Contacts of the helix formed by residues 655 - 672 (chain B) in PDB entry 3N57
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 ASP 655 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599B LEU* 6.0 0.4 - - - +
652B PHE* 5.5 1.2 - - - -
653B GLU 3.3 5.9 + - - +
654B ILE* 1.3 78.4 - - - +
656B GLU* 1.3 64.2 + - - +
657B LYS* 2.8 35.9 + - - +
658B ARG* 3.0 30.7 + - + +
659B PHE 3.2 17.5 + - - -
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Residues in contact with GLU 656 (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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654B ILE 3.7 3.2 + - - -
655B ASP* 1.3 75.4 + - - +
657B LYS* 1.3 60.8 + - + +
659B PHE* 3.4 8.5 - - + +
660B GLU* 3.1 35.1 + - + +
709B LEU* 3.6 37.4 - - + +
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Residues in contact with LYS 657 (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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352B SER 3.8 21.4 + - - -
353B LYS* 4.1 14.6 + - - +
354B GLY* 4.2 7.5 - - - -
655B ASP* 2.8 17.2 + - - +
656B GLU* 1.3 72.6 - - + +
658B ARG* 1.3 66.4 + - + +
660B GLU* 3.4 6.4 + - - +
661B ILE* 3.2 36.8 + - + +
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Residues in contact with ARG 658 (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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351B LYS* 3.6 40.6 + - - +
352B SER* 6.5 0.2 - - - +
354B GLY* 4.7 1.2 - - - -
356B VAL 4.8 0.8 + - - -
357B ASN* 2.9 27.3 + - - +
599B LEU* 3.8 13.7 - - + -
602B ASP* 2.7 38.0 + - - +
655B ASP* 3.0 33.6 + - + +
657B LYS* 1.3 75.3 - - - +
659B PHE* 1.3 61.0 + - - +
661B ILE* 3.4 27.4 + - - +
662B ILE* 3.0 44.0 + - + +
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Residues in contact with PHE 659 (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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595B LEU* 5.0 5.7 - - + +
599B LEU* 3.7 15.2 - - + +
654B ILE* 3.8 10.8 - - + -
655B ASP 3.2 11.3 + - - +
656B GLU* 3.4 14.4 - - + +
658B ARG* 1.3 78.9 - - - +
660B GLU* 1.3 87.6 + - + +
662B ILE* 4.0 0.9 - - - +
663B LYS* 3.0 44.4 + - + +
707B VAL* 4.1 23.1 - - + -
708B THR* 4.0 4.5 - - - -
709B LEU* 3.8 43.5 - - + -
712B LEU* 3.8 31.9 - - + -
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Residues in contact with GLU 660 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656B GLU* 3.1 25.8 + - + +
657B LYS* 3.9 6.3 - - - +
658B ARG 3.4 0.4 - - - -
659B PHE* 1.3 97.6 - - + +
661B ILE* 1.3 62.5 + - + +
663B LYS* 3.7 16.1 - - - +
664B GLU* 3.4 20.6 + - - +
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Residues in contact with ILE 661 (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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354B GLY* 4.1 19.1 - - - +
357B ASN* 3.4 36.3 - - - +
380B THR* 3.6 24.5 - - + +
657B LYS* 3.2 27.8 + - + +
658B ARG* 3.7 26.0 - - - +
660B GLU* 1.3 75.4 - - + +
662B ILE* 1.3 66.0 + - + +
664B GLU* 3.2 10.6 + - - +
665B ALA* 3.1 19.8 + - - +
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Residues in contact with ILE 662 (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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357B ASN* 5.3 3.6 - - - +
594B TYR* 5.6 0.4 - - + -
595B LEU* 3.9 18.6 - - + -
598B GLU* 4.0 30.1 - - + +
599B LEU* 3.6 24.7 - - + -
602B ASP* 3.7 33.9 - - + +
658B ARG* 3.0 29.5 + - + +
659B PHE 4.2 1.8 - - - +
661B ILE* 1.3 74.0 - - + +
663B LYS* 1.3 60.5 + - - +
665B ALA* 3.2 9.3 + - + +
666B TYR* 2.9 28.5 + - + +
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Residues in contact with LYS 663 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595B LEU* 4.0 17.0 - - + +
659B PHE* 3.0 40.2 + - + +
660B GLU* 3.7 19.5 + - - +
662B ILE* 1.3 77.5 - - - +
664B GLU* 1.3 55.8 + - - +
666B TYR* 3.2 3.8 + - - +
667B MET* 2.9 32.8 + - - +
704B LEU* 3.2 48.1 + - + +
705B ASP* 4.0 14.5 + - - +
707B VAL* 3.4 23.2 + - + -
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Residues in contact with GLU 664 (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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311B ARG* 2.8 45.8 + - - -
381B GLU* 3.7 26.7 - - + +
660B GLU 3.4 10.6 + - - +
661B ILE* 3.2 12.3 + - - +
663B LYS* 1.3 78.5 - - - +
665B ALA* 1.3 62.2 + - - +
667B MET* 3.4 21.5 + - + +
668B ARG* 2.9 39.3 + - - +
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Residues in contact with ALA 665 (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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357B ASN* 4.9 11.7 - - - +
661B ILE 3.1 12.3 + - - +
662B ILE* 3.2 11.9 + - + +
664B GLU* 1.3 76.7 + - - +
666B TYR* 1.3 58.2 + - - +
668B ARG* 3.4 26.8 + - - +
669B SER* 3.0 26.9 + - - -
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Residues in contact with TYR 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B SER 5.1 0.7 + - - -
591B ASN* 2.8 39.3 + - + -
594B TYR* 3.4 47.9 - + + +
595B LEU* 4.0 23.6 - - + -
662B ILE* 2.9 16.7 + - + +
663B LYS 3.5 4.0 - - - +
665B ALA* 1.3 75.1 - - - +
667B MET* 1.3 63.0 + - - +
669B SER* 3.3 9.6 + - - -
670B LEU* 3.0 54.0 + - + +
700B LEU* 4.2 9.4 - - - +
704B LEU* 3.7 23.6 - - + -
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Residues in contact with MET 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663B LYS* 2.9 16.5 + - - +
664B GLU* 3.4 24.5 - - + +
666B TYR* 1.3 76.9 - - - +
668B ARG* 1.3 63.3 + - + +
670B LEU* 3.5 5.0 + - - +
671B ASN* 3.1 41.6 + - - +
701B LYS* 4.9 8.1 - - + +
704B LEU* 3.7 23.0 - - + +
705B ASP* 5.0 11.4 - - - +
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Residues in contact with ARG 668 (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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309B ASP* 2.9 55.4 + - + +
310B ILE* 3.7 16.0 - - - +
311B ARG* 3.2 28.8 - - - +
357B ASN* 5.8 2.6 - - - +
379B LEU 4.5 4.9 + - - -
664B GLU* 2.9 45.5 + - - +
665B ALA* 3.7 21.2 - - - +
666B TYR 3.2 0.2 - - - -
667B MET* 1.3 84.1 - - + +
669B SER* 1.3 55.5 + - - +
671B ASN* 3.0 8.5 + - + +
672B ASN* 2.7 44.9 + - - +
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Residues in contact with SER 669 (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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594B TYR* 5.2 5.0 + - - -
665B ALA 3.0 14.7 + - - -
666B TYR* 3.4 20.9 - - - -
668B ARG* 1.3 74.8 - - - +
670B LEU* 1.3 63.0 + - - +
672B ASN* 3.4 17.7 + - - +
673B PHE* 3.7 8.7 + - - +
697B LYS* 5.8 0.7 - - - -
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Residues in contact with LEU 670 (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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666B TYR* 3.0 56.7 + - + +
667B MET 3.6 4.7 - - - +
669B SER* 1.3 75.3 - - - +
671B ASN* 1.3 61.6 + - - +
672B ASN 3.4 0.5 + - - -
673B PHE* 3.4 18.2 + - - +
697B LYS* 3.7 37.9 - - + +
700B LEU* 4.1 20.6 - - + -
701B LYS* 4.0 43.7 + - + +
704B LEU* 4.0 10.1 - - + -
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Residues in contact with ASN 671 (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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309B ASP* 5.8 4.0 - - + +
667B MET* 3.1 30.2 + - - +
668B ARG* 3.0 11.7 + - - +
670B LEU* 1.3 76.2 - - - +
672B ASN* 1.3 61.6 + - - +
673B PHE 3.0 5.6 + - - -
674B ARG* 3.1 28.6 + - - +
701B LYS* 3.3 35.7 - - - +
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Residues in contact with ASN 672 (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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308B LYS* 3.5 34.6 - - + +
309B ASP* 2.8 52.3 + - - +
310B ILE* 4.1 7.3 - - - +
668B ARG* 2.7 31.2 + - - +
669B SER* 3.8 10.6 - - - +
670B LEU 3.3 0.8 - - - -
671B ASN* 1.3 71.5 - - - +
673B PHE* 1.3 59.4 + - - +
674B ARG* 3.1 5.1 + - - +
675B ALA* 2.9 25.4 + - - +
676B GLU* 3.8 2.4 + - - +
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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