Contacts of the helix formed by residues 560 - 564 (chain B) in PDB entry 4YHF
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 PRO 560 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520B ARG 4.7 3.8 - - - +
521B ASP* 3.5 14.4 - - - +
525B ARG* 3.4 29.4 - - - +
551B TYR* 3.8 23.8 - - + +
558B LYS 3.6 1.1 - - - +
559B PHE* 1.3 98.3 - - + +
561B VAL* 1.3 59.0 + - - +
562B ARG 3.3 2.5 - - - -
563B TRP* 3.3 22.1 + - + -
564B SER* 2.7 28.7 + - - +
574B PHE* 6.6 0.2 - - + -
717B EDO 4.4 7.6 - - - +
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Residues in contact with VAL 561 (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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554B SER* 3.8 23.1 - - - +
556B GLY 5.1 0.2 - - - +
559B PHE* 2.9 29.8 + - + +
560B PRO* 1.3 70.9 - - - +
562B ARG* 1.3 60.4 + - - +
563B TRP 3.0 5.4 + - - -
564B SER* 3.1 18.4 + - - +
569B LEU* 3.9 23.1 - - + +
603B ASN* 3.4 50.4 - - + +
606B THR* 4.3 9.2 - - + +
607B ALA* 4.0 15.3 - - + +
610B ILE* 5.8 2.3 - - - +
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Residues in contact with ARG 562 (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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560B PRO 3.3 0.8 - - - -
561B VAL* 1.3 75.7 - - - +
563B TRP* 1.3 83.2 + - + +
564B SER 3.5 0.9 - - - -
581B TRP* 4.8 1.4 + - - -
585B VAL* 3.7 15.4 - - - +
596B MET* 3.9 30.0 - - - +
597B PRO* 3.0 24.2 + - + +
598B TYR* 2.8 61.8 + - + -
601B PHE 2.8 20.4 + - - -
602B THR* 3.7 9.1 - - - +
603B ASN* 3.4 26.2 + - - +
606B THR* 3.6 16.7 + - + -
715B NA 4.4 3.0 - - - -
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Residues in contact with TRP 563 (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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521B ASP* 5.5 0.2 - - - +
522B LEU 3.4 22.0 - - - +
523B ALA* 3.2 5.0 - - + +
525B ARG* 3.0 38.1 - - - -
560B PRO* 3.3 16.5 + - + +
561B VAL 3.0 0.8 - - - -
562B ARG* 1.3 104.7 - - + +
564B SER* 1.3 60.1 + - - +
565B PRO* 4.2 0.5 - - - +
581B TRP* 3.3 18.2 - - - -
582B ALA* 3.5 12.7 + - + +
585B VAL* 3.5 29.5 - - + +
589B GLU* 3.0 42.4 + - - -
596B MET* 5.7 1.6 - - + -
597B PRO* 4.1 17.7 - - + -
717B EDO 3.5 22.1 - - - +
727B CL 3.6 15.9 - - + -
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Residues in contact with SER 564 (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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559B PHE* 3.4 12.0 - - - -
560B PRO* 2.7 21.8 + - - +
561B VAL 3.1 13.4 + - - +
562B ARG 3.5 0.8 - - - -
563B TRP* 1.3 76.6 - - - +
565B PRO* 1.3 69.8 - - - +
568B VAL* 3.9 11.1 - - - +
569B LEU* 3.7 25.4 - - - +
581B TRP* 3.4 14.8 + - - +
610B ILE* 4.4 4.3 - - - +
717B EDO 3.4 14.2 - - - -
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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