Contacts of the strand formed by residues 269 - 273 (chain A) in PDB entry 2FWN
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 VAL 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A ALA* 4.3 11.0 - - + +
197A LEU* 4.1 21.1 - - + -
200A ALA* 3.8 25.8 - - + -
202A ASN 4.2 0.3 - - - +
203A PRO* 3.2 6.4 - - + +
204A ALA 3.0 24.4 + - - +
267A HIS* 4.5 0.3 - - - +
268A ASP* 1.3 91.1 + - + +
270A VAL* 1.3 71.9 + - - +
271A LEU 4.7 0.2 - - - +
294A ARG* 3.3 18.6 - - + +
296A ILE* 4.1 25.6 - - + -
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Residues in contact with VAL 270 (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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204A ALA* 3.3 8.7 - - + +
206A VAL* 3.9 28.3 - - + -
264A LEU* 3.8 31.9 - - + -
267A HIS* 4.0 13.5 - - + -
269A VAL* 1.3 80.3 - - - +
271A LEU* 1.3 60.3 + - - +
272A VAL* 3.8 10.5 + - + -
293A THR* 3.6 26.0 - - + -
294A ARG 2.9 11.6 + - - +
295A LEU* 3.4 7.9 - - + +
296A ILE* 2.8 29.1 + - - +
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Residues in contact with LEU 271 (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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193A LEU* 4.8 5.8 - - + -
197A LEU* 4.0 37.7 - - + -
204A ALA 2.9 12.2 + - - +
205A ILE* 3.3 14.8 - - + +
206A VAL 2.9 24.8 + - - +
223A LEU* 3.9 17.7 - - + -
227A LEU* 5.2 1.3 - - + -
269A VAL* 4.0 1.2 + - + -
270A VAL* 1.3 72.5 - - - +
272A VAL* 1.3 60.3 + - - +
273A ILE* 3.9 25.3 + - + -
296A ILE* 3.4 29.8 - - + +
298A VAL* 4.2 19.1 - - + -
325A LEU* 4.2 6.7 - - + -
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Residues in contact with VAL 272 (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 VAL* 3.2 17.9 - - + +
270A VAL* 4.2 4.9 - - + -
271A LEU* 1.3 74.6 - - - +
273A ILE* 1.3 64.4 + - - +
275A ALA* 3.9 27.6 - - + +
277A VAL* 4.1 15.3 - - + -
278A PHE* 4.0 19.7 - - + -
295A LEU* 3.8 36.3 - - + -
296A ILE 2.8 9.9 + - - +
297A SER* 3.4 6.7 - - - +
298A VAL* 2.8 28.5 + - - +
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Residues in contact with ILE 273 (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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205A ILE* 4.9 2.0 - - + -
206A VAL 2.8 9.7 + - - -
207A LEU* 3.4 24.5 - - + -
208A GLY 2.9 24.1 + - - -
211A VAL* 3.4 17.6 - - + +
220A CYS* 4.3 8.5 - - - -
223A LEU* 3.8 29.2 - - + -
271A LEU* 3.9 22.2 - - + +
272A VAL* 1.3 79.2 - - - +
274A GLY* 1.3 65.1 + - - +
275A ALA 3.3 1.8 - - - -
298A VAL* 3.5 13.5 - - + +
318A ILE* 3.9 20.9 - - + +
321A MET* 6.0 0.4 - - + -
322A ALA* 5.1 9.9 - - + +
325A LEU* 4.8 7.6 - - + -
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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