Contacts of the helix formed by residues 658 - 675 (chain V) in PDB entry 1I84
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 658 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542V ASP* 2.9 29.5 + - + +
545V CYS* 5.8 2.4 - - - -
546V TRP* 4.7 16.9 - - + -
601V ASN* 2.6 32.7 + - - -
602V MET* 6.0 0.4 - - - +
656V PHE 4.1 1.4 + - - -
657V ARG* 1.3 78.6 - - - +
659V VAL* 1.3 51.4 + - - +
660V GLY 3.6 1.4 + - - -
661V GLN* 3.1 30.1 + - + +
662V LEU* 2.7 36.0 + - - +
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Residues in contact with VAL 659 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477V PHE* 3.7 25.4 - - + -
481V CYS* 6.0 1.1 - - - -
600V LYS 4.0 14.1 - - - +
601V ASN* 3.3 20.1 + - - +
602V MET 5.6 0.2 - - - -
603V ASP* 4.7 15.7 - - + +
657V ARG 3.9 1.8 + - - -
658V THR* 1.3 70.9 + - - +
660V GLY* 1.3 66.6 + - - +
662V LEU* 2.7 31.2 + - + +
663V TYR* 2.8 17.6 + - + +
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Residues in contact with GLY 660 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477V PHE* 4.6 1.8 - - - -
481V CYS* 6.2 1.1 - - - -
538V LEU* 3.7 32.4 - - - +
542V ASP* 4.5 4.3 - - - -
601V ASN* 3.5 9.5 + - - -
658V THR* 3.4 2.3 + - - -
659V VAL* 1.3 87.4 - - - +
661V GLN* 1.3 55.9 + - - +
663V TYR* 4.2 5.1 - - - +
664V LYS* 2.8 29.1 + - - +
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Residues in contact with GLN 661 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531V PRO* 5.8 5.9 - - - +
542V ASP* 4.3 13.1 + - - +
657V ARG* 4.5 10.1 - - - +
658V THR* 3.1 26.8 + - + +
659V VAL 2.8 1.4 + - - -
660V GLY* 1.3 75.1 - - - +
662V LEU* 1.3 61.9 + - - +
663V TYR 3.2 1.3 - - - -
664V LYS* 4.0 24.2 - - + +
665V GLU* 2.9 75.0 + - - +
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Residues in contact with LEU 662 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630V ARG* 3.5 32.5 - - - +
657V ARG* 3.6 37.9 - - + +
658V THR 2.7 12.2 + - - +
659V VAL* 2.7 14.1 + - + +
661V GLN* 1.3 79.7 - - - +
663V TYR* 1.3 65.3 + - - +
665V GLU* 3.6 5.4 - - + +
666V GLN* 3.5 15.5 + - - +
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Residues in contact with TYR 663 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270V TYR* 4.6 9.9 - + + -
271V LEU* 3.2 45.5 - - + +
481V CYS* 4.1 18.8 - - + -
484V TYR* 4.1 12.3 - + - -
485V THR* 3.0 23.7 + - - +
538V LEU* 5.8 2.9 - - + -
659V VAL* 2.8 16.7 + - + +
660V GLY* 4.2 5.6 - - - +
662V LEU* 1.3 73.0 - - - +
664V LYS* 1.3 63.3 - - + +
665V GLU 2.2 20.9 + - - -
666V GLN* 2.5 32.7 + - + +
667V LEU* 2.9 53.7 + - + +
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Residues in contact with LYS 664 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484V TYR* 4.3 18.4 - - + +
529V GLU* 2.4 47.1 + - + +
530V ARG* 4.7 0.8 - - - +
531V PRO* 4.9 8.4 - - - +
538V LEU* 4.6 17.7 - - + -
542V ASP* 6.0 0.7 - - - -
660V GLY 2.8 24.7 + - - +
661V GLN* 3.9 29.6 - - - +
663V TYR* 1.3 85.9 - - + +
665V GLU* 1.3 57.8 + - - +
667V LEU* 4.1 11.0 - - + +
668V THR* 2.8 19.5 + - + +
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Residues in contact with GLU 665 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657V ARG* 3.8 24.1 + - - +
661V GLN* 2.9 57.7 + - - +
662V LEU* 3.6 8.5 - - + +
663V TYR 2.2 16.8 + - - -
664V LYS* 1.3 71.3 - - - +
666V GLN* 1.3 61.0 + - - +
667V LEU 3.2 0.2 - - - -
668V THR* 2.7 21.6 + - - +
669V LYS* 3.5 12.0 + - - +
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Residues in contact with GLN 666 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268V GLU* 3.3 26.3 + - - +
269V THR 3.6 11.3 + - - +
270V TYR* 3.3 35.6 - - + -
440V ARG* 4.9 7.4 + - - +
662V LEU 3.5 8.3 + - - +
663V TYR* 2.5 25.8 + - + +
665V GLU* 1.3 72.7 - - - +
667V LEU* 1.3 59.9 + - - +
668V THR 2.9 5.2 - - - -
669V LYS* 2.8 45.1 + - + +
670V LEU* 3.0 8.0 + - - +
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Residues in contact with LEU 667 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270V TYR* 4.9 5.6 - - + -
484V TYR* 4.0 24.9 - - + +
485V THR* 3.4 21.8 - - + -
488V LYS* 4.5 17.2 - - + +
663V TYR* 2.9 54.5 + - + +
664V LYS* 4.4 8.5 - - + +
665V GLU 3.2 0.4 - - - -
666V GLN* 1.3 81.4 - - - +
668V THR* 1.3 57.9 + - - +
670V LEU* 4.0 24.5 - - + +
671V MET* 3.5 23.7 + - + +
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Residues in contact with THR 668 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488V LYS* 6.2 4.3 - - - -
529V GLU* 6.0 1.6 - - - +
664V LYS* 2.8 18.9 + - + +
665V GLU* 2.7 17.9 + - - -
667V LEU* 1.3 76.9 - - - +
669V LYS* 1.3 60.9 + - - +
671V MET* 3.8 8.3 - - + +
672V THR* 2.7 33.3 + - - +
675V ARG* 6.2 1.6 - - - +
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Residues in contact with LYS 669 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268V GLU* 6.0 2.0 - - - +
665V GLU 3.5 7.2 + - - +
666V GLN* 2.8 34.7 + - + +
668V THR* 1.3 79.5 - - - +
670V LEU* 1.3 56.9 + - - +
672V THR* 2.8 28.7 + - - +
673V THR* 3.2 12.3 + - + +
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Residues in contact with LEU 670 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251V PHE* 3.5 34.5 - - + -
268V GLU* 6.1 0.4 - - + -
270V TYR* 3.1 43.3 - - + +
464V LEU* 4.6 12.8 - - + -
466V ILE* 5.4 4.5 - - + -
485V THR* 5.7 0.2 - - + -
666V GLN 3.0 12.5 + - - +
667V LEU* 4.1 15.3 - - + +
669V LYS* 1.3 71.5 - - - +
671V MET* 1.3 74.4 + - + +
672V THR 2.7 14.8 + - - -
673V THR* 3.0 19.3 + - + +
674V LEU* 3.2 23.8 + - + +
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Residues in contact with MET 671 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464V LEU* 6.0 0.2 - - + -
485V THR* 5.6 3.1 - - + -
488V LYS* 4.3 28.3 - - + +
489V LEU* 5.2 12.1 - - + +
492V LEU* 4.0 29.4 - - - -
667V LEU* 3.5 30.0 + - + +
668V THR* 4.1 11.2 - - + +
669V LYS 3.4 0.8 - - - -
670V LEU* 1.3 98.7 - - + +
672V THR* 1.3 57.5 + - - +
674V LEU* 4.2 9.8 - - + +
675V ARG* 3.0 64.8 + - - +
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Residues in contact with THR 672 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668V THR 2.7 16.8 + - - -
669V LYS* 2.8 16.0 + - - +
670V LEU 2.7 5.9 + - - -
671V MET* 1.3 73.7 - - - +
673V THR* 1.3 66.3 + - + +
675V ARG* 3.3 17.1 + - - +
676V ASN* 3.4 19.5 + - - +
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Residues in contact with THR 673 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251V PHE* 4.3 14.1 - - + -
460V PHE* 4.4 8.0 - - - -
669V LYS* 3.3 17.3 - - + +
670V LEU* 3.6 11.9 - - + +
672V THR* 1.3 75.3 - - + +
674V LEU* 1.3 69.4 + - - +
676V ASN* 2.6 29.4 + - - +
677V THR* 2.9 23.3 + - - +
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Residues in contact with LEU 674 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172V SER* 4.6 10.2 + - - +
174V LEU* 3.8 30.7 - - + -
251V PHE* 3.5 32.3 - - + -
464V LEU* 4.2 10.3 - - + -
489V LEU* 5.4 1.6 - - + -
492V LEU* 3.8 28.4 - - + +
670V LEU* 3.2 27.9 + - + +
671V MET* 4.2 13.7 - - + +
673V THR* 1.3 82.8 + - - +
675V ARG* 1.3 58.7 + - - +
676V ASN 3.1 2.8 + - - -
677V THR* 3.0 28.0 + - + +
679V PRO* 5.0 4.3 - - - +
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Residues in contact with ARG 675 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488V LYS* 4.4 15.6 + - - +
491V GLN* 6.0 3.8 - - - +
492V LEU* 4.6 31.3 - - + +
495V HIS* 6.0 7.1 - - - +
496V THR* 6.2 2.2 - - + -
668V THR* 6.2 1.4 - - - +
671V MET* 3.0 47.4 + - - +
672V THR* 3.3 11.5 + - - +
673V THR 3.1 0.8 - - - -
674V LEU* 1.3 77.9 - - + +
676V ASN* 1.3 61.8 + - - +
677V THR 3.5 3.6 - - - +
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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
------------------------------------------------------------
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