Contacts of the helix formed by residues 256 - 263 (chain I) in PDB entry 6NR8
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 256 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254I ILE* 3.1 20.0 + - + +
255I THR* 1.3 93.4 + - - +
257I PRO* 1.3 65.6 - - - +
258I GLU* 3.2 11.7 + - + +
259I LYS* 3.5 15.8 + - + +
260I LEU* 3.4 16.9 - - - +
248K LYS* 4.4 1.1 - - - -
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Residues in contact with PRO 257 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255I THR 3.7 7.9 - - - +
256I ASP* 1.3 84.0 - - - +
258I GLU* 1.3 62.5 + - + +
259I LYS 3.3 0.4 - - - -
260I LEU* 3.1 16.5 + - + +
261I ASP* 3.0 25.3 + - - +
246K GLU* 3.8 22.8 - - + +
248K LYS* 3.7 21.3 - - + +
277K GLN* 4.1 24.2 - - + +
278K LEU* 5.4 1.1 - - + -
280K GLU* 5.8 2.2 - - - +
281K ASP* 4.0 14.3 - - - +
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Residues in contact with GLU 258 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256I ASP* 3.2 9.9 - - + +
257I PRO* 1.3 78.6 - - + +
259I LYS* 1.3 63.5 + - - +
261I ASP* 3.1 17.5 + - - +
262I GLN* 3.2 18.6 + - - +
281K ASP* 5.9 2.5 - - - +
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Residues in contact with LYS 259 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250I VAL* 3.7 35.1 - - + +
254I ILE* 5.2 7.0 - - + -
256I ASP* 3.5 18.5 + - + +
257I PRO 3.3 0.2 - - - -
258I GLU* 1.3 78.3 - - - +
260I LEU* 1.3 61.0 + - - +
261I ASP 3.4 0.3 + - - -
262I GLN* 3.1 41.2 + - + +
263I ILE* 3.9 9.4 - - + +
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Residues in contact with LEU 260 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250I VAL* 3.7 34.1 - - + +
251I GLN 4.4 9.6 - - - +
252I VAL* 5.8 1.1 - - + -
254I ILE* 5.0 3.1 - - + +
256I ASP 3.4 19.3 - - - +
257I PRO* 3.1 11.2 + - + +
259I LYS* 1.3 79.2 - - - +
261I ASP* 1.3 61.0 + - - +
263I ILE* 3.8 16.4 - - - +
264I ARG* 4.2 7.3 + - - +
246K GLU* 3.1 24.1 - - + +
247K TYR* 3.4 42.1 - - + +
248K LYS* 3.5 24.9 - - + +
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Residues in contact with ASP 261 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257I PRO 3.0 12.4 + - - +
258I GLU* 3.1 13.6 + - - +
260I LEU* 1.3 79.4 - - - +
262I GLN* 1.3 62.7 + - - +
263I ILE 3.3 0.2 - - - -
264I ARG* 3.2 16.3 + - - +
265I GLN* 3.8 11.5 + - - +
242K ASP 3.4 16.5 - - - +
243K SER* 3.7 17.0 + - - +
246K GLU* 3.6 15.3 - - - +
281K ASP* 5.4 4.0 - - - +
285K LEU* 5.2 0.3 - - - +
334K ARG* 3.4 23.7 + - - -
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Residues in contact with GLN 262 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258I GLU 3.2 12.8 + - - +
259I LYS* 3.1 48.8 - - - +
261I ASP* 1.3 77.8 - - - +
263I ILE* 1.3 70.6 + - + +
264I ARG 3.2 0.2 - - - -
265I GLN* 3.6 7.8 + - - +
266I ARG* 2.8 40.1 + - - +
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Residues in contact with ILE 263 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247I LYS* 3.2 47.5 + - - +
248I LEU* 5.4 0.2 - - - -
249I GLY* 4.2 19.3 - - - +
250I VAL* 3.8 28.9 - - + +
259I LYS* 3.9 12.1 - - + +
260I LEU* 3.8 15.0 - - - +
262I GLN* 1.3 85.1 - - + +
264I ARG* 1.3 65.6 + - + +
265I GLN 3.3 0.4 - - - -
266I ARG* 3.5 9.5 + - - +
267I GLU* 3.7 2.5 + - - +
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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