Contacts of the helix formed by residues 643 - 656 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568C ASP* 3.2 23.6 - - + +
634C TRP* 4.8 15.9 + - - -
637C ARG* 2.7 30.8 + - - +
638C PRO* 3.7 2.6 - - - +
639C GLY 3.1 30.1 + - - +
640C GLU* 3.3 18.8 + - + +
642C ASN* 1.3 79.7 - - - +
644C VAL* 1.3 68.8 + - - +
645C GLU* 3.3 4.9 - - + +
646C ALA* 3.0 13.5 + - - +
647C ILE* 3.1 14.4 + - - +
993C THR 5.5 7.2 + - - -
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Residues in contact with VAL 644 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568C ASP* 3.1 36.9 + - - +
569C GLN 4.5 0.4 - - - +
570C GLY 4.4 0.7 - - - +
571C VAL 4.3 10.8 - - - +
572C PHE* 4.1 12.1 - - + -
631C LEU* 3.4 21.1 - - + -
643C LYS* 1.3 73.8 - - - +
645C GLU* 1.3 66.2 + - - +
646C ALA 3.1 0.5 + - - -
647C ILE* 3.1 7.1 + - - -
648C THR* 3.0 35.5 + - + +
667C ASN* 3.5 37.9 - - + +
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Residues in contact with GLU 645 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640C GLU* 5.6 5.7 - - - +
643C LYS* 3.3 4.1 - - + +
644C VAL* 1.3 78.3 - - - +
646C ALA* 1.3 60.7 + - - +
648C THR* 3.0 21.5 + - - -
649C MET* 3.2 12.5 + - + +
667C ASN* 5.0 9.0 - - - +
833C PRO* 6.1 1.0 - - - +
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Residues in contact with ALA 646 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640C GLU 3.3 25.3 + - - +
641C GLU* 3.4 19.5 - - + +
643C LYS* 3.0 3.3 + - - +
645C GLU* 1.3 78.1 + - - +
647C ILE* 1.3 65.4 + - - +
649C MET* 3.1 11.6 + - + +
650C ARG* 3.0 36.0 + - - +
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Residues in contact with ILE 647 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572C PHE* 3.9 24.0 - - + -
597C TYR* 4.3 1.2 + - - -
598C TYR* 5.2 2.9 - - + -
602C GLU* 3.8 25.6 - - + +
605C ASN* 3.9 15.0 - - + +
606C VAL* 5.2 1.1 - - + -
631C LEU* 3.9 23.6 - - + -
641C GLU 4.2 1.6 - - - +
642C ASN 3.6 19.5 - - - +
643C LYS 3.1 20.6 + - - +
644C VAL* 3.7 4.9 - - - +
646C ALA* 1.3 76.5 - - - +
648C THR* 1.4 58.2 + - - +
650C ARG* 3.5 27.1 + - - +
651C ALA* 2.9 28.9 + - - +
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Residues in contact with THR 648 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572C PHE* 4.0 16.8 - - + -
644C VAL* 3.0 29.9 + - + +
645C GLU* 3.0 15.1 + - - -
647C ILE* 1.4 74.4 - - - +
649C MET* 1.3 62.4 + - - +
651C ALA* 2.9 8.5 + - - +
652C THR* 2.6 39.3 + - - -
665C ALA* 4.1 14.6 - - + -
666C PHE* 4.0 24.6 - - - +
667C ASN* 4.0 3.1 + - - +
830C GLN* 6.0 0.2 + - - -
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Residues in contact with MET 649 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645C GLU* 3.2 13.0 + - + +
646C ALA* 3.1 11.9 + - + +
648C THR* 1.3 80.5 + - - +
650C ARG* 1.3 69.4 + - + +
652C THR* 4.0 4.9 - - - +
653C ARG* 3.0 56.5 + - - +
833C PRO* 5.3 15.3 - - + -
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Residues in contact with ARG 650 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597C TYR* 3.6 12.9 + - - +
602C GLU* 2.8 33.5 + - - -
605C ASN* 3.9 4.9 - - - +
641C GLU* 2.8 41.0 + - - +
642C ASN* 4.4 2.0 + - - -
646C ALA* 3.0 26.3 + - - +
647C ILE* 3.6 13.6 - - - +
649C MET* 1.3 80.5 - - + +
651C ALA* 1.3 58.1 + - - +
653C ARG* 3.2 31.5 + - - +
654C ALA* 2.9 29.5 + - - +
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Residues in contact with ALA 651 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597C TYR* 3.5 26.4 + - + -
598C TYR* 3.9 23.8 - - + +
647C ILE 2.9 17.0 + - - +
648C THR* 3.1 13.0 - - - +
650C ARG* 1.3 77.2 - - - +
652C THR* 1.3 56.5 + - - +
654C ALA* 3.3 1.6 + - - +
655C PHE* 3.0 36.8 + - + -
665C ALA* 4.1 4.5 - - + -
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Residues in contact with THR 652 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648C THR* 2.6 22.8 + - - -
649C MET* 4.1 5.5 - - - -
651C ALA* 1.3 73.4 - - - +
653C ARG* 1.3 61.9 + - - +
655C PHE* 4.0 7.8 - - - +
656C SER* 3.2 20.8 + - - -
663C VAL 4.1 3.2 - - - +
664C PHE* 3.6 38.8 - - + -
665C ALA 3.0 25.1 + - - +
715C SER* 4.1 13.7 + - - +
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Residues in contact with ARG 653 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649C MET* 3.0 48.6 + - - +
650C ARG* 3.5 28.1 + - - +
652C THR* 1.3 75.0 - - - +
654C ALA* 1.3 66.3 + - - +
656C SER* 2.3 31.6 + - - +
657C GLN* 4.1 4.2 + - - +
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Residues in contact with ALA 654 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597C TYR* 3.8 29.4 - - + -
650C ARG 2.9 16.5 + - - +
651C ALA 3.6 5.4 - - - +
653C ARG* 1.3 79.0 - - - +
655C PHE* 1.3 66.5 + - + +
657C GLN* 3.3 21.8 + - - +
658C ILE* 4.4 1.6 + - - +
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Residues in contact with PHE 655 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574C THR* 3.9 11.4 - - + -
593C GLU 4.6 1.3 - - - -
594C VAL* 3.9 15.9 - - + -
597C TYR* 3.6 36.6 - + + -
598C TYR* 3.3 41.3 - + - -
651C ALA* 3.0 26.5 + - + +
652C THR* 4.2 6.5 - - - +
653C ARG 3.1 0.4 - - - -
654C ALA* 1.3 78.0 - - + +
656C SER* 1.3 58.6 + - - +
657C GLN 2.8 11.2 + - - -
658C ILE* 2.9 38.9 + - + +
661C ALA 5.2 2.3 - - - +
663C VAL* 3.3 40.6 + - + +
664C PHE 4.8 1.3 - - - -
665C ALA* 4.8 0.9 - - + -
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Residues in contact with SER 656 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652C THR 3.2 13.0 + - - -
653C ARG* 2.3 32.0 + - - +
655C PHE* 1.3 76.7 - - - +
657C GLN* 1.3 70.9 + - - +
658C ILE 3.4 5.6 - - - +
663C VAL 5.1 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