Contacts of the helix formed by residues 509 - 523 (chain B) in PDB entry 5CHG
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 509 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420B ARG* 3.5 26.8 - - - +
508B GLY* 1.3 78.2 + - - -
510B ALA* 1.3 59.6 + - - +
511B HIS* 3.7 3.4 + - - +
512B PHE* 3.2 11.4 + - - +
513B ASN* 2.8 26.5 + - - -
573B ARG 2.9 16.4 + - - -
574B ASP* 2.5 30.8 + - - -
603B DGT 3.8 2.2 - - - -
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Residues in contact with ALA 510 (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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509B SER* 1.3 74.7 - - - +
511B HIS* 1.3 63.5 + - - +
513B ASN* 3.2 3.3 + - - +
514B ARG* 3.1 51.5 + - - +
603B DGT 3.8 39.3 + - + +
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Residues in contact with HIS 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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509B SER* 3.3 4.8 + - - +
510B ALA* 1.3 78.2 - - - +
512B PHE* 1.3 57.5 + - - +
514B ARG* 3.2 23.9 + - + +
515B SER* 2.9 35.4 + - - -
575B TRP* 2.9 90.6 + + + -
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Residues in contact with PHE 512 (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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504B LEU* 4.1 15.5 - - + -
508B GLY 3.6 14.4 - - - -
509B SER* 3.2 11.1 + - - +
511B HIS* 1.3 81.0 + - - +
513B ASN* 1.3 62.7 + - - +
515B SER* 3.1 7.3 + - - -
516B MET* 2.9 67.0 + - + +
560B PHE* 3.9 18.8 - + - -
568B ARG* 4.2 24.2 - - - -
572B GLU 5.2 0.2 - - - -
573B ARG* 3.5 49.1 - - + +
575B TRP* 4.0 24.4 + - - +
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Residues in contact with ASN 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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504B LEU* 3.6 21.1 - - - +
505B TYR* 2.8 40.7 + - + -
508B GLY* 3.9 3.2 - - - -
509B SER 2.8 12.0 + - - +
510B ALA 3.4 7.9 - - - +
512B PHE* 1.3 77.9 - - - +
514B ARG* 1.3 59.9 + - - +
516B MET* 3.3 5.7 + - - +
517B ARG* 2.8 31.7 + - - +
527B LEU* 5.1 2.6 - - - +
603B DGT 3.2 41.6 + - - +
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Residues in contact with ARG 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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510B ALA* 3.1 30.5 + - - +
511B HIS* 3.6 40.1 - - + +
513B ASN* 1.3 76.3 - - - +
515B SER* 1.3 56.0 + - - +
517B ARG* 3.3 27.8 + - - +
518B ALA* 2.9 28.2 + - - +
601B SO4 3.6 29.0 + - - +
603B DGT 3.9 13.6 + - - +
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Residues in contact with SER 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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511B HIS* 2.9 26.5 + - - -
512B PHE* 3.3 15.3 - - - -
514B ARG* 1.3 77.3 - - - +
516B MET* 1.3 61.0 + - - +
518B ALA* 3.1 9.5 + - - +
519B LEU* 3.0 25.0 + - - +
575B TRP 4.9 3.4 + - - -
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Residues in contact with MET 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B LEU* 4.8 11.4 - - + -
512B PHE* 2.9 50.9 + - + +
513B ASN* 3.8 5.4 - - - +
515B SER* 1.3 74.6 - - - +
517B ARG* 1.3 65.5 + - - +
519B LEU* 3.2 7.7 + - - +
520B ALA* 3.0 24.1 + - - +
527B LEU* 3.9 18.2 - - + +
559B VAL* 4.9 1.1 - - + -
560B PHE* 3.6 35.4 - - + -
563B LEU* 3.6 25.7 - - + +
565B LEU* 3.8 21.1 - - + -
568B ARG* 6.2 0.2 - - - -
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Residues in contact with ARG 517 (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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505B TYR* 5.7 2.6 - - - -
513B ASN 2.8 17.4 + - - +
514B ARG* 3.6 23.4 + - - +
515B SER 3.3 0.2 - - - -
516B MET* 1.3 77.0 - - - +
518B ALA* 1.3 61.5 + - - +
520B ALA* 3.5 7.3 + - - +
521B LYS* 3.4 26.8 + - + +
526B SER* 6.1 0.4 - - - -
527B LEU* 3.8 31.7 + - + +
601B SO4 2.7 44.7 + - - -
603B DGT 3.9 10.7 + - - -
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Residues in contact with ALA 518 (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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514B ARG 2.9 13.9 + - - +
515B SER* 3.1 12.1 + - - +
517B ARG* 1.3 76.0 - - - +
519B LEU* 1.3 64.5 + - - +
521B LYS* 3.2 19.2 + - - +
522B THR* 3.4 17.1 + - - +
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Residues in contact with LEU 519 (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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515B SER 3.0 12.7 + - - +
516B MET* 3.2 11.9 + - - +
518B ALA* 1.3 75.4 - - - +
520B ALA* 1.3 62.5 + - - +
522B THR* 2.8 35.6 + - + +
523B LYS* 3.5 10.2 + - + +
563B LEU* 3.4 37.5 - - + +
565B LEU* 3.7 34.5 - - + -
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Residues in contact with ALA 520 (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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516B MET 3.0 15.9 + - - +
517B ARG 3.7 6.3 - - - +
519B LEU* 1.3 77.8 - - - +
521B LYS* 1.3 54.5 + - - +
523B LYS* 3.2 6.7 + - - -
525B MET* 2.7 48.7 + - + +
527B LEU* 4.1 22.2 - - + +
532B LEU* 4.1 3.8 - - + -
563B LEU* 3.6 22.1 - - + +
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Residues in contact with LYS 521 (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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517B ARG* 3.4 15.4 + - + +
518B ALA* 3.2 12.7 + - - +
519B LEU 3.2 1.0 - - - -
520B ALA* 1.3 75.0 - - - +
522B THR* 1.3 59.6 + - + +
523B LYS 3.1 2.2 - - - -
524B GLY* 3.0 17.8 + - - -
525B MET 3.5 13.0 - - - +
526B SER* 5.7 1.8 - - - -
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Residues in contact with THR 522 (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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518B ALA 3.5 14.1 - - - +
519B LEU* 2.8 32.5 + - + +
521B LYS* 1.3 77.1 - - + +
523B LYS* 1.3 61.8 + - - +
524B GLY 3.3 1.2 + - - -
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Residues in contact with LYS 523 (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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519B LEU* 3.6 15.7 - - + +
520B ALA 3.2 7.0 + - - +
521B LYS 3.1 0.8 - - - -
522B THR* 1.3 82.5 - - - +
524B GLY* 1.3 64.5 + - - +
525B MET* 3.2 24.5 + - + +
534B THR* 5.7 1.0 - - - +
562B LEU 3.7 25.4 - - - +
563B LEU* 3.7 28.2 + - + +
564B GLY* 4.8 5.0 - - - +
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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