Contacts of the helix formed by residues 671 - 683 (chain B) in PDB entry 2NUP
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 671 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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670B THR* 1.3 79.4 + - - +
672B PHE* 1.3 68.9 + - - +
673B TYR 3.2 2.7 - - - -
674B LYS* 2.8 37.2 + - + +
675B LYS* 2.8 49.7 + - + +
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Residues in contact with PHE 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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617B GLY* 3.8 32.1 - - - -
621B GLN* 3.7 24.5 - - - -
646B VAL* 3.6 29.4 - - + -
647B GLY* 3.6 20.4 - - - -
670B THR* 3.3 16.8 + - + +
671B ASP* 1.3 80.0 + - - +
673B TYR* 1.3 84.9 + + - +
675B LYS* 3.3 9.8 + - + +
676B LEU* 2.9 48.9 + - + +
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Residues in contact with TYR 673 (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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616B LEU* 4.1 4.3 - - + +
617B GLY* 4.1 8.3 + - - -
620B LEU* 4.0 25.1 - - + -
642B PRO* 3.7 16.6 - - - +
647B GLY* 2.6 32.8 + - - -
649B LEU* 3.9 14.1 - - + -
670B THR* 4.2 12.3 + - + +
671B ASP 3.2 0.4 - - - -
672B PHE* 1.3 100.5 - + - +
674B LYS* 1.3 61.2 + - - +
676B LEU* 4.0 3.6 - - - -
677B ALA* 3.2 22.5 + - - +
701B SER* 3.5 31.9 - - - +
702B LEU* 3.7 23.6 - - + -
704B CYS* 4.0 2.2 - - + -
705B ILE* 3.6 24.4 - - + +
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Residues in contact with LYS 674 (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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670B THR 5.6 0.2 + - - -
671B ASP* 2.8 26.7 + - + +
673B TYR* 1.3 76.9 - - - +
675B LYS* 1.3 68.6 + - + +
677B ALA* 3.3 6.0 + - - +
678B LEU* 3.1 43.8 + - + +
704B CYS* 3.8 21.7 - - + +
708B TYR* 3.9 27.0 - - + +
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Residues in contact with LYS 675 (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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671B ASP* 2.8 41.3 + - + +
672B PHE* 3.6 9.9 - - + +
674B LYS* 1.3 78.3 - - + +
676B LEU* 1.3 63.3 + - - +
678B LEU* 3.0 15.7 + - + +
679B ASP* 2.7 33.8 + - - +
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Residues in contact with LEU 676 (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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620B LEU* 3.6 34.1 - - + -
621B GLN* 4.4 16.8 - - + +
624B PHE* 4.5 26.7 - - + -
672B PHE* 2.9 44.8 + - + +
673B TYR* 4.1 1.1 - - + +
675B LYS* 1.3 75.4 - - - +
677B ALA* 1.3 57.2 + - - +
679B ASP* 3.1 13.0 + - + +
680B CYS* 2.9 31.5 + - - -
705B ILE* 3.8 20.4 - - + -
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Residues in contact with ALA 677 (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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673B TYR 3.2 17.8 + - - +
674B LYS 3.4 6.1 - - - +
675B LYS 3.2 0.6 - - - -
676B LEU* 1.3 79.5 - - - +
678B LEU* 1.3 56.9 + - - +
680B CYS* 3.2 8.0 + - - +
681B SER* 2.8 30.2 + - - -
704B CYS 3.4 19.5 - - - +
705B ILE* 3.6 20.6 - - - +
708B TYR* 3.8 16.2 - - + -
709B SER* 4.0 3.9 - - - -
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Residues in contact with LEU 678 (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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674B LYS* 3.1 34.3 - - + +
675B LYS* 3.0 14.5 + - + +
677B ALA* 1.3 75.3 - - - +
679B ASP* 1.3 60.2 + - - +
681B SER* 3.3 6.7 - - - -
682B GLY* 2.9 24.8 + - - -
708B TYR* 3.9 23.3 - - + +
767B PHE* 3.4 42.6 - - + -
769B ARG* 5.2 1.7 + - - -
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Residues in contact with ASP 679 (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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624B PHE* 3.9 22.9 - - + -
675B LYS* 2.7 31.6 + - - +
676B LEU* 3.1 16.7 + - + +
678B LEU* 1.3 75.0 - - - +
680B CYS* 1.3 67.1 + - - +
682B GLY* 3.2 9.6 + - - -
683B GLN* 3.4 17.0 + - - +
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Residues in contact with CYS 680 (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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620B LEU 5.7 0.7 - - - -
624B PHE* 3.9 29.4 - - - -
634B MET* 5.3 3.6 - - - -
676B LEU* 2.9 26.3 + - - -
677B ALA* 3.5 9.0 - - - +
679B ASP* 1.3 74.9 - - - +
681B SER* 1.3 54.8 + - - +
683B GLN* 2.7 25.6 + - - +
685B VAL* 3.0 46.4 + - + +
687B VAL* 3.8 23.8 - - + -
705B ILE* 5.0 0.4 - - - -
709B SER* 4.7 0.9 - - - -
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Residues in contact with SER 681 (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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677B ALA 2.8 17.7 + - - -
678B LEU* 3.3 11.4 - - - -
680B CYS* 1.3 77.4 - - - +
682B GLY* 1.3 61.8 + - - -
683B GLN 3.1 1.2 + - - -
684B GLN* 3.1 19.2 + - - +
685B VAL 3.6 0.8 + - - -
708B TYR 4.0 10.8 + - - -
709B SER* 4.6 0.7 - - - -
767B PHE* 3.7 22.5 - - - +
769B ARG* 4.3 6.5 + - - -
775B SER* 3.8 11.1 + - - -
777B PRO* 3.6 27.7 - - - +
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Residues in contact with GLY 682 (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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678B LEU 2.9 14.2 + - - -
679B ASP 3.2 4.8 + - - -
681B SER* 1.3 75.1 - - - +
683B GLN* 1.3 65.4 + - - +
684B GLN* 3.5 7.3 + - - +
769B ARG* 3.7 18.3 - - - +
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Residues in contact with GLN 683 (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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499B ARG* 4.7 4.9 + - - +
624B PHE* 3.7 19.1 - - + -
628B SER* 2.8 44.9 + - - +
630B THR 4.5 1.0 - - - -
631B GLY* 3.4 15.6 + - - -
679B ASP 3.7 11.7 - - - +
680B CYS 2.7 8.5 + - - +
682B GLY* 1.3 81.3 + - - +
684B GLN* 1.3 72.8 + - - +
685B VAL* 3.2 5.6 - - + -
23C ASP* 4.1 4.9 + - - +
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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