Contacts of the strand formed by residues 337 - 342 (chain A) in PDB entry 6F3T
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 LEU 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A LEU* 3.4 32.8 - - + -
242A PRO* 3.7 31.2 - - + -
243A LEU* 4.0 21.1 - - + -
246A HIS* 4.5 7.2 - - + -
304A LYS* 3.3 19.3 + - - +
305A PHE* 3.4 14.6 - - + +
307A LEU* 4.6 7.0 - - + -
332A ILE 4.8 0.4 - - - +
333A VAL* 3.1 35.6 + - + +
334A GLN* 4.1 1.6 - - - +
336A HIS* 1.3 89.3 - - + +
338A TYR* 1.3 62.3 + - - +
339A ILE* 4.1 5.8 - - + +
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Residues in contact with TYR 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LYS* 4.1 20.6 - - + +
305A PHE 2.8 11.3 + - - +
306A VAL* 3.3 9.9 - - + -
307A LEU* 2.9 26.3 + - - +
337A LEU* 1.3 74.1 - - - +
339A ILE* 1.3 67.2 + - - +
340A ASP* 3.7 35.9 + - + -
364A LYS* 3.6 49.3 - - + +
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Residues in contact with ILE 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LEU* 4.9 6.7 - - + -
307A LEU* 3.3 16.2 - - + +
309A ILE* 3.6 33.2 - - + -
314A TYR* 4.0 30.5 - - + -
317A LEU* 4.0 21.3 - - + -
321A LEU* 5.9 0.4 - - + -
333A VAL* 4.2 20.4 - - + -
337A LEU* 4.4 11.6 + - + +
338A TYR* 1.3 83.8 - - - +
340A ASP* 1.3 58.9 + - - +
341A ILE* 3.3 17.6 + - + +
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Residues in contact with ASP 340 (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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306A VAL* 4.4 5.8 - - + -
307A LEU 2.7 12.9 + - - +
308A ARG* 3.0 48.9 + - + +
309A ILE 3.4 4.0 + - - +
338A TYR* 3.6 30.0 + - + -
339A ILE* 1.3 68.5 - - - +
341A ILE* 1.3 68.0 + - - +
342A PHE* 3.6 1.9 + - - -
364A LYS* 3.5 4.4 - - - +
365A ARG* 2.9 32.6 + - - +
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Residues in contact with ILE 341 (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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308A ARG* 5.1 0.7 + - - -
309A ILE 3.3 5.4 - - - +
310A SER 4.1 0.4 - - - -
311A ARG* 3.6 67.8 + - + +
314A TYR* 3.3 48.7 - - + -
339A ILE* 3.3 20.2 + - + +
340A ASP* 1.3 79.8 + - - +
342A PHE* 1.3 64.1 + - - +
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Residues in contact with PHE 342 (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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235A GLU* 3.3 22.2 - - - -
308A ARG* 3.7 31.4 - - + +
309A ILE* 3.0 39.2 + - - -
310A SER* 3.3 19.8 - - - -
311A ARG 3.1 20.2 + - - -
340A ASP 4.3 0.9 - - - -
341A ILE* 1.3 74.1 - - - +
343A ASP* 1.3 73.0 + - - +
344A GLY* 3.4 2.9 + - - -
345A MET 3.6 15.0 - - - -
347A ARG* 3.9 16.4 - - + -
756A THR* 3.7 24.2 - - - +
758A HIS* 3.7 21.5 - + - -
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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