Contacts of the helix formed by residues 643 - 655 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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568A ASP* 3.1 25.6 - - + +
634A TRP* 4.5 21.6 + - - -
637A ARG* 2.5 32.1 + - - +
638A PRO* 4.1 1.4 - - - +
639A GLY 3.3 23.0 + - - +
640A GLU* 3.2 15.9 + - + +
642A ASN* 1.3 83.3 - - - +
644A VAL* 1.3 67.3 + - - +
645A GLU* 3.2 6.7 - - + +
646A ALA* 3.0 5.1 + - - -
647A ILE* 3.0 22.7 + - - +
993A THR* 6.0 3.0 - - - -
994A GLY* 5.3 10.9 - - - +
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Residues in contact with VAL 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A ASP* 2.8 40.6 + - - +
569A GLN 4.6 0.2 - - - +
570A GLY 4.6 1.8 - - - +
571A VAL 4.4 10.1 - - - +
572A PHE* 4.2 13.9 - - + -
631A LEU* 3.6 20.2 - - + -
643A LYS* 1.3 73.7 - - - +
645A GLU* 1.3 57.7 + - - +
647A ILE* 4.2 7.4 - - - -
648A THR* 2.8 48.9 + - - +
667A ASN* 3.5 36.3 - - + +
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Residues in contact with GLU 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566A ASP* 5.2 11.6 - - - +
640A GLU* 4.7 10.6 - - - +
643A LYS* 3.1 5.2 + - + +
644A VAL* 1.3 78.9 - - - +
646A ALA* 1.3 57.7 + - + +
648A THR* 3.9 4.1 - - - +
649A MET* 3.1 29.0 + - + +
667A ASN* 5.3 7.7 - - - +
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Residues in contact with ALA 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640A GLU* 3.7 24.9 + - + +
641A GLU* 3.9 8.7 - - + +
643A LYS 3.0 4.2 + - - +
645A GLU* 1.3 74.5 - - - +
647A ILE* 1.3 68.5 + - - +
648A THR 3.1 1.1 - - - -
649A MET* 3.8 16.8 - - + +
650A ARG* 2.8 47.5 + - - +
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Residues in contact with ILE 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572A PHE* 3.8 26.9 - - + -
598A TYR* 5.2 2.7 - - + -
602A GLU* 3.6 24.9 - - + +
605A ASN* 3.7 31.0 - - + +
606A VAL* 5.6 0.9 - - + -
631A LEU* 3.7 27.6 - - + -
637A ARG* 4.2 0.2 - - - +
642A ASN* 3.4 24.9 - - - +
643A LYS 3.0 15.1 + - - +
644A VAL* 3.9 4.5 - - - +
646A ALA* 1.3 76.4 - - - +
648A THR* 1.3 62.0 + - - +
650A ARG* 4.0 7.8 - - - +
651A ALA* 3.2 23.4 + - - +
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Residues in contact with THR 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A PHE* 3.9 14.5 - - - -
644A VAL* 2.8 36.4 + - - +
645A GLU* 3.9 4.5 - - - +
647A ILE* 1.3 76.1 - - - +
649A MET* 1.3 61.9 + - + +
651A ALA* 3.2 2.6 + - - +
652A THR* 2.8 33.6 + - - +
665A ALA* 2.7 43.8 - - - +
666A PHE* 3.6 9.7 + - - +
667A ASN* 4.7 2.7 - - + +
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Residues in contact with MET 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645A GLU* 3.1 16.8 + - + +
646A ALA* 3.2 15.7 + - + +
648A THR* 1.3 81.4 - - + +
650A ARG* 1.3 77.4 + - + +
652A THR* 3.9 6.0 - - - -
653A ARG* 3.1 49.4 + - - +
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Residues in contact with ARG 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597A TYR* 3.7 10.9 + - - +
602A GLU* 3.2 33.3 + - - -
605A ASN* 4.2 6.3 - - - +
641A GLU* 2.9 34.9 + - - +
642A ASN* 4.6 1.8 + - - -
646A ALA* 2.8 33.1 + - - +
647A ILE* 4.0 6.9 - - - +
649A MET* 1.3 88.1 - - + +
651A ALA* 1.3 61.3 + - - +
653A ARG* 3.5 21.7 + - - +
654A ALA* 3.0 27.4 + - - +
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Residues in contact with ALA 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572A PHE* 5.6 0.2 - - + -
597A TYR* 3.5 29.8 + - + -
598A TYR* 4.1 11.2 - - + +
647A ILE 3.2 16.6 + - - +
648A THR 3.2 3.7 + - - +
650A ARG* 1.3 76.8 - - - +
652A THR* 1.3 61.8 + - - +
654A ALA* 3.1 1.6 + - - +
655A PHE* 2.8 50.6 + - + -
665A ALA* 4.4 4.0 - - + -
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Residues in contact with THR 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648A THR* 2.8 21.3 + - - +
649A MET* 3.9 6.7 - - - -
651A ALA* 1.3 78.0 - - - +
653A ARG* 1.3 61.3 + - - +
655A PHE* 3.6 9.6 + - - +
656A SER* 3.2 21.3 + - - -
662A MET* 6.2 0.4 - - + -
663A VAL 4.5 3.2 - - - +
664A PHE* 4.3 20.4 - - + -
665A ALA 3.2 26.4 + - - +
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Residues in contact with ARG 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649A MET* 3.1 51.5 + - - +
650A ARG* 3.8 26.4 + - - +
652A THR* 1.3 75.5 - - - +
654A ALA* 1.3 62.5 + - - +
656A SER* 2.8 28.1 + - - +
657A GLN* 5.0 3.6 + - - +
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Residues in contact with ALA 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A TYR* 3.7 28.5 - - + -
650A ARG 3.0 19.2 + - - +
651A ALA 3.5 4.7 - - - +
653A ARG* 1.3 78.2 - - - +
655A PHE* 1.3 64.3 + - + +
656A SER 3.3 0.9 + - - -
657A GLN* 3.4 19.4 + - - +
658A ILE* 4.8 1.9 - - - +
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Residues in contact with PHE 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574A THR* 4.0 13.0 - - + -
593A GLU 4.6 1.1 - - - -
594A VAL* 3.9 22.9 - - + -
597A TYR* 3.8 35.0 - + + -
598A TYR* 3.4 36.1 - + - -
651A ALA* 2.8 27.0 + - + +
652A THR* 3.9 5.8 - - - +
653A ARG 3.3 0.2 - - - -
654A ALA* 1.3 74.1 - - + +
656A SER* 1.3 64.4 + - - +
657A GLN 3.0 3.8 + - - -
658A ILE* 3.2 37.4 + - + +
661A ALA 5.3 1.2 - - - +
663A VAL* 3.7 42.6 - - + +
665A ALA* 4.8 2.2 - - + -
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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