Contacts of the helix formed by residues 511 - 519 (chain A) in PDB entry 4Z1H
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 SER 511 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500A LEU* 4.0 17.5 - - - +
507A LEU 3.2 20.0 - - - -
508A ALA* 3.3 16.0 + - - -
509A GLU 3.4 0.4 - - - -
510A HIS* 1.3 76.4 - - - +
512A PRO* 1.3 59.7 - - - +
513A TYR* 3.7 16.1 + - - +
514A TYR* 2.6 27.5 + - - +
515A GLU* 2.8 17.8 - - - +
551A GLU* 5.7 0.2 + - - -
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Residues in contact with PRO 512 (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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510A HIS 3.7 5.8 - - - +
511A SER* 1.3 85.9 - - - +
513A TYR* 1.3 72.4 + - + +
514A TYR 3.0 1.7 + - - -
515A GLU* 3.0 28.9 + - + +
516A ALA* 3.3 12.0 + - - +
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Residues in contact with TYR 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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500A LEU* 4.9 2.0 - - + -
511A SER* 3.3 11.4 - - - +
512A PRO* 1.3 85.7 - - + +
514A TYR* 1.3 59.1 + - - +
516A ALA* 3.6 15.5 - - - +
517A MET* 4.4 1.6 - - - +
550A VAL* 3.1 50.4 - - + +
551A GLU* 3.6 46.8 + - + +
552A THR 4.8 0.4 - - - -
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Residues in contact with TYR 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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473A SER* 3.4 34.3 + - - -
500A LEU* 4.1 12.8 - - + -
508A ALA 3.4 17.0 - - - +
509A GLU* 3.3 36.0 - - + +
511A SER* 2.6 18.4 + - - +
513A TYR* 1.3 71.4 - - - +
515A GLU* 1.3 56.0 + - + -
516A ALA 2.9 4.7 - - - -
517A MET* 2.5 28.7 + - + +
518A LYS* 3.1 51.2 + - + +
522A THR 5.3 2.5 - - - -
524A VAL* 3.9 28.3 - - + -
526A PHE* 4.3 7.4 - + - -
550A VAL* 4.4 4.5 - - + +
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Residues in contact with GLU 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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509A GLU 3.6 12.1 - - - +
510A HIS* 3.7 8.9 - - - +
511A SER 2.8 30.7 + - - +
512A PRO* 3.0 32.3 - - + +
514A TYR* 1.3 73.7 - - + +
516A ALA* 1.3 59.8 + - - +
517A MET 2.9 1.9 + - - -
518A LYS* 3.3 27.4 + - + +
519A LYS* 4.3 3.5 + - - +
520A LYS 5.4 0.2 + - - -
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Residues in contact with ALA 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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512A PRO 3.3 11.7 + - - +
513A TYR* 3.6 18.8 - - - +
514A TYR 2.9 0.2 + - - -
515A GLU* 1.3 76.3 - - - +
517A MET* 1.3 64.7 + - + +
520A LYS* 4.0 20.0 + - - +
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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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498A TYR* 3.7 39.7 - - + -
513A TYR 4.4 3.4 - - - +
514A TYR* 2.5 20.6 + - + +
516A ALA* 1.3 77.9 - - + +
518A LYS* 1.3 64.1 + - - +
519A LYS 3.4 2.2 - - - -
520A LYS* 3.4 40.0 + - - +
522A THR* 3.4 37.1 + - - +
524A VAL* 3.8 19.1 - - + -
550A VAL* 3.8 27.8 - - + -
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Residues in contact with LYS 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 TYR* 3.1 39.5 + - + +
515A GLU* 3.3 26.6 + - + +
517A MET* 1.3 79.1 - - - +
519A LYS* 1.3 63.2 + - + +
521A ASP* 3.8 10.4 + - - +
522A THR 4.5 3.0 + - - +
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Residues in contact with LYS 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 GLU 4.3 4.6 + - - +
518A LYS* 1.3 82.8 - - + +
520A LYS* 1.3 56.7 + - - +
521A ASP* 2.9 26.4 + - - +
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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
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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