Contacts of the helix formed by residues 663 - 672 (chain A) in PDB entry 1NU6
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 663 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A TRP* 3.8 7.9 - - + -
202A VAL* 4.2 11.9 - - + -
206A GLU* 2.4 38.7 - - - +
256A TYR* 3.3 23.4 + - + +
257A PRO 3.2 10.3 - - - +
662A TYR* 1.3 95.8 + - - +
664A SER* 1.3 62.9 + - - +
665A VAL* 3.1 5.1 + - - +
666A TYR* 2.9 24.3 + - - +
667A THR* 2.7 27.3 + - - -
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Residues in contact with SER 664 (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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202A VAL* 4.2 0.2 - - - +
257A PRO* 2.8 24.1 + - - +
258A LYS 4.0 6.1 - - - -
259A ALA* 4.2 5.4 - - - +
263A ASN* 2.8 33.4 + - - -
299A TYR* 4.4 0.7 - - - -
318A ARG* 4.0 0.9 - - - -
662A TYR 3.7 0.4 + - - -
663A ASP* 1.3 72.9 - - - +
665A VAL* 1.3 74.1 + - - +
668A GLU* 3.0 55.5 + - - +
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Residues in contact with VAL 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A VAL* 3.7 22.4 - - + -
206A GLU* 3.8 23.1 - - + +
207A VAL* 3.8 27.4 - - + -
299A TYR* 3.7 35.0 - - + +
301A CYS* 6.1 2.5 - - - -
316A LEU* 6.3 0.2 - - + -
320A GLN* 3.0 27.9 + - - +
663A ASP* 3.1 3.5 + - - +
664A SER* 1.3 84.8 + - - +
666A TYR* 1.3 62.7 + - - +
669A ARG* 3.6 21.6 + - - +
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Residues in contact with TYR 666 (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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206A GLU* 3.9 21.3 - - - +
357A PHE* 4.9 11.3 - + - -
547A TYR* 4.7 9.0 + - - -
549A GLY* 4.5 1.6 - - - -
550A PRO* 3.7 14.2 + - - +
598A LEU* 5.1 0.2 - - + -
631A TYR* 3.5 22.6 - + - -
659A TRP* 4.0 22.4 - + - -
662A TYR* 3.7 23.8 - + + -
663A ASP* 2.9 14.6 + - - +
665A VAL* 1.3 77.0 - - - +
667A THR* 1.3 71.8 + - - +
669A ARG* 3.3 27.1 - - - +
670A TYR* 3.0 51.3 - + - -
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Residues in contact with THR 667 (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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259A ALA* 4.0 7.2 - - + -
598A LEU* 5.6 1.1 - - - -
659A TRP* 3.5 43.3 - - + +
662A TYR* 3.3 26.5 - - - +
663A ASP 2.7 22.5 + - - -
666A TYR* 1.3 84.6 - - - +
668A GLU* 1.3 59.3 + - - +
670A TYR* 3.2 4.8 + - - +
671A MET* 2.7 34.0 + - + +
683A TYR* 3.6 17.3 - - + +
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Residues in contact with GLU 668 (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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259A ALA* 4.6 1.3 - - - -
260A GLY 2.8 17.4 + - - +
299A TYR* 4.1 3.3 + - - -
318A ARG* 2.6 67.0 + - - +
319A ILE* 6.0 0.5 - - - -
320A GLN* 4.5 7.1 + - - +
664A SER* 3.0 30.0 + - - +
667A THR* 1.3 73.6 - - - +
669A ARG* 1.3 66.1 + - - +
672A GLY* 2.9 43.6 + - - +
673A LEU* 3.7 13.2 - - + +
683A TYR* 4.0 7.0 - - - +
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Residues in contact with ARG 669 (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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206A GLU* 5.3 4.4 + - - -
320A GLN* 2.6 46.9 + - + +
353A TRP* 3.6 49.4 - - + +
354A VAL 5.2 2.9 - - - -
356A ARG 4.1 3.6 + - - -
357A PHE* 2.8 41.2 + - - +
358A ARG* 5.0 1.5 - - - +
595A ASN* 4.5 3.1 - - - +
665A VAL* 3.6 28.0 + - - +
666A TYR* 3.3 29.4 + - - +
667A THR 3.2 0.2 - - - -
668A GLU* 1.3 79.7 - - - +
670A TYR* 1.3 94.3 + - + +
672A GLY 4.9 0.2 + - - -
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Residues in contact with TYR 670 (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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353A TRP* 3.5 43.1 - + + -
356A ARG 4.0 2.0 + - - -
357A PHE* 3.5 20.3 - - - -
550A PRO* 3.4 33.6 - - + +
594A ILE 4.5 0.8 - - - +
595A ASN* 4.8 0.9 - - - -
596A ARG* 2.7 31.0 + - - +
597A ARG 4.2 0.5 + - - -
598A LEU* 3.6 26.4 - - + +
666A TYR* 3.0 57.3 - + - -
667A THR 3.2 2.4 + - - +
669A ARG* 1.3 110.2 + - - +
671A MET* 1.3 63.1 + - - +
672A GLY 3.8 0.4 - - - -
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Residues in contact with MET 671 (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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596A ARG* 3.7 13.5 - - - +
598A LEU* 3.5 49.6 - - + -
659A TRP* 4.2 8.5 - - + -
667A THR* 2.7 25.6 + - + +
670A TYR* 1.3 77.3 - - - +
672A GLY* 1.3 62.4 + - - +
679A ASN* 2.8 34.4 - - - +
682A HIS* 3.4 26.5 - - + +
683A TYR* 3.5 47.7 - - + +
686A SER* 4.1 6.3 - - - +
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Residues in contact with GLY 672 (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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319A ILE* 6.1 4.5 - - - -
596A ARG* 4.3 8.2 - - - +
668A GLU* 2.9 29.0 + - - +
669A ARG 4.9 0.4 + - - -
670A TYR 3.8 0.8 - - - -
671A MET* 1.3 78.8 - - - +
673A LEU* 1.3 60.7 + - - -
678A ASP* 3.6 12.3 - - - -
679A ASN* 4.8 0.2 - - - -
683A TYR* 2.8 19.9 + - - -
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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