Contacts of the helix formed by residues 664 - 668 (chain I) in PDB entry 6PSU
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 664 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521I LEU* 4.1 18.8 - - - +
525I THR* 4.0 14.5 + - - -
562I GLU* 4.2 8.7 - - - -
662I SER* 3.1 8.1 + - - -
663I VAL* 1.3 84.6 - - - +
665I ALA* 1.3 60.5 + - - +
666I SER 3.5 0.2 + - - -
667I LEU* 3.8 12.3 + - - +
668I ILE 5.0 0.3 + - - -
683I ALA* 4.3 7.4 - - - +
686I GLN* 4.3 13.3 + - - +
687I ARG* 6.3 0.2 - - - -
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Residues in contact with ALA 665 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559I CYS* 4.3 2.9 - - - -
561I ILE* 3.4 38.1 - - + -
562I GLU* 4.5 5.5 + - + -
661I VAL* 4.5 4.3 - - + -
662I SER* 2.9 20.9 + - - +
664I GLY* 1.3 72.6 - - - +
666I SER* 1.3 61.1 + - - +
667I LEU 3.1 7.3 + - - -
668I ILE* 3.3 22.8 + - + +
671I LEU* 3.8 10.2 - - + +
683I ALA* 4.3 10.2 - - + +
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Residues in contact with SER 666 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577I VAL* 4.7 4.7 - - - +
658I GLN* 5.4 3.8 + - - -
661I VAL* 3.9 14.3 - - - +
662I SER 2.8 13.2 + - - -
663I VAL* 2.9 25.7 + - - +
665I ALA* 1.3 74.5 - - - +
667I LEU* 1.3 52.4 + - - +
668I ILE 3.2 1.4 - - - +
702I THR* 2.7 35.1 + - - +
704I MET* 3.7 24.1 - - - +
1186I VAL* 4.0 19.1 - - - +
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Residues in contact with LEU 667 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521I LEU* 3.2 30.5 - - + -
663I VAL 4.1 5.2 - - - +
664I GLY 3.8 3.3 + - - +
665I ALA 3.1 2.0 - - - -
666I SER* 1.3 79.6 - - - +
668I ILE* 1.3 63.2 + - - +
669I PRO* 3.3 9.0 - - - +
686I GLN* 3.5 19.3 - - - +
702I THR* 3.9 13.5 - - - +
704I MET* 4.3 9.0 - - + -
705I GLU* 3.3 42.0 - - + +
708I VAL* 4.1 14.4 - - + -
794I LEU* 3.3 22.0 - - + -
796I LEU* 6.0 0.7 - - + -
1069I ARG* 3.4 17.1 + - - +
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Residues in contact with ILE 668 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664I GLY 5.3 0.2 - - - +
665I ALA* 3.7 20.6 - - + +
666I SER 3.2 3.0 - - - +
667I LEU* 1.3 76.5 - - - +
669I PRO* 1.3 80.8 - - + +
670I PHE 3.7 1.2 + - - -
671I LEU* 3.6 30.0 + - + +
674I ASP* 4.2 1.3 - - - +
679I ALA* 3.9 38.4 - - + +
683I ALA* 4.3 9.9 - - - +
686I GLN* 4.9 8.1 - - + -
702I THR* 3.4 11.1 - - - +
1069I ARG* 4.0 17.5 - - + +
1070I HIS* 3.9 23.8 - - + -
1186I VAL* 4.5 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
------------------------------------------------------------
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