Contacts of the helix formed by residues 476 - 485 (chain A) in PDB entry 4IDT
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 476 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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474A GLY 4.7 0.9 - - - +
475A GLY* 1.3 75.3 - - - -
477A LEU* 1.3 65.1 + - - +
478A GLY* 3.3 6.6 + - - -
479A GLN* 2.7 47.5 + - - +
480A LEU* 3.1 12.0 + - - +
519A ASP* 4.0 17.2 + - - -
521A VAL 3.3 11.7 - - - -
522A LEU* 3.8 14.8 - - - -
523A LEU* 3.9 3.0 - - - +
701A T28 3.5 10.8 - - - +
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Residues in contact with LEU 477 (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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476A SER* 1.3 71.0 - - - +
478A GLY* 1.3 55.5 + - - +
480A LEU* 3.3 6.3 + - + +
481A VAL* 3.0 36.1 + - + +
487A LEU* 3.8 18.4 - - + -
495A TYR* 3.5 40.4 - - + -
518A ALA* 3.4 17.5 - - + +
521A VAL* 2.7 44.5 + - + +
523A LEU* 3.7 12.0 - - + +
585A MET* 4.1 13.2 - - + -
589A MET* 3.8 20.6 - - + -
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Residues in contact with GLY 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A SER* 3.0 2.7 + - - -
477A LEU* 1.3 77.8 - - - +
479A GLN* 1.3 59.7 + - - +
481A VAL* 3.6 4.4 + - - +
482A LYS* 3.2 22.0 + - - +
518A ALA* 3.1 23.3 + - - -
519A ASP* 3.4 24.9 - - - -
588A HIS* 5.3 5.4 - - - -
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Residues in contact with GLN 479 (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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406A LEU 4.6 6.3 + - - -
475A GLY* 3.2 12.3 - - - -
476A SER* 2.7 44.4 + - - +
478A GLY* 1.3 73.0 - - - +
480A LEU* 1.3 66.7 + - - +
482A LYS* 3.3 6.5 + - - +
483A GLU* 3.0 26.0 + - - +
519A ASP* 5.9 0.4 - - - +
666A ARG* 6.1 0.2 - - - -
701A T28 3.6 17.7 - - - +
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Residues in contact with LEU 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A SER 3.1 11.8 + - - +
477A LEU* 3.4 13.0 - - + +
479A GLN* 1.3 77.3 - - - +
481A VAL* 1.3 62.2 + - - +
483A GLU* 3.2 17.9 + - - +
484A GLN* 2.9 49.1 + - + +
487A LEU* 3.5 33.2 - - + -
491A ARG* 5.7 2.0 - - - -
495A TYR* 4.1 12.6 - - + -
523A LEU* 4.3 3.1 - - + -
665A TRP* 3.8 39.7 - - + +
666A ARG* 4.3 13.5 - - - +
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Residues in contact with VAL 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A LEU* 3.0 20.2 + - + +
478A GLY 3.9 5.2 - - - +
480A LEU* 1.3 77.2 - - - +
482A LYS* 1.3 57.5 + - - +
484A GLN 4.7 0.2 - - - +
485A GLY 2.9 42.6 + - - +
486A CYS* 4.8 1.1 - - - -
487A LEU* 4.1 21.8 - - + -
518A ALA* 4.8 4.9 - - + -
588A HIS* 3.6 39.5 - - + +
589A MET* 3.9 29.6 - - + +
592A GLY* 4.3 1.8 - - - +
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Residues in contact with LYS 482 (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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478A GLY 3.2 15.3 + - - +
479A GLN* 3.8 6.7 - - - +
480A LEU 3.2 0.2 - - - -
481A VAL* 1.3 81.7 - - - +
483A GLU* 1.3 61.9 + - - +
484A GLN 3.5 0.2 + - - -
485A GLY* 3.6 7.5 + - - -
669A TYR* 4.4 5.9 + - - -
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Residues in contact with GLU 483 (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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479A GLN 3.0 17.1 + - - +
480A LEU* 3.4 12.6 - - - +
482A LYS* 1.3 77.2 - - - +
484A GLN* 1.3 84.2 + - + +
666A ARG* 3.2 36.4 + - - +
669A TYR* 3.5 15.2 - - - +
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Residues in contact with GLN 484 (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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480A LEU* 2.9 30.7 + - + +
481A VAL 4.4 0.2 - - - +
483A GLU* 1.3 107.3 + - - +
485A GLY* 1.3 55.7 + - - +
486A CYS 2.8 23.7 + - - +
487A LEU* 4.3 9.2 - - + -
488A PRO* 6.4 0.2 - - + -
666A ARG* 3.0 35.6 - - - +
667A GLY 3.1 25.3 + - - +
668A GLU 3.7 9.6 - - - +
669A TYR* 3.4 9.6 - - - +
670A LYS 2.9 24.4 + - - -
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Residues in contact with GLY 485 (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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481A VAL* 2.9 16.9 + - - +
482A LYS* 3.6 4.1 + - - -
483A GLU 3.5 1.2 - - - -
484A GLN* 1.3 74.9 - - - +
486A CYS* 1.3 58.2 + - - -
592A GLY* 3.0 26.7 - - - +
669A TYR* 3.4 20.7 - - - -
670A LYS 3.3 11.9 - - - -
672A PRO* 4.0 9.6 - - - +
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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