Contacts of the strand formed by residues 244 - 251 (chain A) in PDB entry 2FIB
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 TYR 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A ASP* 2.6 30.9 + - - -
192A THR* 6.1 0.4 - - - -
236A ILE* 3.1 29.4 - - + -
237A SER* 3.5 19.5 - - - -
239A GLN* 3.1 23.6 + - + +
242A ILE* 3.2 44.9 + - + +
243A PRO* 1.3 74.1 - - - +
245A ALA* 1.3 60.1 + - - +
264A MET* 2.8 12.4 + - - +
265A PHE* 2.7 46.2 + - + +
386A ILE* 4.4 14.8 - - + -
387A ILE* 3.7 23.1 - - - -
388A PRO* 3.9 14.1 - - + -
389A PHE* 4.3 2.0 - - - -
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Residues in contact with ALA 245 (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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191A TRP* 4.7 1.6 - - + -
244A TYR* 1.3 74.5 - - - +
246A LEU* 1.3 60.9 + - - +
247A ARG 4.1 0.3 + - - -
261A ASP* 5.7 0.2 - - + -
262A TYR 3.1 11.4 - - - +
264A MET 4.4 0.7 - - - +
265A PHE* 4.5 1.3 - - - -
385A LYS 4.0 0.3 - - - +
386A ILE* 3.5 6.4 - - - +
387A ILE* 2.9 36.6 + - + +
389A PHE* 4.0 15.2 - - + +
392A LEU* 3.5 35.7 - - + -
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Residues in contact with LEU 246 (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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191A TRP* 5.3 0.2 - - - -
194A PHE* 3.9 27.8 - - + -
245A ALA* 1.3 75.2 - - - +
247A ARG* 1.3 76.8 + - - +
248A VAL* 4.2 10.8 - - + -
260A ALA 3.7 0.9 - - - +
261A ASP* 3.2 5.7 - - - +
262A TYR* 2.8 54.6 + - + +
265A PHE* 3.5 42.9 - - + +
276A LEU* 5.3 0.2 - - + -
278A TYR* 6.5 0.2 - - + -
290A PHE* 4.2 18.8 - - + -
384A MET* 4.4 11.0 - - + -
385A LYS 3.6 11.2 - - - +
386A ILE* 4.2 1.1 - - - -
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Residues in contact with ARG 247 (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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191A TRP* 3.6 39.5 - - + -
245A ALA 4.1 0.6 + - - -
246A LEU* 1.3 75.9 - - - +
248A VAL* 1.3 73.6 + - - +
249A GLU* 4.3 9.9 + - + +
259A THR* 4.4 20.7 + - - +
260A ALA 3.5 3.4 - - - +
261A ASP* 2.8 38.2 + - - +
383A THR 3.6 1.2 - - - +
384A MET* 3.4 3.3 - - - -
385A LYS* 2.9 55.1 + - + +
392A LEU* 3.9 14.5 - - - +
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Residues in contact with VAL 248 (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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246A LEU* 4.2 21.3 - - + -
247A ARG* 1.3 76.6 - - - +
249A GLU* 1.3 62.1 + - - +
250A LEU* 3.8 18.8 - - + +
258A SER 4.0 0.3 - - - +
259A THR* 3.4 4.3 - - - -
260A ALA* 3.0 41.2 + - + +
262A TYR* 4.7 4.3 - - + -
286A ALA* 5.6 0.2 - - - +
290A PHE* 4.9 1.3 - - + -
344A LEU* 3.7 24.7 - - + -
369A TRP* 4.1 27.6 - - + -
383A THR 3.3 4.9 - - - +
384A MET* 4.4 17.0 - - + -
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Residues in contact with GLU 249 (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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183A GLU* 5.2 2.9 - - - +
247A ARG* 4.3 11.8 + - + -
248A VAL* 1.3 73.9 - - - +
250A LEU* 1.3 65.6 + - - +
257A THR* 3.9 22.7 - - + +
258A SER 3.5 2.5 - - - -
259A THR* 4.1 13.8 - - + +
381A LYS 4.6 0.3 - - - -
382A THR* 3.4 4.7 - - - -
383A THR* 2.8 49.4 + - - +
385A LYS* 3.0 30.2 + - - -
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Residues in contact with LEU 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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248A VAL* 3.8 19.7 - - + -
249A GLU* 1.3 84.9 - - - +
251A GLU* 1.3 61.9 + - - +
256A ARG 3.7 0.5 - - - +
257A THR* 3.1 10.3 - - - +
258A SER* 2.8 56.7 + - - +
286A ALA* 4.0 9.0 - - + -
344A LEU* 3.8 21.5 - - + -
369A TRP* 3.7 37.7 - - + -
372A TRP* 3.9 15.2 - - + -
379A MET* 4.6 8.5 - - + -
381A LYS 3.6 1.6 - - - +
382A THR* 3.9 13.7 - - + -
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Residues in contact with GLU 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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250A LEU* 1.3 75.7 - - - +
252A ASP* 1.3 73.4 + - - +
255A GLY* 4.3 17.0 + - - +
256A ARG 3.6 6.5 - - - +
257A THR* 4.0 17.1 + - + +
372A TRP* 4.3 0.4 - - - -
379A MET* 3.5 10.8 - - - +
380A LYS* 2.9 35.9 + - - +
381A LYS* 2.9 56.7 + - + +
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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