Contacts of the helix formed by residues 503 - 508 (chain A) in PDB entry 6T8G
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 503 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473A SER* 2.4 36.1 + - - -
477A ASN* 5.5 3.4 + - - +
500A LYS* 4.2 22.4 + - - +
502A LEU* 1.3 97.1 - - + +
504A LEU* 1.3 68.5 + - + +
505A SER 3.2 6.1 + - - -
506A ILE* 3.3 25.1 + - - +
595A ASP* 5.1 4.0 - - - +
801A ADP 4.2 6.6 + - - -
548F ARG* 3.8 34.7 + - + +
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Residues in contact with LEU 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A SER* 5.7 3.1 - - - +
476A VAL* 4.4 21.1 - - + -
477A ASN* 3.9 23.3 - - - +
496A MET* 3.6 37.1 - - + +
497A ILE 4.9 1.8 - - - +
498A ASP* 3.7 22.3 + - + +
500A LYS 5.2 0.4 + - - -
503A GLU* 1.3 82.3 - - + +
505A SER* 1.3 57.5 + - - +
506A ILE* 3.1 7.5 + - - +
507A TYR* 3.9 13.5 + - + +
517A VAL* 3.5 12.4 - - + +
593A VAL* 5.9 2.0 - - + +
594A VAL 5.4 0.9 - - - -
595A ASP* 3.5 44.6 - - + +
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Residues in contact with SER 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A ASP* 3.9 6.8 + - - -
501A MET 5.4 4.5 - - - -
502A LEU 4.7 11.0 - - - -
503A GLU 3.2 2.4 - - - +
504A LEU* 1.3 75.0 - - - +
506A ILE* 1.3 62.9 + - - +
507A TYR 3.2 2.8 + - - -
508A GLU* 3.3 20.6 + - - +
517A VAL* 4.3 12.7 - - - +
543F ALA* 6.2 2.9 - - - -
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Residues in contact with ILE 506 (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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477A ASN* 4.9 4.0 - - - +
503A GLU 3.3 19.0 + - - +
504A LEU* 4.5 0.9 - - - -
505A SER* 1.3 76.5 - - - +
507A TYR* 1.3 89.7 + - + +
508A GLU 3.2 3.2 + - - +
698A ASP* 5.5 3.1 - - + +
701A VAL* 3.9 20.9 - - + -
702A HIS* 4.4 23.3 - - + +
705A VAL* 3.5 21.7 - - + +
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Residues in contact with TYR 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A ASN* 2.4 42.3 + - - -
480A LEU* 3.5 28.9 - - + +
481A LEU* 3.4 21.5 - - + +
484A LEU* 5.0 10.8 - - + -
494A LEU* 5.8 2.0 - - + -
496A MET* 3.6 37.9 - - + -
504A LEU* 4.1 7.0 - - + +
505A SER 3.2 1.2 - - - -
506A ILE* 1.3 84.7 - - + +
508A GLU* 1.3 62.0 - - - +
509A GLY 3.3 3.5 + - - -
510A ILE* 3.3 30.1 - - + +
513A LEU* 3.9 8.3 - - + +
517A VAL* 5.1 0.2 - - - -
701A VAL* 3.5 23.6 - - + +
705A VAL* 4.0 16.4 - - + -
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Residues in contact with GLU 508 (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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505A SER* 3.3 18.8 + - - +
506A ILE 3.2 6.2 - - - +
507A TYR* 1.3 76.9 - - - +
509A GLY* 1.3 58.4 + - - +
513A LEU* 3.4 7.5 - - - +
516A PRO* 3.7 12.8 - - - +
517A VAL* 2.9 39.9 + - + +
705A VAL* 4.9 0.9 - - - +
709A LYS* 3.8 14.7 + - - +
716A TYR* 2.3 34.6 + - - +
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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