Contacts of the strand formed by residues 272 - 276 (chain A) in PDB entry 6WNX
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 ILE 272 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A VAL* 3.6 23.3 - - + -
265A SER 3.2 10.3 - - - +
266A ALA* 4.1 8.1 - - + -
271A THR* 1.3 74.1 - - - +
273A LYS* 1.3 65.4 + - - +
274A VAL* 4.8 2.9 - - + -
285A THR* 3.4 4.5 - - - +
286A LEU* 2.6 57.1 + - + +
293A ILE* 4.0 9.6 - - + +
296A LEU* 3.9 12.6 - - + -
303A VAL* 4.3 6.1 - - + -
305A SER* 3.8 18.4 - - - +
315A TRP* 3.4 44.4 - - + +
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Residues in contact with LYS 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A GLY* 3.2 27.8 + - - +
249A HIS* 3.6 16.8 - - + +
250A ARG* 6.2 1.2 - - - +
264A VAL* 3.5 3.3 - - - +
265A SER* 2.9 46.3 + - - +
269A ASP* 4.5 3.1 - - - -
271A THR* 3.8 20.8 - - - +
272A ILE* 1.3 79.0 - - - +
274A VAL* 1.3 61.8 + - - +
275A TRP* 3.3 22.5 + - + +
282A PHE* 4.0 16.3 - - + -
284A ARG 3.6 3.1 - - - -
285A THR* 3.7 23.6 + - - +
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Residues in contact with VAL 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A TYR* 3.4 48.9 - - + -
263A ILE 3.4 4.9 - - - +
264A VAL* 4.7 3.1 - - + +
272A ILE* 4.8 6.3 - - + -
273A LYS* 1.3 73.2 - - - +
275A TRP* 1.3 58.4 + - - +
282A PHE* 3.8 4.3 - - - -
283A VAL* 2.9 33.4 + - + -
284A ARG* 2.8 37.4 + - + +
286A LEU* 4.1 11.0 - - + -
317A ILE* 4.0 23.3 - - + -
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Residues in contact with TRP 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ILE* 3.9 15.8 - - + +
246A LEU* 3.6 37.9 - - + -
247A VAL 4.3 5.4 - - - -
248A GLY* 4.1 24.9 - - - -
249A HIS* 4.6 2.5 - + - -
262A TYR* 3.2 8.5 - - - -
263A ILE* 2.8 59.1 + - + +
265A SER* 2.9 25.8 + - - -
273A LYS* 3.3 28.7 + - + -
274A VAL* 1.3 74.6 - - - +
276A SER* 1.3 62.4 + - - +
280A CYS 4.3 3.6 - - - +
281A GLU 3.3 9.6 - - - +
282A PHE* 3.5 40.4 - + + -
283A VAL* 4.1 6.1 - - - +
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Residues in contact with SER 276 (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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261A LYS 3.8 7.7 + - - -
262A TYR* 4.7 2.0 - - - -
263A ILE* 4.2 3.5 - - - +
275A TRP* 1.3 70.0 - - - +
277A THR* 1.3 59.9 + - - +
278A SER* 3.3 21.5 + - - -
279A THR* 3.0 27.5 + - - +
280A CYS* 2.8 29.8 + - - -
281A GLU* 2.8 11.9 + - - -
283A VAL* 3.8 12.7 - - - +
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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