Contacts of the strand formed by residues 337 - 343 (chain A) in PDB entry 3LX9
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 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332A ARG* 6.2 0.4 - - - -
333A GLN* 3.2 5.6 - - - +
334A GLY 2.9 32.1 + - - +
335A ASP* 3.3 26.7 - - + -
336A ASN* 1.3 78.5 - - - +
338A GLU* 1.3 66.1 + - - +
353A MET* 6.2 0.2 - - + -
354A ILE 3.3 13.5 - - - -
355A ASN* 4.2 9.2 - - - -
363A ARG* 3.3 50.9 - - + -
364A SER 3.5 22.4 - - - -
365A TYR* 3.4 49.8 - + + -
407A ILE* 4.1 14.8 - - + -
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Residues in contact with GLU 338 (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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243A LEU* 5.4 2.0 - - - +
244A ASP* 4.0 3.9 - - - +
247A SER* 4.6 1.2 + - - -
330A GLN* 2.7 29.6 + - - +
332A ARG 3.3 5.4 - - - +
333A GLN* 4.2 6.5 - - + +
336A ASN 5.8 0.2 - - - -
337A PHE* 1.3 80.3 - - - +
339A VAL* 1.3 63.1 + - - +
340A TRP* 2.8 33.0 + - + +
352A ALA 3.7 0.7 - - - +
353A MET* 3.3 4.3 - - - +
354A ILE* 2.8 52.2 + - + +
356A ARG* 2.6 46.4 + - + +
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Residues in contact with VAL 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A GLN* 3.6 2.9 - - - -
331A LEU* 2.7 44.1 + - + -
332A ARG* 2.8 28.1 + - + +
337A PHE* 5.8 0.2 - - + -
338A GLU* 1.3 77.9 - - - +
340A TRP* 1.3 60.7 + - - +
351A VAL* 4.0 21.3 - - + -
352A ALA 3.3 7.4 - - - +
353A MET* 4.3 8.1 - - + -
365A TYR* 3.5 41.7 - - + +
367A ILE* 4.2 16.8 - - + -
372A LEU* 4.4 0.9 - - + -
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Residues in contact with TRP 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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243A LEU* 3.8 34.8 - - + -
246A THR* 4.4 8.7 - - + -
247A SER* 3.7 29.4 - - - -
250A GLN* 5.0 1.1 - - - -
286A LEU* 3.3 24.2 - - + -
289A ILE* 3.9 21.5 - - + -
290A MET* 4.0 21.5 - - + -
327A GLN* 6.2 0.2 - - - -
328A GLY 5.1 0.9 - - - -
329A TYR* 3.2 22.7 - - - -
330A GLN* 3.8 14.3 - - + +
331A LEU 4.1 0.2 - - - +
338A GLU* 2.8 36.1 + - + -
339A VAL* 1.3 82.0 - - - +
341A GLU* 1.3 61.0 + - - +
351A VAL* 3.4 6.4 - - - +
352A ALA* 2.7 43.6 + - + +
354A ILE* 3.9 8.7 - - + +
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Residues in contact with GLU 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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289A ILE* 4.3 3.1 - - - -
328A GLY* 3.1 2.6 - - - -
329A TYR* 2.7 71.9 + - + +
331A LEU* 3.6 32.5 - - + +
340A TRP* 1.3 76.1 - - - +
342A ARG* 1.3 59.6 + - - +
349A TRP* 4.0 8.9 - - + -
350A ALA 3.2 11.4 - - - +
351A VAL* 4.2 9.8 - - + +
371A SER 4.8 0.2 - - - +
372A LEU* 3.6 5.7 - - - +
373A GLY 2.7 31.4 + - - -
374A LYS* 4.0 8.8 + - - +
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Residues in contact with ARG 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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262A TRP* 5.2 0.6 - - - -
288A ALA 2.9 31.2 + - - -
289A ILE* 3.4 26.7 - - + +
291A ALA* 3.5 16.8 - - - +
319A ILE* 2.9 21.0 + - - -
320A ASN* 3.2 19.8 + - - +
322A ASP* 3.8 15.3 + - - +
325A GLY* 3.7 28.1 - - - +
326A LYS 2.7 26.9 + - - +
328A GLY* 3.6 11.7 - - - +
341A GLU* 1.3 75.9 - - - +
343A PRO* 1.3 69.4 + - - +
344A LEU* 3.5 16.0 + - + +
349A TRP* 3.4 6.9 - - - -
350A ALA* 2.8 37.3 + - + +
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Residues in contact with PRO 343 (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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322A ASP* 4.4 2.8 - - - +
324A LEU* 4.6 2.4 - - + +
326A LYS* 3.8 47.4 - - + +
327A GLN 4.3 4.9 - - - +
329A TYR* 4.3 15.9 - - + -
342A ARG* 1.3 98.3 + - + +
344A LEU* 1.3 64.4 + - - +
348A ALA 4.2 0.2 - - - +
349A TRP* 3.4 40.8 - - + -
374A LYS* 5.6 1.8 - - - +
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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