Contacts of the helix formed by residues 643 - 656 (chain B) in PDB entry 5NC5
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 LYS 643 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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568B ASP* 3.4 22.4 - - + +
634B TRP* 4.3 15.7 + - + +
637B ARG* 3.1 24.6 + - - +
638B PRO* 4.4 1.8 - - - +
639B GLY 3.7 23.8 - - - +
640B GLU* 3.9 17.5 + - + +
641B GLU 3.5 1.2 - - - -
642B ASN* 1.3 83.3 - - - +
644B VAL* 1.3 69.1 + - - +
645B GLU* 3.3 4.5 - - + +
646B ALA* 2.9 14.4 + - - +
647B ILE* 3.0 13.6 + - - +
993B THR* 5.6 5.8 - - - -
994B GLY* 4.7 22.9 - - - +
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Residues in contact with VAL 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B ASP* 2.7 47.9 + - - +
569B GLN 4.6 1.6 - - - +
570B GLY 4.8 0.7 - - - +
571B VAL 4.2 12.1 - - - +
572B PHE* 3.9 17.7 - - + -
631B LEU* 3.5 20.9 - - + -
643B LYS* 1.3 71.9 - - - +
645B GLU* 1.3 66.8 + - - +
646B ALA 3.1 0.3 + - - -
647B ILE* 3.1 8.5 + - - +
648B THR* 2.8 39.5 + - - +
667B ASN* 3.8 28.5 - - + +
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Residues in contact with GLU 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B ASP* 5.2 12.3 - - - +
643B LYS* 3.2 3.8 + - + +
644B VAL* 1.3 81.1 - - - +
646B ALA* 1.3 62.9 + - - +
648B THR* 3.5 6.5 - - - -
649B MET* 3.2 53.5 + - + +
667B ASN* 5.3 9.4 + - + +
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Residues in contact with ALA 646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640B GLU* 3.1 28.9 - - + +
641B GLU* 3.4 17.0 - - - +
643B LYS* 2.9 8.5 + - - +
645B GLU* 1.3 81.2 - - - +
647B ILE* 1.3 63.7 + - - +
649B MET* 3.2 4.5 + - - +
650B ARG* 3.1 34.4 + - - +
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Residues in contact with ILE 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B PHE* 3.9 23.8 - - + -
598B TYR* 4.9 4.7 - - + -
602B GLU* 3.6 38.8 - - + +
605B ASN* 4.0 18.6 - - + +
606B VAL* 5.7 0.7 - - + -
631B LEU* 4.1 20.0 - - + -
642B ASN 3.8 15.3 - - - +
643B LYS 3.0 24.9 + - - +
644B VAL* 3.6 7.9 - - - +
646B ALA* 1.3 74.7 - - - +
648B THR* 1.3 52.3 + - - +
650B ARG* 3.2 11.6 + - - +
651B ALA* 2.7 37.6 + - + +
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Residues in contact with THR 648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B PHE* 4.2 8.8 - - - -
644B VAL* 2.8 36.6 + - - +
645B GLU* 3.5 8.3 - - - +
647B ILE* 1.3 71.7 - - - +
649B MET* 1.3 69.5 + - + +
651B ALA* 3.1 3.6 + - - +
652B THR* 2.7 41.1 + - - +
665B ALA* 3.7 31.6 - - - +
666B PHE* 4.1 9.7 - - - -
667B ASN* 4.1 10.0 + - + +
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Residues in contact with MET 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B GLU* 3.2 52.7 + - + +
646B ALA* 3.2 5.4 + - - +
648B THR* 1.3 93.4 - - + +
650B ARG* 1.3 63.6 + - + +
652B THR* 3.4 5.1 + - - -
653B ARG* 3.0 33.7 + - - +
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Residues in contact with ARG 650 (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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597B TYR* 3.8 9.0 - - - +
602B GLU* 3.5 29.6 + - - +
605B ASN* 4.2 4.2 - - - +
641B GLU* 2.8 38.8 + - - +
642B ASN* 4.3 3.2 + - - -
646B ALA* 3.1 25.7 + - - +
647B ILE* 3.5 13.5 - - - +
649B MET* 1.3 74.8 - - + +
651B ALA* 1.3 65.1 + - - +
653B ARG* 3.2 31.7 + - - +
654B ALA* 2.9 23.2 + - - +
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Residues in contact with ALA 651 (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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572B PHE* 5.1 0.2 - - + -
597B TYR* 3.5 17.6 + - + -
598B TYR* 3.7 36.6 - - + +
647B ILE* 2.7 22.1 + - + +
648B THR 3.4 4.5 - - - +
650B ARG* 1.3 73.2 - - - +
652B THR* 1.3 62.5 + - - +
654B ALA* 3.1 3.6 + - - +
655B PHE* 3.1 29.5 + - + -
665B ALA* 4.0 8.3 - - + -
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Residues in contact with THR 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B THR* 2.7 22.6 + - - +
649B MET* 3.9 5.8 - - - -
651B ALA* 1.3 73.8 - - - +
653B ARG* 1.3 60.8 + - - +
655B PHE* 3.6 3.5 + - - +
656B SER* 3.2 19.9 + - - -
663B VAL 4.6 1.9 - - - +
664B PHE* 3.7 29.4 - - + +
665B ALA 3.2 26.8 + - - +
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Residues in contact with ARG 653 (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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649B MET* 3.0 33.1 + - - +
650B ARG* 3.5 35.0 - - - +
652B THR* 1.3 74.3 - - - +
654B ALA* 1.3 63.3 + - - +
656B SER* 2.4 32.3 + - - +
657B GLN* 4.3 3.5 + - - +
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Residues in contact with ALA 654 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B TYR* 3.8 30.5 - - + +
650B ARG 2.9 12.7 + - - +
651B ALA 3.1 8.3 + - - +
653B ARG* 1.3 76.7 - - - +
655B PHE* 1.3 61.7 + - + +
657B GLN* 3.1 27.4 - - - +
658B ILE* 5.0 1.0 - - - +
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Residues in contact with PHE 655 (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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574B THR* 4.3 2.9 - - - -
593B GLU 5.0 0.7 - - - -
594B VAL* 3.9 23.1 - - + -
597B TYR* 3.6 46.4 - + + -
598B TYR* 3.3 28.3 - + - -
651B ALA* 3.1 18.4 + - + +
652B THR* 3.9 3.1 - - - +
653B ARG 3.2 0.4 - - - -
654B ALA* 1.3 76.9 - - + +
656B SER* 1.3 55.1 + - - +
657B GLN 2.7 15.7 + - - -
658B ILE* 2.9 36.6 + - + +
661B ALA 5.3 0.7 - - - +
663B VAL* 3.4 50.1 + - + +
664B PHE* 4.6 2.7 - - - -
665B ALA 5.2 1.3 - - - -
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Residues in contact with SER 656 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652B THR 3.2 12.7 + - - -
653B ARG* 2.4 30.4 + - - +
655B PHE* 1.3 75.5 - - - +
657B GLN* 1.3 69.7 + - - +
658B ILE 3.7 5.7 + - - +
663B VAL 5.4 1.8 - - - -
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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