Contacts of the helix formed by residues 513 - 528 (chain B) in PDB entry 3ZHT
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 THR 513 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486B LEU* 3.9 5.9 - - - +
511B ALA* 3.2 1.5 + - - -
512B GLU* 1.3 73.8 - - - +
514B VAL* 1.4 62.5 + - - +
515B ILE 3.2 0.4 - - - -
516B PRO* 3.2 11.0 - - + +
517B MET* 3.1 20.3 + - - +
711B GLY 2.7 28.1 + - - +
714B PRO* 3.7 19.0 - - + +
717B CYS* 3.5 35.7 - - + -
739B MET* 3.9 9.9 - - - -
770B SER* 3.0 18.1 + - - -
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Residues in contact with VAL 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B LEU* 3.7 27.8 - - + -
511B ALA 3.1 18.5 + - - +
512B GLU 3.1 1.6 - - - -
513B THR* 1.4 78.1 - - - +
515B ILE* 1.4 59.0 + - + +
517B MET* 4.0 3.1 - - - -
518B MET* 2.8 55.3 + - + +
545B VAL* 5.7 1.3 - - + -
642B LEU* 4.2 5.2 - - + -
674B ILE* 3.8 29.8 - - + -
676B VAL* 4.0 15.5 - - + -
739B MET* 3.6 18.1 - - + -
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Residues in contact with ILE 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B LYS* 3.9 24.7 - - - +
489B ALA* 3.7 19.7 - - + -
508B LEU* 3.8 17.3 - - + -
512B GLU 3.0 13.0 + - - +
514B VAL* 1.4 74.4 - - + +
516B PRO* 1.4 67.2 - - + +
517B MET 3.2 0.7 + - - -
518B MET* 3.2 2.5 + - - -
519B ASP* 3.0 18.8 + - - +
544B ASN* 3.7 17.9 - - - +
545B VAL* 3.8 36.3 - - + +
548B ASN* 3.9 22.2 - - + -
549B ILE* 3.3 21.3 - - + +
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Residues in contact with PRO 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B ILE* 4.3 22.1 - - + +
485B LYS* 4.0 22.9 - - + +
486B LEU* 4.3 19.7 - - + -
512B GLU 3.3 12.8 - - - +
513B THR* 3.2 26.2 - - + +
515B ILE* 1.4 84.1 - - + +
517B MET* 1.4 54.5 + - - -
519B ASP* 3.6 9.4 - - + +
520B ALA* 3.0 28.6 + - - +
714B PRO* 4.6 12.6 - - + +
718B ALA* 4.6 4.5 - - + +
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Residues in contact with MET 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B THR 3.1 18.6 + - - +
514B VAL* 3.6 5.8 - - - +
515B ILE 3.2 0.2 - - - -
516B PRO* 1.4 74.5 - - - +
518B MET* 1.4 64.2 + - - +
520B ALA* 3.2 5.0 + - - -
521B VAL* 3.1 19.1 + - - +
674B ILE* 3.9 32.1 - - + -
709B VAL* 3.7 24.0 - - + -
714B PRO 5.9 0.2 + - - -
717B CYS* 3.6 45.3 - - + +
718B ALA* 4.8 2.9 - - - +
721B ALA* 3.4 15.3 - - + +
737B ILE* 3.7 21.5 - - + -
739B MET* 3.7 16.4 - - + +
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Residues in contact with MET 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B VAL* 2.8 31.1 + - + +
515B ILE* 4.9 0.4 - - - -
517B MET* 1.4 68.9 - - - +
519B ASP* 1.3 64.8 + - - +
521B VAL* 3.2 10.0 + - - +
522B ILE* 3.1 28.6 + - - +
535B ILE* 3.9 32.5 - - + -
545B VAL* 3.8 34.3 - - + -
549B ILE* 3.7 20.2 - - + -
640B LEU* 4.1 9.9 - - + -
642B LEU* 3.8 31.0 - - + -
674B ILE* 4.0 18.6 - - + -
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Residues in contact with ASP 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B TYR* 2.7 42.1 + - - -
485B LYS* 3.8 16.1 + - - -
515B ILE 3.0 16.6 + - - +
516B PRO* 3.6 11.2 - - + +
518B MET* 1.3 76.3 - - - +
520B ALA* 1.4 57.4 + - - +
522B ILE* 3.6 1.9 + - - -
523B ASP* 2.9 29.3 + - - +
548B ASN 4.9 1.0 - - - +
549B ILE* 3.6 11.8 - - + +
586B TYR* 2.9 33.5 + - - -
722B ARG* 5.1 2.4 + - - -
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Residues in contact with ALA 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B PRO 3.0 17.3 + - - +
517B MET 3.2 6.3 + - - +
519B ASP* 1.4 75.4 + - - +
521B VAL* 1.4 59.3 + - - +
524B GLN* 2.9 32.1 + - - +
718B ALA* 3.6 35.0 - - + +
721B ALA* 3.8 4.7 - - + -
722B ARG* 3.7 25.4 + - + +
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Residues in contact with VAL 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B MET 3.1 15.4 + - - +
518B MET* 3.2 7.8 + - - +
520B ALA* 1.4 75.2 - - - +
522B ILE* 1.3 59.0 + - + +
524B GLN 3.2 2.1 + - - -
525B CYS* 2.9 40.2 + - - -
533B VAL* 5.0 2.5 - - + -
638B VAL* 5.7 0.7 - - + -
640B LEU* 4.1 25.1 - - + -
672B ILE* 4.2 17.9 - - + -
674B ILE* 4.2 21.1 - - + -
721B ALA* 3.6 21.8 - - + +
725B VAL* 3.5 21.3 - - + +
737B ILE* 5.0 0.7 - - + -
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Residues in contact with ILE 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B MET 3.1 17.1 + - - +
519B ASP* 4.0 4.5 - - - +
521B VAL* 1.3 71.0 - - - +
523B ASP* 1.3 59.6 + - - +
525B CYS* 3.2 3.3 + - - +
526B ALA* 2.9 27.7 + - - +
533B VAL* 4.1 28.7 - - + -
535B ILE* 4.5 1.1 - - + -
549B ILE* 3.4 33.7 - - + +
586B TYR* 3.4 33.9 - - + -
595B ILE* 3.6 14.8 - - + +
597B VAL* 3.6 20.0 - - + -
640B LEU* 4.4 13.0 - - + -
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Residues in contact with ASP 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B TYR* 6.4 1.3 - - - -
519B ASP* 2.9 20.6 + - - +
520B ALA 3.9 0.7 - - - +
522B ILE* 1.3 77.0 - - - +
524B GLN* 1.3 57.1 + - - +
526B ALA* 3.3 2.4 + - - -
527B GLU* 2.9 26.3 + - - +
586B TYR* 3.6 20.7 + - - +
588B GLN* 3.2 45.7 + - - +
589B MET* 4.4 3.6 + - - +
590B PHE* 5.3 2.2 + - - -
591B GLY 5.4 0.3 + - - -
722B ARG* 2.7 36.2 + - - +
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Residues in contact with GLN 524 (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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520B ALA 2.9 18.7 + - - +
521B VAL 3.6 3.8 - - - +
523B ASP* 1.3 73.2 - - - +
525B CYS* 1.3 63.8 + - - +
527B GLU* 3.3 17.7 + - - +
528B HIS* 3.1 34.3 + - + -
722B ARG* 3.1 56.5 + - - +
725B VAL* 3.7 15.7 - - + -
726B ASP* 2.9 30.5 + - - +
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Residues in contact with CYS 525 (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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521B VAL* 2.9 27.6 + - - -
522B ILE 3.2 7.2 + - - +
524B GLN* 1.3 74.8 - - - +
526B ALA* 1.4 60.0 + - - +
528B HIS 3.2 6.2 + - - -
530B LEU* 3.1 40.2 + - + +
533B VAL* 3.9 12.6 - - + -
595B ILE* 3.7 17.5 - - + -
638B VAL* 3.9 28.7 - - - -
725B VAL* 3.8 23.3 - - - -
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Residues in contact with ALA 526 (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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522B ILE 2.9 12.9 + - - +
523B ASP* 3.5 10.1 - - - +
524B GLN 3.3 0.2 - - - -
525B CYS* 1.4 73.3 - - - +
527B GLU* 1.3 59.1 + - - +
529B GLY* 2.9 20.0 + - - +
530B LEU 4.7 1.6 - - - +
586B TYR* 5.0 1.1 - - + -
588B GLN* 3.7 24.9 - - + -
593B ASN* 3.3 24.0 + - + +
594B ASP* 4.6 4.0 - - - -
595B ILE* 3.9 26.4 - - + +
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Residues in contact with GLU 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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523B ASP* 2.9 16.0 + - - +
524B GLN* 3.3 28.5 + - - +
526B ALA* 1.3 74.9 - - - +
528B HIS* 1.4 58.9 + - + +
529B GLY* 3.2 3.2 + - - -
588B GLN* 2.9 29.7 + - - +
591B GLY* 4.9 5.7 - - - -
593B ASN* 4.2 10.9 + - - +
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Residues in contact with HIS 528 (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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524B GLN* 3.1 29.3 + - + -
525B CYS 3.5 9.2 - - - +
526B ALA 3.2 0.4 - - - -
527B GLU* 1.4 76.3 - - + +
529B GLY* 1.3 60.9 + - - +
530B LEU* 3.3 16.7 + - + +
634B ARG* 3.7 11.6 + - - -
725B VAL* 3.7 15.0 - - + -
726B ASP* 2.8 32.5 + - - -
729B GLN* 3.5 34.3 + - + +
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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