Contacts of the helix formed by residues 660 - 669 (chain F) in PDB entry 4YJL
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 ASN 660 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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556B ASP* 5.5 2.9 - - - +
557B VAL* 3.4 34.6 + - + +
558B ASN* 4.7 12.0 + - - +
657F ARG 3.0 17.2 + - - +
658F GLU 3.4 1.0 - - - -
659F ASN* 1.3 78.6 - - - +
661F CYS* 1.3 63.7 + - - +
663F GLN* 3.2 41.8 + - + +
664F THR* 3.2 25.8 + - - +
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Residues in contact with CYS 661 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617F VAL* 3.9 15.5 - - + -
620F LEU* 4.2 5.6 - - - -
639F LEU* 3.7 20.6 - - - -
656F LEU* 3.0 53.0 + - + +
657F ARG* 4.8 1.0 - - - +
659F ASN 3.3 1.2 + - - -
660F ASN* 1.3 75.8 - - - +
662F LEU* 1.3 65.8 + - + +
664F THR* 3.2 5.0 + - - -
665F LEU* 2.9 47.4 + - - +
687F LEU* 4.5 1.1 - - - -
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Residues in contact with LEU 662 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656F LEU* 5.7 0.9 - - + -
657F ARG* 5.3 9.1 - - + +
660F ASN 3.5 0.2 - - - -
661F CYS* 1.3 76.8 - - + +
663F GLN* 1.3 66.7 + - - +
665F LEU* 3.2 6.7 + - + +
666F LEU* 3.1 26.7 + - - +
684F LEU* 4.2 8.6 - - + +
687F LEU* 3.9 37.7 - - + -
694F ASP* 3.5 44.9 - - + +
697F ALA* 4.3 12.8 - - + -
698F LEU* 4.1 20.2 - - + -
701F MET* 3.7 17.0 - - + -
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Residues in contact with GLN 663 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558B ASN* 6.1 1.0 - - - +
657F ARG* 5.2 1.5 + - - +
660F ASN* 3.2 52.9 + - + +
661F CYS 3.3 0.2 - - - -
662F LEU* 1.3 79.3 + - - +
664F THR* 1.3 62.5 + - - +
666F LEU* 3.3 7.6 + - - +
667F GLN* 3.2 25.6 + - - +
701F MET* 3.3 32.8 - - + +
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Residues in contact with THR 664 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617F VAL* 5.5 2.1 - - - +
620F LEU* 3.7 33.0 - - + -
621F THR* 3.8 26.0 - - + +
659F ASN 5.0 1.9 + - - -
660F ASN* 3.2 15.8 + - - +
661F CYS* 3.2 8.4 + - - -
663F GLN* 1.3 75.2 - - - +
665F LEU* 1.3 62.1 + - - +
667F GLN* 3.0 13.3 + - + +
668F HIS* 2.9 37.1 + - + +
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Residues in contact with LEU 665 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620F LEU* 4.2 19.1 - - + -
636F GLY* 6.3 0.4 - - - -
639F LEU* 4.6 2.9 - - + -
661F CYS* 2.9 34.7 + - - +
662F LEU* 3.2 7.6 + - - +
664F THR* 1.3 76.0 - - - +
666F LEU* 1.3 59.9 + - - +
668F HIS* 3.2 25.0 + - - +
669F LEU* 3.3 12.3 + - - +
680F ALA* 3.7 19.5 - - + +
683F THR* 3.6 42.2 - - + +
684F LEU* 4.0 26.0 - - + -
687F LEU* 3.9 10.8 - - + -
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Residues in contact with LEU 666 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662F LEU 3.1 13.4 + - - +
663F GLN* 3.5 8.7 - - - +
664F THR 3.2 0.2 - - - -
665F LEU* 1.3 73.6 - - - +
667F GLN* 1.3 67.0 + - - +
669F LEU* 3.2 31.4 + - + +
670F LYS 4.0 0.3 + - - -
684F LEU* 4.0 13.5 - - + -
698F LEU* 4.0 9.9 - - + -
701F MET* 3.6 47.6 - - + +
703F ALA* 3.6 34.5 - - + -
706F MET* 3.0 32.7 - - - +
707F LEU* 5.5 0.9 - - + -
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Residues in contact with GLN 667 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663F GLN 3.2 14.7 + - - +
664F THR* 3.0 15.8 + - + +
666F LEU* 1.3 76.4 - - - +
668F HIS* 1.3 66.4 + - + +
670F LYS* 3.1 58.6 + - - +
671F SER* 3.9 2.4 + - - -
706F MET* 5.5 1.0 - - - +
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Residues in contact with HIS 668 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620F LEU* 3.0 50.2 + - + +
632F ILE* 3.5 27.0 - - + +
636F GLY* 5.5 1.9 - - - -
664F THR* 2.9 24.0 + - + +
665F LEU* 3.3 23.1 - - - +
666F LEU 3.2 0.4 - - - -
667F GLN* 1.3 73.9 - - + +
669F LEU* 1.3 56.9 + - - +
670F LYS 3.1 2.5 - - - -
671F SER* 3.0 27.6 + - - +
676F ILE* 3.5 22.5 + - + +
677F VAL* 3.4 8.2 - - - +
679F ASN* 6.3 0.4 - - - +
680F ALA* 3.6 16.2 + - + +
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Residues in contact with LEU 669 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665F LEU 3.6 9.4 - - - +
666F LEU* 3.3 36.3 - - + +
667F GLN 3.2 0.6 - - - -
668F HIS* 1.3 77.5 - - - +
670F LYS* 1.3 58.7 + - - +
671F SER 3.3 1.7 + - - +
677F VAL* 3.7 20.5 - - - +
680F ALA* 4.0 11.9 - - + -
681F CYS* 3.8 18.8 - - - -
684F LEU* 3.9 14.1 - - + -
706F MET* 4.2 22.2 - - + +
707F LEU* 4.0 19.3 - - + -
710F LEU* 3.8 33.8 - - + +
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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