Contacts of the strand formed by residues 381 - 386 (chain F) in PDB entry 3IFS
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 ASN 381 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8F ASP 4.7 2.3 - - - +
11F LYS* 4.2 9.1 + - + +
12F ALA* 3.6 24.0 + - - +
327F GLU* 3.3 30.7 + - - +
329F VAL* 3.7 18.4 - - - +
371F LEU* 3.6 42.5 - - + +
374F HIS* 3.7 11.4 + - - +
375F SER* 4.1 9.5 + - - +
379F VAL 2.9 24.9 + - - -
380F PRO* 1.3 74.8 + - - +
382F LEU* 1.3 62.7 + - - +
383F ILE* 4.9 0.7 - - - +
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Residues in contact with LEU 382 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F PHE* 3.9 20.2 - - + -
8F ASP 3.9 3.6 - - - -
9F TYR* 4.0 12.8 - - + -
12F ALA* 3.9 17.3 - - + -
254F TYR* 4.3 9.0 - - + -
257F VAL* 3.7 34.1 - - + -
258F ARG 5.1 1.6 - - - +
261F LEU* 4.3 5.6 - - + -
326F PHE* 3.9 21.8 - - + -
327F GLU 2.8 14.0 + - - +
328F THR* 3.7 21.1 - - + +
329F VAL* 2.8 32.7 + - - +
380F PRO 5.1 0.2 - - - +
381F ASN* 1.3 81.2 - - - +
383F ILE* 1.3 61.7 + - - +
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Residues in contact with ILE 383 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F THR 3.8 0.3 - - - +
7F PHE* 3.4 8.3 - - - -
8F ASP* 2.9 58.4 + - + +
11F LYS* 4.0 18.2 - - + +
329F VAL* 3.5 9.0 - - + +
331F LYS* 4.2 4.5 - - + -
367F TYR* 3.3 30.3 - - + +
371F LEU* 3.8 22.9 - - + -
381F ASN 4.9 1.1 - - - +
382F LEU* 1.3 80.9 - - - +
384F VAL* 1.3 66.8 + - - +
385F ASN* 3.6 29.2 - - - +
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Residues in contact with VAL 384 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F VAL* 3.7 26.5 - - + -
6F THR 3.4 4.7 - - - +
7F PHE* 4.1 14.6 - - + -
254F TYR* 5.5 0.4 - - + -
328F THR* 3.9 24.0 - - + -
329F VAL 2.8 8.6 + - - +
330F LEU* 3.5 17.1 - - + -
331F LYS 2.9 23.7 + - - -
383F ILE* 1.3 77.4 - - - +
385F ASN* 1.3 60.2 + - - +
386F ILE* 3.6 4.1 + - + +
397F LEU* 3.9 18.6 - - + -
400F PHE* 4.2 19.1 - - + -
401F PHE* 4.3 7.0 - - + -
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Residues in contact with ASN 385 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F HIS 4.2 0.2 - - - +
5F VAL* 3.2 12.6 - - - +
6F THR* 2.8 51.9 + - - +
8F ASP* 4.2 16.6 + - - +
331F LYS* 3.5 16.7 - - - +
367F TYR* 5.0 0.3 + - - -
383F ILE* 3.6 23.7 - - - +
384F VAL* 1.3 69.4 - - - +
386F ILE* 1.3 61.6 - - - +
387F PRO* 3.6 2.6 - - + +
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Residues in contact with ILE 386 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F VAL* 4.4 2.5 - - + -
95F MSE 6.2 0.4 - - - -
278F LEU* 4.7 6.1 - - + -
330F LEU* 3.8 33.4 - - + -
331F LYS 2.8 10.5 + - - +
332F VAL* 3.1 14.7 - - + -
333F GLY 2.8 24.9 + - - -
384F VAL* 4.0 6.5 - - + +
385F ASN* 1.3 75.1 - - - +
387F PRO* 1.3 63.4 - - - +
388F GLU 3.3 10.4 + - - +
389F LEU* 4.1 17.0 - - + -
393F THR* 3.5 26.0 - - + -
397F LEU* 3.7 37.7 - - + -
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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