Contacts of the strand formed by residues 370 - 376 (chain B) in PDB entry 1F0C
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 370 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A PHE* 4.2 0.7 - + - -
250A MET* 5.9 0.9 - - + -
252A VAL* 3.7 26.2 - - + -
253A ILE 3.4 14.8 - - - +
254A LEU* 3.9 11.0 - - + -
260A LEU* 4.0 7.1 - - - +
288A ILE* 4.3 6.3 - - + -
289A PRO* 3.7 31.0 - - + -
291A PHE* 4.3 10.1 - + - -
366B ALA* 3.7 14.8 - - + -
368B HIS 3.3 13.7 - - - -
369B PRO* 1.3 75.5 - - - +
371B ILE* 1.3 63.3 + - - +
372B TYR* 3.8 17.7 - + + -
387B ARG* 3.5 2.6 - - - -
388B TYR* 2.8 74.8 + + + +
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Residues in contact with ILE 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A PHE* 4.5 7.6 - - + -
251A VAL 3.9 0.2 - - - +
252A VAL* 3.3 6.6 - - - +
253A ILE* 2.9 57.3 + - + +
260A LEU* 3.8 26.4 - - + +
263A ILE* 5.0 7.0 - - + -
264A GLU* 4.0 31.0 - - + +
267A LEU* 4.4 22.0 - - + -
370B PHE* 1.3 75.8 - - - +
372B TYR* 1.3 70.3 + - - +
373B VAL* 4.2 11.0 - - + -
385B VAL* 4.6 2.5 - - + -
386B GLY 3.4 13.5 - - - +
387B ARG* 4.6 3.8 - - + -
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Residues in contact with TYR 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A VAL 4.2 1.9 + - - -
51A PHE* 3.4 39.5 - + - +
250A MET* 3.9 24.9 - - + -
251A VAL 3.3 5.8 - - - +
252A VAL* 4.4 6.1 - - + -
291A PHE* 3.4 31.0 - + - -
293A VAL* 4.9 4.3 - - - +
338A ILE* 3.6 26.2 - - + +
370B PHE* 3.8 20.9 - + + -
371B ILE* 1.3 75.2 - - - +
373B VAL* 1.3 65.9 + - - +
374B ILE* 5.2 3.8 - - + -
385B VAL* 3.6 0.5 - - - -
386B GLY* 3.0 53.2 + - - +
387B ARG 3.6 15.1 + - - -
388B TYR* 3.8 6.1 - - + -
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Residues in contact with VAL 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A MET* 3.8 20.9 - - + -
249A SER 3.6 0.7 - - - +
250A MET* 3.3 3.3 - - - -
251A VAL* 2.7 43.3 + - - +
253A ILE* 5.1 0.9 - - + -
267A LEU* 5.4 0.2 - - + -
272A PHE* 4.0 32.1 - - + -
371B ILE* 4.2 11.4 - - + -
372B TYR* 1.3 80.2 - - - +
374B ILE* 1.3 73.8 + - - +
375B ARG* 3.8 4.4 + - + -
382B ILE* 4.1 21.8 - - + -
384B PHE 3.4 9.2 - - - +
385B VAL* 4.0 9.9 - - + -
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Residues in contact with ILE 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A PHE* 4.0 31.6 - - + -
244A TYR* 4.1 11.0 - - + +
248A THR* 5.2 0.2 - - - -
249A SER 3.5 7.9 - - - +
250A MET* 4.7 9.4 - - + -
338A ILE* 4.1 18.4 - - + -
345A THR* 3.8 28.7 - - + -
347A ALA* 4.5 3.1 - - + -
372B TYR* 5.2 4.7 - - + -
373B VAL* 1.3 74.6 - - - +
375B ARG* 1.3 62.6 + - - +
382B ILE* 3.8 1.0 - - - -
383B LEU* 2.8 30.3 + - + -
384B PHE* 2.8 47.6 + - + +
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Residues in contact with ARG 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A GLU* 4.9 7.1 + - - -
248A THR* 3.3 7.8 - - - -
249A SER* 3.0 44.4 + - - +
251A VAL* 3.8 23.0 - - + +
272A PHE* 3.6 22.2 - - - -
273A LYS* 5.4 9.9 - - - +
276A CYS* 3.1 35.5 - - - +
373B VAL* 3.8 6.0 + - + -
374B ILE* 1.3 77.1 - - - +
376B HIS* 1.3 68.5 + - - +
377B VAL* 4.9 7.0 + - - +
378B ASP 4.3 4.0 + - - -
380B GLY* 3.4 30.9 + - - -
381B LYS 3.4 11.4 - - - +
382B ILE* 4.1 7.0 - - + -
383B LEU* 4.1 4.3 - - - +
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Residues in contact with HIS 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ASP* 2.9 47.0 + - + +
112A PHE* 4.2 9.9 - + + +
247A ASP* 3.0 27.9 + - - -
248A THR* 3.5 6.8 - - + +
375B ARG* 1.3 78.9 + - - +
377B VAL* 1.3 59.6 + - - +
378B ASP* 2.7 19.4 + - - +
380B GLY* 2.8 24.8 + - - -
381B LYS* 2.8 21.5 + - + +
383B LEU* 3.6 31.9 - - + +
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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