Contacts of the helix formed by residues 517 - 526 (chain A) in PDB entry 6G4N
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 ARG 517 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375A TYR* 4.5 1.6 - - - -
393A ASP* 4.0 23.9 + - - +
397A ASP* 2.7 45.7 + - - -
401A ILE* 3.8 26.7 - - + -
422A PHE* 5.8 3.1 - - + -
515A ARG 3.2 3.4 + - - -
516A LEU* 1.3 85.4 - - + +
518A VAL* 1.3 65.6 + - - +
519A GLN 3.1 4.2 + - - -
520A MET* 3.3 24.2 + - + +
521A CYS* 2.9 31.3 + - - +
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Residues in contact with VAL 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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500A GLN* 5.3 2.7 - - - +
515A ARG* 3.5 34.7 + - + +
516A LEU 3.0 5.1 + - - -
517A ARG* 1.3 77.3 - - - +
519A GLN* 1.3 62.3 + - + +
521A CYS* 3.9 3.5 - - - +
522A VAL* 2.9 45.2 + - + +
378B TRP* 3.3 46.2 - - + +
379B MET* 3.7 13.7 - - + -
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Residues in contact with GLN 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A GLN* 4.6 5.1 + - - +
517A ARG 3.1 1.4 + - - -
518A VAL* 1.3 84.4 - - + +
520A MET* 1.3 73.7 + - + +
521A CYS 3.3 0.2 + - - -
522A VAL* 3.4 4.2 + - - +
523A PHE* 3.4 15.9 + - - +
373B LEU* 3.6 26.6 + - + +
376B THR 2.9 21.3 + - - +
377B ASP* 3.8 4.4 - - - +
378B TRP* 2.8 42.6 + - - +
379B MET* 4.6 1.0 + - + -
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Residues in contact with MET 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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374A GLN* 3.3 50.3 - - + +
375A TYR* 3.4 34.8 - - + +
397A ASP* 3.6 7.9 - - + +
402A CYS* 4.0 0.9 - - - -
517A ARG* 3.3 37.0 + - + +
519A GLN* 1.3 85.8 - - + +
521A CYS* 1.3 58.0 + - - +
523A PHE* 3.2 4.9 - - + +
524A TRP* 2.9 35.1 + - + -
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Residues in contact with CYS 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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401A ILE* 4.3 4.3 - - - -
402A CYS* 2.0 55.0 - - - -
405A MET* 4.3 11.0 - - + -
516A LEU 4.9 0.7 - - - +
517A ARG* 2.9 37.9 + - - +
518A VAL* 3.9 4.5 - - - +
520A MET* 1.3 75.4 - - - +
522A VAL* 1.3 56.3 + - - +
524A TRP 4.1 0.2 - - - +
525A ASN* 2.6 51.7 + - - +
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Residues in contact with VAL 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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518A VAL* 2.9 31.6 + - + +
519A GLN 3.7 5.4 - - - +
521A CYS* 1.3 74.9 - - - +
523A PHE* 1.3 63.7 + - - +
525A ASN* 5.2 0.2 - - - -
526A GLN* 3.0 46.8 + - + +
527A PHE* 3.1 9.2 + - + +
373B LEU* 3.7 23.6 - - + -
378B TRP* 4.0 37.2 - - + +
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Residues in contact with PHE 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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370A ALA* 4.1 15.3 - - + -
371A VAL* 3.7 31.2 - - + -
374A GLN* 3.7 44.9 - - + +
375A TYR* 4.1 3.1 - + - -
519A GLN 3.4 3.8 + - - +
520A MET* 3.2 10.4 + - + +
521A CYS 3.3 0.2 - - - -
522A VAL* 1.3 80.2 - - - +
524A TRP* 1.3 105.0 + + - +
527A PHE* 3.3 23.0 + + - -
528A LEU* 2.9 46.8 + - + +
373B LEU* 3.9 14.7 - - + +
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Residues in contact with TRP 524 (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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360A VAL* 3.7 22.4 - - + -
371A VAL* 3.9 16.8 - - + -
375A TYR* 2.3 42.2 + + - -
394A ILE* 4.1 10.1 - - + -
397A ASP* 3.6 16.7 - - + +
398A HIS* 3.4 45.8 - + + -
402A CYS* 3.8 20.0 - - + -
520A MET 2.9 28.2 + - - +
521A CYS 4.0 0.2 - - - +
523A PHE* 1.3 98.0 - + - +
525A ASN* 1.3 61.4 + - - +
528A LEU* 3.6 25.4 - - + -
529A PRO* 3.2 20.0 - - - +
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Residues in contact with ASN 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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402A CYS* 3.1 38.5 + - - +
403A PRO* 4.1 1.9 - - - +
405A MET* 4.7 1.8 - - - +
406A HIS* 3.9 36.1 - - + +
521A CYS* 2.6 39.0 + - - +
522A VAL* 5.2 0.2 - - - -
524A TRP* 1.3 76.8 - - - +
526A GLN* 1.3 66.8 + - + +
529A PRO* 3.3 14.5 - - - +
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Residues in contact with GLN 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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522A VAL* 3.0 33.7 + - + +
525A ASN* 1.3 87.2 - - + +
527A PHE* 1.3 67.0 + - - +
529A PRO* 3.7 4.3 - - - +
530A LYS* 3.3 20.6 + - - +
378B TRP* 5.9 4.8 - - - -
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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