Contacts of the strand formed by residues 249 - 252 (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 PHE 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A VAL* 3.6 11.9 - - + -
232A TRP 5.0 0.7 - - - -
233A VAL* 3.3 31.0 - - + -
240A CYS* 5.5 0.2 - - - -
242A PHE* 3.7 36.2 - + + -
243A PRO 3.7 13.2 - - - +
244A THR* 3.3 37.5 - - + +
245A ARG* 5.9 0.2 - - - -
246A HIS 2.9 17.6 + - - +
247A PRO 4.3 0.3 - - - +
248A CYS* 1.3 78.6 - - - +
250A ARG* 1.3 76.7 + - - +
251A GLY* 3.3 33.9 - - - -
340A ALA* 4.3 12.5 + - - +
384A TRP* 3.9 22.0 - + - -
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Residues in contact with ARG 250 (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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230A PRO* 3.7 22.2 - - + +
231A VAL 2.7 13.9 + - - +
232A TRP* 3.4 35.8 + - + +
247A PRO 2.9 22.4 + - - -
248A CYS 3.6 11.1 + - - +
249A PHE* 1.3 87.7 + - - +
251A GLY* 1.3 60.7 + - - +
252A LEU 5.1 0.7 - - - +
337A PRO* 3.5 22.1 - - - +
338A THR* 2.8 26.3 + - - +
340A ALA* 4.0 12.3 - - - +
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Residues in contact with GLY 251 (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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231A VAL 4.0 0.4 + - - -
232A TRP* 3.5 7.1 - - - -
233A VAL* 3.0 25.1 + - - -
249A PHE* 3.3 31.9 - - - -
250A ARG* 1.3 80.2 - - - +
252A LEU* 1.3 63.6 + - - -
384A TRP* 5.4 2.5 - - - -
385A GLN* 6.6 0.4 - - - -
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Residues in contact with LEU 252 (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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232A TRP* 4.8 1.6 - - - -
233A VAL* 3.8 7.4 - - + +
234A ALA 3.6 24.2 - - - +
235A PRO* 4.1 2.7 - - + -
236A SER* 4.2 3.4 - - - +
237A ALA* 3.7 24.9 - - + +
249A PHE* 4.8 0.6 - - - -
250A ARG 5.1 0.7 - - - +
251A GLY* 1.3 71.3 - - - -
253A MET* 1.3 76.2 + - - +
254A PRO* 3.5 7.3 - - + +
380A THR* 4.1 15.9 - - + +
381A ALA* 5.1 7.6 - - + -
384A TRP* 3.6 44.8 - - + +
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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