Contacts of the helix formed by residues 658 - 662 (chain C) in PDB entry 5Y7K
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 658 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656C VAL* 3.9 2.8 - - - +
657C SER* 1.3 82.0 + - - +
659C TRP* 1.3 54.8 + - - +
660C GLU* 3.0 42.0 + - + +
661C TYR* 2.7 69.7 + - + +
662C TYR 4.0 0.9 + - - -
683C TYR 5.5 0.2 - - - +
684C ARG* 3.3 33.3 - - - +
687C THR* 3.9 18.0 - - + +
689C MET* 3.6 10.5 - - + -
715C GLN* 3.2 2.8 + - - +
244D GLU* 3.4 38.7 + - - +
245D SER* 3.8 23.0 + - - +
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Residues in contact with TRP 659 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C ALA* 3.5 13.7 - - - +
598C LEU* 3.6 29.8 - - + +
631C TYR* 3.4 41.1 - + - -
634C TYR* 3.3 35.9 + + - -
656C VAL* 3.8 29.6 - - + -
658C ARG* 1.3 70.4 - - - +
660C GLU* 1.3 59.9 + - - +
661C TYR 3.0 2.0 + - - -
662C TYR* 3.4 17.3 + + + +
666C TYR* 4.1 17.3 - + - -
667C THR* 3.6 39.8 + - + +
671C MET* 4.7 5.6 - - + -
683C TYR* 3.8 21.6 + - + +
686C SER* 3.6 24.7 - - - -
801C 8VU 4.0 4.5 - - - -
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Residues in contact with GLU 660 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C LYS* 3.6 3.5 - - - +
259C ALA* 3.9 7.6 - - - -
658C ARG* 2.9 37.0 + - - +
659C TRP* 1.3 77.3 - - - +
661C TYR* 1.3 60.2 + - + +
662C TYR 3.6 0.2 - - - -
674C PRO* 3.9 18.2 - - + +
680C LEU* 4.1 3.9 - - - +
683C TYR* 3.7 33.2 - - + +
684C ARG* 3.1 40.5 + - - -
247D GLN* 2.9 40.9 + - + +
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Residues in contact with TYR 661 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C TYR* 4.1 3.1 + - - -
258C LYS* 2.7 30.0 + - - +
657C SER* 3.9 7.2 - - - -
658C ARG* 2.7 52.0 + - + +
660C GLU* 1.3 77.6 - - + +
662C TYR* 1.3 61.5 + - - +
689C MET* 4.4 0.9 - - + -
712C HIS* 4.2 2.4 + - - -
714C GLN* 3.1 40.2 - - + +
715C GLN* 3.4 33.2 + - + +
718C GLN* 3.6 26.1 + - + +
244D GLU* 2.4 35.9 + - - +
246D LEU 3.3 13.3 + - - -
247D GLN* 3.8 9.6 - - - -
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Residues in contact with TYR 662 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C GLU* 4.2 0.3 + - - +
206C GLU* 3.3 4.2 + - - -
256C TYR* 3.4 13.0 - - - -
258C LYS* 3.3 2.3 - - - -
259C ALA 3.0 24.4 + - - -
656C VAL* 4.6 2.0 - - + -
659C TRP* 3.4 26.0 + + + +
661C TYR* 1.3 79.0 - - - +
663C ASP* 1.3 84.2 + - - +
666C TYR* 3.5 27.6 - + - -
667C THR* 3.5 20.9 - - - +
710C ASN* 2.6 41.5 + - - -
711C VAL* 3.9 16.8 - - + -
715C GLN* 3.8 12.9 - - - +
801C 8VU 2.8 39.5 + + - -
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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