Contacts of the strand formed by residues 336 - 342 (chain v) in PDB entry 6FF7
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 ALA 336 (chain v).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288v VAL* 3.9 19.4 - - - +
289v CYS* 5.0 3.7 - - - +
304v GLN* 5.4 8.6 - - + +
334v PRO 3.4 5.0 + - - +
335v VAL* 1.3 75.7 - - - +
337v ALA* 1.3 61.9 + - - +
338v ALA 4.3 7.2 - - - +
339v MET* 5.8 1.6 - - + -
349v VAL* 4.0 15.5 - - + -
350v ALA 3.4 29.8 - - - +
351v SER* 3.7 1.8 - - - +
352v GLU* 4.5 2.2 - - - -
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Residues in contact with ALA 337 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14v ILE 4.3 16.4 - - - +
15v SER* 4.5 13.1 - - - +
288v VAL* 3.3 22.0 - - - +
289v CYS* 4.8 1.0 - - - -
336v ALA* 1.3 74.5 - - - +
338v ALA* 1.3 60.6 + - + +
350v ALA 2.9 10.8 + - - +
352v GLU* 4.1 18.8 - - + +
61x LYS* 5.2 11.4 - - + -
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Residues in contact with ALA 338 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15v SER 5.0 2.0 - - - +
16v PHE* 4.8 5.8 - - - -
17v ALA* 4.1 35.3 - - + +
289v CYS* 4.9 5.4 - - - -
336v ALA* 3.5 4.7 - - - +
337v ALA* 1.3 81.3 - - + +
339v MET* 1.3 61.2 + - - +
348v PHE 4.2 0.9 - - - +
349v VAL* 4.3 0.3 - - - -
350v ALA* 3.3 32.2 + - + +
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Residues in contact with MET 339 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17v ALA* 4.6 8.8 - - - +
18v ILE* 5.9 0.2 - - - -
289v CYS* 4.6 13.3 - - + +
291v ALA* 3.7 33.6 - - + +
302v LEU 5.2 1.3 - - - +
336v ALA* 6.0 1.8 - - + -
338v ALA* 1.3 76.2 - - - +
340v CYS* 1.3 64.4 + - - +
341v VAL* 4.0 0.9 - - + +
348v PHE 3.5 9.2 - - - +
349v VAL* 4.8 5.2 - - + +
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Residues in contact with CYS 340 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17v ALA* 5.3 8.7 - - + -
18v ILE* 4.8 5.8 - - - +
19v HIS* 4.0 28.7 - - + +
30v ILE* 5.6 6.7 - - + -
339v MET* 1.3 75.7 - - - +
341v VAL* 1.3 65.6 + - - +
342v LEU* 3.8 5.4 + - - +
347v LEU* 4.0 0.7 - - - -
348v PHE* 3.0 40.5 + - + +
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Residues in contact with VAL 341 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19v HIS* 4.6 9.9 - - - +
291v ALA* 5.0 14.5 - - + +
292v THR 4.8 15.4 + - - +
293v HIS* 4.8 12.1 - - + -
302v LEU* 5.6 5.8 - - + -
339v MET* 4.0 3.0 - - + +
340v CYS* 1.3 74.8 - - - +
342v LEU* 1.3 60.0 + - - +
346v PHE 3.6 8.7 - - - +
347v LEU* 4.4 8.7 - - + +
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Residues in contact with LEU 342 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28v GLN* 5.4 9.9 - - + -
340v CYS 4.5 4.0 - - - +
341v VAL* 1.3 76.2 - - - +
343v LYS* 1.3 67.3 + - - +
345v GLY* 3.8 7.4 + - - -
346v PHE* 2.9 36.2 + - + +
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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