Contacts of the helix formed by residues 611 - 615 (chain B) in PDB entry 1R9J
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 GLY 611 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610A PHE* 3.7 25.7 - - - -
611A GLY* 4.3 16.0 + - - -
613A GLU* 6.5 0.2 - - - -
614A LYS* 5.9 1.6 - - - +
580B GLN* 5.3 1.9 + - - +
609B SER 3.0 0.8 + - - -
610B PHE* 1.3 77.3 - - - +
612B TRP* 1.3 63.3 + - - +
613B GLU* 3.2 6.1 + - - +
614B LYS* 3.3 27.8 + - - +
615B TYR* 4.8 1.0 - - - -
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Residues in contact with TRP 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A ASN* 5.5 0.4 - - - -
481B ARG* 3.9 5.0 - - - +
550B VAL* 4.0 20.4 - - + -
551B ALA* 5.4 4.7 - - - -
552B SER* 5.1 1.1 - - - -
577B MET* 4.1 14.6 - - + -
580B GLN* 3.4 26.0 - - - +
603B SER* 3.5 26.9 - - - +
604B VAL 5.3 0.4 - - - -
605B GLU* 2.8 46.3 + - + -
608B VAL 3.9 10.9 + - - -
609B SER* 2.9 18.7 + - - +
610B PHE 3.4 3.7 - - - -
611B GLY* 1.3 73.7 - - - +
613B GLU* 1.3 55.5 - - - +
614B LYS 3.0 6.3 - - - -
615B TYR* 2.8 45.7 + + + +
616B SER* 3.0 22.8 + - - +
619B HIS* 3.4 31.2 + + + -
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Residues in contact with GLU 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A GLY* 6.4 0.4 - - - -
613A GLU* 2.2 54.1 - - + +
614A LYS* 3.2 41.0 - - + +
663A LEU 5.4 0.2 - - - +
664A LYS* 3.6 10.2 + - - +
665A ASN* 3.1 46.7 + - + +
666A SER 4.8 0.3 + - - -
609B SER 4.4 2.4 + - - +
611B GLY 3.2 4.4 - - - +
612B TRP* 1.3 76.9 - - - +
614B LYS* 1.3 56.2 + - - +
615B TYR 3.1 1.8 - - - -
616B SER 3.8 5.8 - - - -
664B LYS* 2.9 33.1 + - - +
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Residues in contact with LYS 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A PHE* 4.8 20.3 - - + -
613A GLU* 3.4 22.9 + - + +
580B GLN* 4.9 1.6 + - - +
584B ASP* 2.7 31.7 + - - -
611B GLY 3.3 18.7 + - - +
612B TRP 2.9 1.2 + - - -
613B GLU* 1.3 78.1 - - - +
615B TYR* 1.3 99.5 + - + +
664B LYS* 3.9 16.4 - - - +
666B SER* 4.5 15.4 + - - -
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Residues in contact with TYR 615 (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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550B VAL* 5.3 4.0 - - + -
577B MET* 4.0 11.4 - - + -
580B GLN* 3.5 34.6 + - + +
583B PHE* 3.9 16.3 - + - -
584B ASP* 2.5 40.8 + - - -
595B LEU* 3.9 27.7 - - + +
601B VAL* 3.7 19.7 - - - +
611B GLY 4.8 1.6 - - - -
612B TRP* 2.8 34.4 + + + +
613B GLU 3.1 0.2 - - - -
614B LYS* 1.3 119.5 + - + +
616B SER* 1.3 59.0 + - - +
617B HIS* 4.8 0.3 - - - -
664B LYS* 3.8 14.7 - - - +
666B SER* 6.0 2.9 - - - -
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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
------------------------------------------------------------
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