Contacts of the helix formed by residues 508 - 517 (chain B) in PDB entry 4ZG9
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504B PHE* 5.3 1.3 - - + -
505B GLU* 3.5 21.5 - - + +
506B ASN 3.0 1.4 - - - -
507B ILE* 1.3 86.5 - - + +
509B LEU* 1.3 64.9 + - - +
510B TYR 3.5 0.2 - - - -
511B ASN* 3.5 20.9 + - - +
512B VAL* 3.6 3.8 + - - +
526B GLY* 3.6 7.7 - - - -
527B THR* 2.8 41.5 + - - +
530B SER* 2.7 24.8 + - - +
531B LEU* 3.4 29.9 - - + +
826B ARG* 3.8 12.2 + - - +
854B THR* 3.7 12.9 - - + +
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Residues in contact with LEU 509 (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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202B MET* 4.0 10.1 - - - -
217B LEU* 4.2 11.4 - - + +
355B ILE* 4.8 8.7 - - + -
357B VAL* 4.0 30.1 - - + -
488B PHE* 3.5 32.5 - - + -
504B PHE* 3.7 25.8 - - + -
505B GLU 4.5 0.4 + - - -
506B ASN 3.5 8.0 + - - +
507B ILE 3.4 0.8 - - - -
508B GLU* 1.3 74.5 - - - +
510B TYR* 1.3 66.1 + - - +
511B ASN 3.1 2.5 - - - -
512B VAL* 2.8 13.5 + - + +
513B MET* 2.7 40.4 + - + +
531B LEU* 4.1 7.2 - - + +
534B LEU* 5.1 0.7 - - + -
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Residues in contact with TYR 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B LEU 4.2 5.5 + - - +
218B ALA 3.3 26.0 - - - -
219B THR* 3.4 13.7 - - - -
220B GLY* 3.5 22.9 - - - +
258B GLN 3.4 14.7 + - - -
260B LEU* 3.9 13.9 - - + -
263B THR* 2.5 29.9 + - - +
506B ASN 4.7 1.6 + - - -
507B ILE 4.3 1.9 + - - +
508B GLU 3.5 1.0 - - - -
509B LEU* 1.3 75.3 - - - +
511B ASN* 1.3 56.3 + - - +
513B MET* 3.4 13.4 + - + +
514B CYS* 2.9 43.2 + - - -
521B PRO* 3.7 5.2 - - + -
522B ALA* 3.2 31.1 + - + +
524B ASN* 3.2 31.9 - - - -
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Residues in contact with ASN 511 (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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508B GLU* 3.5 12.0 + - - +
510B TYR* 1.3 79.6 - - - +
512B VAL* 1.3 58.3 + - + +
514B CYS* 3.3 8.1 + - - +
515B ASP* 3.0 31.1 + - - +
521B PRO* 3.3 12.5 - - - +
524B ASN* 2.7 41.3 + - - -
526B GLY* 4.0 7.0 + - - -
527B THR 4.0 3.6 - - - +
528B HIS* 3.2 53.0 + - + +
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Residues in contact with VAL 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B ILE* 5.5 0.7 - - + -
495B PHE* 4.6 10.1 - - + -
508B GLU 3.8 3.6 - - - +
509B LEU* 2.8 19.6 + - + +
511B ASN* 1.3 72.0 - - + +
513B MET* 1.3 68.1 + - + +
515B ASP* 3.1 11.0 + - - +
516B LEU* 3.0 37.2 + - + +
528B HIS* 6.4 0.2 - - + -
531B LEU* 3.4 49.4 - - + +
534B LEU* 5.1 4.9 - - + -
535B LEU* 4.4 21.5 - - + -
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Residues in contact with MET 513 (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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166B LEU* 4.0 7.5 - - + +
168B ILE* 3.7 35.0 - - + -
217B LEU* 3.3 30.1 - - + +
218B ALA* 5.0 2.2 - - - -
260B LEU* 3.7 27.6 - - + -
355B ILE* 3.8 24.5 - - + -
357B VAL* 6.5 0.7 - - - -
509B LEU* 2.7 38.2 + - + +
510B TYR* 3.8 10.1 - - - +
512B VAL* 1.3 71.7 - - + +
514B CYS* 1.3 63.7 + - - +
516B LEU* 3.5 9.9 + - - +
517B LEU* 3.4 25.6 + - - +
909B 4O2 6.2 1.8 - - - -
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Residues in contact with CYS 514 (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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260B LEU* 3.8 11.4 - - - -
263B THR* 4.1 11.0 - - - -
510B TYR* 2.9 38.6 + - - +
511B ASN 3.4 8.7 - - - +
512B VAL 3.1 0.2 - - - -
513B MET* 1.3 75.7 - - - +
515B ASP* 1.3 62.5 + - - +
517B LEU* 2.9 12.1 + - - -
519B LEU* 3.0 40.3 + - + +
521B PRO* 3.7 33.0 - - + -
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Residues in contact with ASP 515 (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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494B THR* 6.2 0.2 - - - -
511B ASN 3.0 14.8 + - - +
512B VAL* 3.1 13.3 + - - +
514B CYS* 1.3 75.2 - - - +
516B LEU* 1.3 61.5 + - - +
517B LEU 3.1 1.4 + - - -
518B GLY* 3.2 12.0 + - - +
519B LEU 4.7 6.5 - - - +
528B HIS* 2.9 41.8 + - - -
532B ASN* 4.4 8.8 - - - +
535B LEU* 4.4 17.5 - - + +
538B ASN* 5.6 5.2 - - - -
539B THR* 5.1 11.6 + - - +
540B PHE* 3.6 17.6 + - - +
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Residues in contact with LEU 516 (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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163B ARG* 5.1 2.1 - - - +
164B PRO* 4.4 14.6 - - - +
166B LEU* 4.0 19.2 - - + +
353B ASN* 3.7 14.7 + - - +
355B ILE* 3.9 17.0 - - + -
494B THR* 3.6 38.8 + - + -
495B PHE* 3.7 28.0 - - + -
512B VAL* 3.0 24.0 + - + +
513B MET* 3.7 10.1 - - - +
514B CYS 3.3 0.2 - - - -
515B ASP* 1.3 74.5 - - - +
517B LEU* 1.3 65.2 + - + +
518B GLY 3.5 0.2 - - - -
535B LEU* 3.7 17.0 - - + -
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Residues in contact with LEU 517 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ARG* 3.6 37.5 + - - +
164B PRO 4.5 4.0 - - - +
166B LEU* 4.3 17.5 - - + -
260B LEU* 4.6 8.7 - - + -
264B ALA* 5.0 1.6 - - + -
269B VAL* 4.1 8.2 - - + +
302B SER* 3.8 25.1 - - - +
303B VAL* 3.9 31.0 - - + -
513B MET 3.4 14.3 + - - +
514B CYS 2.9 3.4 + - - -
516B LEU* 1.3 82.2 - - - +
518B GLY* 1.3 63.7 + - - +
519B LEU* 3.4 36.4 + - + +
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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