Contacts of the helix formed by residues 660 - 672 (chain N) in PDB entry 5G04
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 THR 660 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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639N HIS 4.5 0.2 - - - +
640N THR 3.7 17.7 - - - +
642N GLY 4.3 4.5 - - - +
644N VAL* 3.9 1.3 - - - -
659N VAL* 1.3 78.3 - - - +
661N PRO* 1.4 70.4 - - + +
662N VAL* 4.0 12.3 - - + +
663N GLN* 2.9 27.7 + - - +
664N ALA 3.0 10.0 + - - -
695N ARG* 3.4 43.8 + - - +
729N LEU* 3.4 22.5 + - - +
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Residues in contact with PRO 661 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B TRP* 5.5 2.2 - - - +
612N PRO* 4.7 3.5 - - + +
615N ILE* 5.7 1.8 - - + -
639N HIS* 3.3 46.3 + - + +
642N GLY* 3.3 32.8 - - - +
643N LEU 4.0 1.6 - - - +
644N VAL* 3.7 28.5 - - + -
659N VAL 3.8 4.9 - - - +
660N THR* 1.4 86.4 - - + +
662N VAL* 1.3 56.4 + - - +
664N ALA* 3.4 3.4 + - + +
665N VAL* 3.0 29.8 + - - +
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Residues in contact with VAL 662 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609N LEU* 3.6 27.8 - - + -
639N HIS* 4.0 14.6 - - + +
640N THR* 4.2 7.4 - - - +
660N THR* 3.1 6.0 + - + -
661N PRO* 1.3 74.8 - - - +
663N GLN* 1.3 60.8 + - - +
665N VAL* 3.0 25.8 - - - +
666N ILE* 3.2 19.2 + - + +
685N VAL* 4.6 0.7 - - - +
687N MET* 3.6 26.2 - - + -
695N ARG* 3.3 49.8 - - + +
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Residues in contact with GLN 663 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659N VAL* 3.3 27.7 - - + +
660N THR* 2.9 9.0 + - - +
662N VAL* 1.3 78.3 - - + +
664N ALA* 1.3 64.0 + - - +
666N ILE* 3.4 5.0 + - + -
667N LEU* 3.1 18.4 + - - +
695N ARG* 3.3 44.4 + - + +
698N VAL* 3.4 30.3 - - - +
699N TRP* 3.2 56.0 + - + +
728N VAL* 4.0 5.6 + - - +
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Residues in contact with ALA 664 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612N PRO* 5.7 2.7 - - + -
644N VAL* 3.6 31.4 - - + -
646N MET* 3.7 21.4 - - - +
659N VAL* 3.8 8.8 - - + +
660N THR 3.0 5.0 + - - +
661N PRO* 3.5 9.4 - - + +
662N VAL 3.4 0.2 - - - -
663N GLN* 1.3 77.0 - - - +
665N VAL* 1.3 55.8 + - - +
667N LEU* 3.5 7.6 + - - +
668N LEU* 3.0 34.2 + - + +
699N TRP* 5.1 0.4 - - - -
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Residues in contact with VAL 665 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609N LEU* 4.8 3.6 - - + -
610N GLU 4.1 8.7 - - - +
612N PRO* 3.7 41.9 - - + +
639N HIS* 5.1 0.2 - - - +
661N PRO 3.0 17.1 + - - +
662N VAL* 3.0 25.8 - - - +
664N ALA* 1.3 73.0 - - - +
666N ILE* 1.3 58.9 + - - +
668N LEU* 3.7 5.8 - - + -
669N TYR* 2.8 53.4 + - + -
685N VAL* 3.7 22.7 - - + -
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Residues in contact with ILE 666 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662N VAL 3.2 19.9 + - - +
663N GLN* 3.5 19.3 - - + +
665N VAL* 1.3 76.3 - - - +
667N LEU* 1.3 57.4 + - - +
669N TYR* 3.4 4.7 + - - +
670N PHE* 3.0 31.9 + - + +
681N LEU* 3.5 45.6 - - + +
685N VAL* 4.2 7.2 - - + -
687N MET* 5.2 1.8 - - - -
692N LEU* 3.9 17.7 - - + +
695N ARG* 4.9 9.6 - - + -
696N MET* 5.7 0.7 - - - +
699N TRP* 4.0 22.7 - - + +
705N LEU* 5.0 2.5 - - + -
713N PHE* 4.2 15.3 - - + -
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Residues in contact with LEU 667 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B VAL* 4.3 17.2 - - + +
646N MET* 6.0 2.7 - - + -
648N VAL* 4.1 28.0 - - + -
650N LEU* 5.6 12.8 - - + -
657N VAL* 4.7 7.9 - - + -
663N GLN 3.1 7.1 + - - +
664N ALA* 3.8 10.1 - - - +
665N VAL 3.4 0.2 - - - -
666N ILE* 1.3 75.2 - - - +
668N LEU* 1.3 57.5 + - + +
670N PHE* 3.3 13.2 + - + +
671N GLN* 2.9 26.3 + - - +
699N TRP* 3.7 35.9 - - + -
704N VAL* 4.5 25.6 - - + +
705N LEU* 4.7 11.4 - - + -
715N VAL* 6.1 3.6 - - + -
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Residues in contact with LEU 668 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B VAL* 4.1 9.2 - - + +
5B ILE* 4.4 6.1 - - + -
612N PRO* 3.7 27.6 - - + -
613N GLU 5.5 0.7 - - - +
614N ASP* 3.4 28.9 - - - +
646N MET* 3.8 31.9 - - + -
664N ALA* 3.0 21.6 + - + +
665N VAL* 3.8 7.2 - - + +
666N ILE 3.3 0.2 - - - -
667N LEU* 1.3 73.0 - - - +
669N TYR* 1.3 63.5 + - - +
671N GLN* 3.2 45.7 + - - +
672N ASP* 3.3 9.7 - - - +
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Residues in contact with TYR 669 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610N GLU* 4.4 7.7 + - - +
665N VAL* 2.8 45.7 + - + +
666N ILE 3.6 5.6 - - - +
668N LEU* 1.3 74.2 - - - +
670N PHE* 1.3 61.9 + - - +
672N ASP* 3.0 32.7 - - - +
673N GLN 3.2 6.6 - - - +
676N TRP* 3.5 35.6 + + + +
681N LEU* 4.4 6.1 - - + -
684N ALA* 2.8 46.2 + - + +
685N VAL* 4.0 13.0 - - + -
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Residues in contact with PHE 670 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 4.7 6.5 - - - +
666N ILE* 3.0 21.9 + - + +
667N LEU* 3.3 17.9 + - + +
669N TYR* 1.3 73.4 - - - +
671N GLN* 1.3 65.8 + - - +
672N ASP 3.4 3.8 - - - +
673N GLN 3.2 15.1 - - - +
674N ALA* 3.2 33.6 - - + -
675N SER* 3.7 12.8 - - - -
676N TRP* 4.2 9.0 - + + -
681N LEU* 5.8 0.9 - - + -
705N LEU* 3.5 30.1 - - + -
713N PHE* 3.5 29.4 - + + -
714N SER 3.8 1.1 - - - -
715N VAL* 3.4 46.6 - - + +
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Residues in contact with GLN 671 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 3.3 47.8 - - - +
2B LYS* 3.8 4.3 - - - +
3B VAL* 2.8 46.5 + - + +
614N ASP* 5.2 0.8 + - - -
650N LEU* 5.6 1.6 - - - -
667N LEU 2.9 13.4 + - - +
668N LEU* 3.2 33.8 + - - +
670N PHE* 1.3 75.8 - - - +
672N ASP* 1.3 62.8 + - - +
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Residues in contact with ASP 672 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 4.8 5.5 - - - +
668N LEU 3.3 11.8 - - - +
669N TYR* 3.0 25.1 - - - +
670N PHE 3.4 2.3 - - - +
671N GLN* 1.3 82.6 + - - +
673N GLN* 1.3 84.5 + - + +
674N ALA* 3.5 1.9 + - - +
676N TRP* 4.5 7.8 - - - -
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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