Contacts of the helix formed by residues 508 - 517 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504A PHE* 4.4 3.4 - - + -
505A GLU* 2.8 27.1 + - + +
507A ILE* 1.3 85.0 - - + +
509A LEU* 1.3 64.7 + - - +
510A TYR 3.3 1.6 + - - -
511A ASN* 3.4 15.1 + - - +
512A VAL* 3.5 12.1 + - - +
525A ASN 4.4 0.3 - - - +
526A GLY* 3.7 7.3 - - - -
527A THR* 2.9 32.7 + - - +
530A SER* 3.1 20.6 + - - +
531A LEU* 3.4 25.7 - - + +
826A ARG* 3.9 13.3 + - - -
854A THR* 3.9 20.1 - - + +
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Residues in contact with LEU 509 (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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202A MET* 3.8 11.2 - - - -
217A LEU* 3.8 15.5 - - + -
355A ILE* 4.6 14.1 - - + -
357A VAL* 3.7 31.4 - - + -
488A PHE* 3.4 31.9 - - + -
504A PHE* 4.0 16.2 - - + -
505A GLU 4.3 0.2 + - - -
506A ASN 3.4 10.3 + - - +
508A GLU* 1.3 79.2 - - - +
510A TYR* 1.3 64.5 + - - +
512A VAL* 2.9 28.0 + - + +
513A MET* 2.9 28.8 + - + +
531A LEU* 5.0 1.6 - - + -
534A LEU* 5.3 0.2 - - + -
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Residues in contact with TYR 510 (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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217A LEU 3.9 6.5 + - - +
218A ALA* 3.2 21.5 - - - -
219A THR 3.5 13.0 - - - -
220A GLY* 3.5 22.2 - - - +
258A GLN 3.6 18.2 + - - -
260A LEU* 4.0 12.3 - - + -
263A THR* 2.7 28.3 + - - +
506A ASN 4.6 0.8 + - - -
507A ILE 4.3 2.1 + - - +
508A GLU 3.3 1.4 + - - -
509A LEU* 1.3 77.0 - - - +
511A ASN* 1.3 63.5 + - - +
513A MET* 3.3 11.7 + - + +
514A CYS* 3.1 42.3 + - - -
521A PRO* 3.7 6.1 - - + -
522A ALA* 2.9 36.8 + - + +
524A ASN* 3.4 30.1 - - - -
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Residues in contact with ASN 511 (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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507A ILE 5.1 0.2 + - - -
508A GLU* 3.4 11.1 + - - +
509A LEU 3.2 0.2 - - - -
510A TYR* 1.3 79.3 - - - +
512A VAL* 1.3 61.5 + - + +
514A CYS* 3.7 2.4 + - - +
515A ASP* 3.3 26.0 + - - +
521A PRO* 3.3 18.3 - - - +
524A ASN* 3.1 36.8 + - - +
526A GLY* 3.8 3.2 - - - -
527A THR 3.7 11.2 - - - +
528A HIS* 3.4 52.5 + - + +
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Residues in contact with VAL 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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355A ILE* 5.3 0.4 - - + -
495A PHE* 4.5 18.4 - - + -
508A GLU 3.5 5.8 + - - +
509A LEU* 2.9 20.7 + - + +
511A ASN* 1.3 75.7 - - + +
513A MET* 1.3 63.5 + - + +
515A ASP* 3.0 12.3 + - - +
516A LEU* 2.9 38.8 + - + +
528A HIS* 6.5 0.2 - - + -
531A LEU* 3.6 46.9 - - + +
534A LEU* 5.1 4.5 - - + -
535A LEU* 4.6 13.5 - - + -
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Residues in contact with MET 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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166A LEU* 4.0 10.3 - - + +
168A ILE* 3.6 36.3 - - + -
217A LEU* 3.7 29.2 - - + +
218A ALA* 5.0 3.4 - - - -
260A LEU* 3.8 25.8 - - + -
355A ILE* 3.8 25.1 - - + -
509A LEU* 2.9 33.8 + - + +
510A TYR* 3.8 8.7 - - - +
512A VAL* 1.3 76.8 - - + +
514A CYS* 1.3 61.5 + - - +
516A LEU* 3.3 6.0 + - - +
517A LEU* 3.2 27.5 + - - +
908A 4O2 5.9 2.2 - - - -
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Residues in contact with CYS 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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260A LEU* 3.7 20.2 - - - -
263A THR* 4.2 9.2 - - - -
510A TYR* 3.1 42.6 + - - +
511A ASN 3.9 5.6 - - - +
513A MET* 1.3 75.1 - - - +
515A ASP* 1.3 58.2 + - - +
517A LEU 2.9 17.8 + - - -
518A GLY 2.9 12.0 + - - -
519A LEU* 2.9 34.4 + - + +
521A PRO* 3.9 20.4 - - + -
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Residues in contact with ASP 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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511A ASN 3.3 9.5 + - - +
512A VAL* 3.0 15.5 + - - +
514A CYS* 1.3 74.6 - - - +
516A LEU* 1.3 62.1 + - - +
517A LEU 3.1 1.6 + - - -
518A GLY* 3.2 11.3 + - - +
519A LEU 4.7 4.7 - - - +
528A HIS* 2.9 35.0 + - - -
532A ASN* 4.2 12.5 - - - +
535A LEU* 4.3 12.1 - - + +
538A ASN* 3.4 41.4 + - - +
540A PHE* 4.3 11.0 + - - +
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Residues in contact with LEU 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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163A ARG* 5.0 1.6 - - - +
164A PRO* 4.2 16.3 - - - +
166A LEU* 3.5 37.6 - - + +
353A ASN* 4.1 13.5 + - + +
355A ILE* 4.2 7.9 - - + -
494A THR* 3.6 34.9 + - + -
495A PHE* 3.8 24.7 - - + -
512A VAL* 2.9 24.3 + - + +
513A MET* 3.7 6.5 - - - +
514A CYS 3.3 0.4 - - - -
515A ASP* 1.3 71.4 - - - +
517A LEU* 1.3 63.2 + - + +
518A GLY 3.6 0.4 - - - -
535A LEU* 4.0 21.8 - - + -
538A ASN* 4.0 12.0 + - - +
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Residues in contact with LEU 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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163A ARG* 4.0 23.9 + - - +
164A PRO 4.5 5.6 - - - +
166A LEU* 3.9 30.3 - - + -
260A LEU* 4.4 10.5 - - + -
264A ALA* 4.7 3.6 - - + -
269A VAL* 4.3 7.2 - - + +
302A SER* 4.0 24.7 - - - +
303A VAL* 3.9 26.5 - - + -
513A MET 3.4 16.6 - - - +
514A CYS 2.9 4.4 + - - +
516A LEU* 1.3 81.5 - - - +
518A GLY* 1.3 64.3 + - - +
519A LEU* 3.3 31.7 + - + +
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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