ARG* 3.4 34.1 + - - +
515A VAL* 3.3 28.9 + - - +
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Residues in contact with LYS 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A ALA* 4.4 2.9 - - + +
506A ALA* 2.9 37.9 + - + +
507A THR* 3.8 22.3 - - - +
508A GLU 2.8 17.7 + - - +
509A THR 3.6 4.3 - - - +
511A THR* 1.3 79.4 + - - +
513A ILE* 1.3 61.2 + - - +
515A VAL* 3.6 2.1 + - - +
516A CYS* 3.4 27.9 + - - -
538A PRO* 4.0 22.6 - - + +
539A ASN* 2.9 35.8 + - - +
541A LEU* 5.1 1.6 - - - +
553A TYR 4.7 3.8 + - - -
556A ASN* 3.9 29.6 - - - +
557A PHE* 4.1 5.8 - - - +
560A ALA* 3.8 9.2 - - + -
564A ILE* 4.9 1.6 - - - -
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Residues in contact with ILE 513 (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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509A THR* 3.1 33.1 + - + +
510A ASP* 3.2 13.9 + - - +
512A LYS* 1.3 73.3 - - - +
514A ARG* 1.3 65.8 + - - +
516A CYS* 3.4 1.4 + - - +
517A THR* 2.6 44.6 + - - +
560A ALA* 4.2 16.6 - - + +
563A VAL* 3.9 28.5 - - + -
564A ILE* 4.6 12.1 - - + -
567A THR* 5.8 4.9 - - - -
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Residues in contact with ARG 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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501A ASP* 2.5 44.6 + - - -
503A GLU* 4.1 20.0 + - - +
510A ASP 2.8 20.0 + - - +
511A THR* 3.4 36.2 + - - +
512A LYS 3.4 0.2 - - - -
513A ILE* 1.3 73.6 - - - +
515A VAL* 1.3 62.3 + - - +
517A THR* 3.6 5.4 - - - -
518A ARG* 2.9 37.0 + - + +
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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
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474A LEU* 4.4 13.4 - - + +
497A VAL* 5.3 0.9 - - + -
498A MET 3.8 22.0 - - - +
499A ALA* 3.9 9.0 - - - -
500A PHE 3.8 19.1 - - - +
501A ASP* 3.7 37.7 - - + +
506A ALA* 4.7 4.3 - - + -
511A THR 3.3 15.9 + - - +
512A LYS 4.0 3.4 - - - +
514A ARG* 1.3 84.4 - - - +
516A CYS* 1.3 60.2 + - - +
518A ARG* 3.4 6.0 + - - +
519A ALA* 2.8 34.3 + - + +
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Residues in contact with CYS 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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497A VAL 5.0 1.3 - - - -
498A MET 5.5 0.2 - - - -
499A ALA* 4.5 18.2 - - - -
512A LYS 3.4 19.3 + - - +
513A ILE 4.0 1.3 - - - +
515A VAL* 1.3 80.3 - - - +
517A THR* 1.3 57.2 + - - +
520A TYR* 2.8 27.4 + - - +
536A PHE* 3.2 51.6 - - + -
538A PRO* 4.9 6.1 - - - -
564A ILE* 3.8 24.5 - - + -
568A LEU* 3.9 7.0 - - + -
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Residues in contact with THR 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A ILE* 2.6 37.1 + - - +
514A ARG* 3.6 5.2 - - - -
516A CYS* 1.3 76.1 - - - +
518A ARG* 1.3 64.3 + - - +
520A TYR* 3.7 2.8 - - - +
521A HIS* 3.1 22.2 + - + +
567A THR* 5.3 3.8 - - - -
568A LEU* 4.0 26.5 - - + +
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Residues in contact with ARG 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A LEU* 3.7 26.5 - - - +
478A GLU* 3.8 34.1 + - - +
501A ASP* 4.5 7.1 + - - +
502A GLU* 3.0 38.2 + - - -
514A ARG* 2.9 22.5 + - + +
515A VAL* 3.6 5.6 - - - +
517A THR* 1.3 76.0 - - - +
519A ALA* 1.3 65.1 + - - +
521A HIS* 3.1 9.7 + - + +
522A LEU* 3.1 34.0 + - + +
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Residues in contact with ALA 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A LEU* 4.6 7.6 - - + +
481A PHE* 4.0 19.5 - - + -
497A VAL* 3.8 16.6 - - + -
515A VAL* 2.8 18.8 + - + +
516A CYS 3.7 3.4 - - - +
518A ARG* 1.3 73.5 - - - +
520A TYR* 1.3 66.6 + - - +
522A LEU* 3.0 6.8 + - - +
523A LEU* 2.9 29.0 + - - +
536A PHE* 3.8 16.4 - - + -
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Residues in contact with TYR 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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516A CYS 2.8 21.7 + - - +
517A THR 3.7 5.4 - - - +
519A ALA* 1.3 72.1 - - - +
521A HIS* 1.3 59.8 + - + +
523A LEU* 4.7 4.5 - - - -
524A VAL* 2.9 66.5 + - + +
531A PRO* 3.8 13.9 - - + +
534A ILE* 4.4 4.9 - - + -
536A PHE* 3.6 20.5 - + + -
568A LEU* 3.7 34.8 - - + -
569A PRO* 2.5 54.1 + - + +
571A ALA* 4.3 5.8 - - + -
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Residues in contact with HIS 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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517A THR 3.1 14.1 + - - +
518A ARG* 3.3 12.3 - - + +
519A ALA 3.1 0.4 - - - -
520A TYR* 1.3 77.9 - - - +
522A LEU* 1.3 60.3 + - + +
524A VAL* 5.2 0.4 - - - -
525A LYS* 3.0 38.1 + - + +
526A LYS* 3.6 0.7 + - - +
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Residues in contact with LEU 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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474A LEU* 4.2 20.9 - - + -
478A GLU* 3.6 46.7 - - + +
481A PHE* 4.2 11.0 - - + -
482A LEU* 3.9 20.4 - - + -
518A ARG* 3.1 31.1 + - + +
519A ALA 3.0 6.3 + - - +
521A HIS* 1.3 77.2 - - + +
523A LEU* 1.3 63.5 + - - +
526A LYS* 3.1 36.6 + - + +
527A LEU* 3.2 8.1 + - - +
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Residues in contact with LEU 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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481A PHE* 3.8 14.8 - - + -
485A ALA* 3.5 32.5 - - + -
495A MET* 3.4 26.9 - - + -
497A VAL* 3.9 17.0 - - + -
519A ALA 2.9 21.9 + - - +
520A TYR 4.0 0.4 - - - +
522A LEU* 1.3 76.4 - - - +
524A VAL* 1.3 57.7 + - - +
527A LEU* 3.3 13.9 - - + +
528A GLY 3.1 10.0 + - - -
529A PHE* 2.9 32.1 + - + +
534A ILE* 3.5 34.1 - - + -
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Residues in contact with VAL 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A TYR* 2.9 58.8 + - + +
521A HIS* 5.2 0.2 - - - -
523A LEU* 1.3 75.9 - - - +
525A LYS* 1.3 62.0 + - - +
528A GLY* 3.1 23.0 + - - -
529A PHE 3.9 15.5 - - - +
531A PRO* 4.1 12.8 - - + -
534A ILE* 4.0 14.4 - - + -
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Residues in contact with LYS 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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521A HIS* 3.0 19.5 + - + +
524A VAL* 1.3 82.5 - - - +
526A LYS* 1.3 67.3 + - + +
527A LEU 3.3 0.5 + - - -
528A GLY* 3.8 3.1 + - - -
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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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478A GLU* 5.9 1.3 - - - +
482A LEU* 4.7 13.0 - - + -
486A ARG* 5.8 1.3 - - - +
521A HIS 3.6 0.6 + - - +
522A LEU* 3.1 32.8 + - + +
525A LYS* 1.3 79.3 - - + +
527A LEU* 1.3 70.6 + - + +
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Residues in contact with LEU 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A LEU* 3.6 39.9 - - + +
485A ALA* 3.8 30.7 - - + +
486A ARG* 3.7 37.5 - - + +
489A LYS* 5.4 6.6 - - + +
522A LEU 3.2 4.4 + - - +
523A LEU* 3.3 19.3 - - + +
526A LYS* 1.3 89.2 - - + +
528A GLY* 1.3 63.7 + - - +
529A PHE* 3.4 8.8 + - + +
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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
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523A LEU 3.1 3.6 + - - -
524A VAL 3.1 16.7 + - - -
525A LYS 3.8 3.9 + - - -
527A LEU* 1.3 78.6 - - - +
529A PHE* 1.3 65.4 + - - +
530A ASN* 3.4 2.9 + - - -
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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