Contacts of the strand formed by residues 381 - 388 (chain A) in PDB entry 1FIB
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 LYS 381 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A LYS* 5.8 7.2 - - - +
197A ARG* 3.2 10.8 - - - +
198A LEU* 3.8 26.7 - - + +
250A LEU* 3.6 0.7 - - - -
251A GLU* 2.9 68.0 + - + +
379A MET* 3.6 1.9 - - - +
380A LYS* 1.3 105.9 - - + +
382A THR* 1.3 72.4 + - - +
383A THR* 5.8 1.1 - - - +
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Residues in contact with THR 382 (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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195A GLN* 2.9 21.3 + - - -
196A LYS* 3.5 5.5 - - - +
197A ARG* 3.1 44.5 + - + +
249A GLU 3.3 7.6 - - - -
250A LEU* 3.9 19.7 - - + -
344A LEU* 4.2 11.7 - - + -
367A ILE* 3.6 31.2 - - + -
379A MET* 4.0 4.9 - - + -
381A LYS* 1.3 80.8 - - - +
383A THR* 1.3 67.3 + - - +
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Residues in contact with THR 383 (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* 4.5 4.0 - - - +
193A VAL* 4.0 22.9 - - + -
195A GLN* 3.5 4.9 - - - +
196A LYS* 3.2 25.8 + - + +
247A ARG 3.6 1.0 - - - +
248A VAL* 3.5 5.4 - - - +
249A GLU* 2.8 53.4 + - - +
381A LYS* 5.8 0.9 - - - +
382A THR* 1.3 79.1 + - - +
384A MET* 1.3 67.4 + - - +
385A LYS* 3.9 26.0 - - + -
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Residues in contact with MET 384 (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 VAL* 3.8 1.6 - - - +
194A PHE* 3.0 60.4 + - + -
195A GLN* 3.1 34.7 + - + +
227A TRP* 4.4 1.8 - - - -
246A LEU* 4.4 18.8 - - + -
247A ARG 3.6 4.7 - - - -
248A VAL* 4.6 7.6 - - + -
265A PHE* 5.9 0.7 - - + -
290A PHE* 4.8 5.2 - - + -
334A TRP* 3.8 29.2 - - + -
335A TRP* 4.4 10.5 - - + -
344A LEU* 3.7 28.9 - - + -
383A THR* 1.3 77.3 - - - +
385A LYS* 1.3 61.7 + - - +
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Residues in contact with LYS 385 (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* 2.7 40.1 + - - +
191A TRP* 3.8 31.6 - - + +
192A THR 3.2 16.2 - - - +
193A VAL* 4.0 9.4 - - + -
194A PHE* 4.4 1.8 - - - -
245A ALA 3.8 0.2 - - - +
246A LEU* 3.5 1.7 - - - +
247A ARG* 2.9 59.7 + - - +
249A GLU* 2.7 30.9 + - - -
383A THR* 3.9 13.5 - - + -
384A MET* 1.3 76.7 - - - +
386A ILE* 1.3 67.7 + - - +
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Residues in contact with ILE 386 (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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190A GLY 4.3 0.5 - - - +
191A TRP* 3.7 2.9 - - - -
192A THR* 3.0 46.6 + - + +
194A PHE* 3.8 23.1 - - + -
233A ILE* 5.3 4.0 - - + +
236A ILE* 3.6 35.4 - - + -
237A SER* 4.6 13.2 - - - +
244A TYR* 4.3 16.9 - - + -
245A ALA 3.3 10.8 - - - +
246A LEU* 4.2 4.0 - - + -
265A PHE* 3.8 27.4 - - + -
385A LYS* 1.3 80.1 - - - +
387A ILE* 1.3 62.7 + - - +
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Residues in contact with ILE 387 (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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154A GLN* 3.4 21.8 - - - +
189A ASN* 3.8 21.8 - - + -
190A GLY 3.6 13.5 - - - +
191A TRP* 3.5 40.6 - - + -
244A TYR* 3.4 5.9 - - - -
245A ALA* 2.8 36.9 + - + +
386A ILE* 1.3 75.3 - - - +
388A PRO* 1.4 85.0 - - + +
391A ARG* 3.7 25.8 - - + +
392A LEU* 5.0 0.2 - - + -
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Residues in contact with PRO 388 (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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151A LYS* 4.5 7.9 - - - +
152A ASP* 4.2 7.6 - - - +
154A GLN* 3.6 28.9 - - + -
190A GLY 5.0 0.4 - - - +
242A ILE* 4.6 10.3 - - + -
243A PRO 3.5 10.3 - - - +
244A TYR* 4.1 19.3 - - + -
387A ILE* 1.4 96.7 - - + +
389A PHE* 1.3 56.0 + - - +
390A ASN* 3.2 19.1 - - - +
391A ARG* 2.8 35.3 + - + +
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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