Contacts of the helix formed by residues 678 - 682 (chain A) in PDB entry 3NKO
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 PRO 678 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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629A TYR* 3.7 11.7 - - + +
676A LEU 3.6 7.8 - - - +
677A PHE* 1.3 107.3 - - + +
679A PRO* 1.3 72.5 - - + +
680A TYR* 4.1 9.0 - - + +
681A LEU* 3.0 39.3 + - + -
712A GLN* 3.6 25.8 - - + +
716A VAL* 5.7 0.2 - - + -
1012A EDO 3.4 18.2 - - - +
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Residues in contact with PRO 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A ILE* 3.7 33.0 - - + -
675A PHE* 4.0 16.4 - - + -
677A PHE 3.5 7.2 - - - +
678A PRO* 1.3 81.0 - - + +
680A TYR* 1.3 58.2 + - + +
681A LEU 2.8 6.6 + - - -
682A SER* 3.0 14.3 + - - +
688A LYS* 3.1 23.3 + - + -
691A ALA* 3.7 24.0 - - + -
692A PHE* 3.8 22.9 - - + -
1012A EDO 3.5 15.3 - - - +
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Residues in contact with TYR 680 (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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636A GLU 4.1 0.3 - - - +
637A VAL* 3.5 17.5 - - + -
638A SER* 3.0 47.7 + - - +
639A SER* 4.4 1.8 - - - -
640A ILE* 3.7 42.2 - - + +
678A PRO* 3.0 7.3 - - + -
679A PRO* 1.3 76.4 - - - +
681A LEU* 1.3 62.8 + - + +
682A SER 3.5 0.4 - - - -
688A LYS* 4.7 0.4 - - - +
709A THR* 3.6 23.1 + - + +
712A GLN* 4.5 1.3 - - + -
713A ARG* 3.9 44.2 - - + -
1012A EDO 3.5 31.4 - - - -
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Residues in contact with LEU 681 (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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612A ASP* 4.3 1.2 - - - +
629A TYR* 4.3 2.0 - - + -
631A ILE* 3.8 36.3 - - + +
635A ALA* 5.6 3.4 - - + -
636A GLU 4.6 7.4 - - - +
637A VAL* 3.4 34.5 - - + -
677A PHE* 3.8 13.8 - - + -
678A PRO* 3.0 31.8 + - + +
679A PRO 2.8 1.4 + - - -
680A TYR* 1.3 79.4 - - - +
682A SER* 1.3 69.5 + - - +
683A SER* 3.7 0.9 + - - -
712A GLN 3.9 13.7 - - - +
716A VAL* 3.7 28.9 - - + -
717A LYS* 4.6 8.1 - - + -
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Residues in contact with SER 682 (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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612A ASP* 3.1 8.7 - - - -
636A GLU 4.5 8.0 - - - +
638A SER* 3.5 4.7 + - - -
677A PHE* 4.2 5.8 - - - -
678A PRO 4.0 1.2 + - - -
679A PRO 3.0 7.4 + - - -
680A TYR 3.5 0.4 - - - -
681A LEU* 1.3 82.0 - - - +
683A SER* 1.3 62.0 + - - +
684A SER* 3.7 4.8 + - - -
687A ALA 4.5 0.2 - - - -
688A LYS* 2.5 66.9 + - - +
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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