Contacts of the strand formed by residues 340 - 345 (chain A) in PDB entry 7ENL
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 ASP 340 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A PHE* 3.5 26.4 - - + -
315A ILE 4.2 7.0 - - - +
316A GLN* 3.3 9.0 - - - +
317A ILE 2.9 31.9 + - - -
339A ALA* 1.3 77.7 - - - +
341A ALA* 1.3 61.1 - - - +
366A GLY 5.5 1.6 - - - +
367A TRP* 3.3 22.5 - - + -
368A GLY 3.2 9.0 + - - -
431A HIS* 3.1 34.5 + - + -
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Residues in contact with ALA 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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316A GLN* 3.6 33.2 - - + +
317A ILE 2.8 8.9 + - - +
318A VAL* 4.0 9.9 - - + -
319A ALA* 2.8 35.4 + - - +
340A ASP* 1.3 82.4 - - - +
342A LEU* 1.3 56.7 - - - +
367A TRP* 3.8 8.1 - - - -
368A GLY 3.6 15.7 - - - +
369A VAL* 4.6 1.1 - - - +
370A MET* 5.3 1.1 - - + +
394A GLN* 4.7 1.3 - - - +
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Residues in contact with LEU 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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318A VAL* 4.4 3.1 - - - -
319A ALA 3.7 2.5 - - - -
323A THR* 3.7 24.5 - - + +
325A THR* 4.4 8.1 - - + -
330A ILE* 3.6 26.5 - - + -
341A ALA* 1.3 73.7 - - - +
343A LEU* 1.3 69.4 - - - +
344A LEU* 3.5 17.8 + - + -
358A ALA* 3.8 17.9 - - + +
359A ALA* 4.3 2.0 - - - -
362A SER* 3.4 26.9 - - - +
367A TRP* 4.0 5.2 - - + -
368A GLY 3.3 9.4 + - - +
369A VAL* 3.4 14.2 - - + -
370A MET 2.9 26.0 + - - +
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Residues in contact with LEU 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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295A GLU* 3.2 19.7 - - - +
318A VAL* 4.1 8.2 - - + +
319A ALA 3.0 18.5 + - - +
320A ASP* 3.3 13.9 - - + -
323A THR* 5.1 0.2 + - - -
325A THR* 3.6 11.8 + - - -
342A LEU* 1.3 77.5 - - - +
344A LEU* 1.3 63.0 + - - +
345A LYS* 3.3 28.1 + - - +
348A GLN* 4.3 2.6 + - - -
370A MET* 3.4 23.1 - - + +
372A SER* 3.5 22.9 - - - +
396A LYS* 3.9 17.3 - - + -
439A 2PG 3.2 26.2 - - - +
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Residues in contact with LEU 344 (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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325A THR* 4.1 15.9 - - + -
342A LEU* 3.5 8.9 + - + -
343A LEU* 1.3 73.0 - - - +
345A LYS* 1.3 63.0 - - - +
346A VAL* 3.8 28.5 - - + +
355A SER* 3.8 17.0 - - - +
359A ALA* 3.4 32.3 - - + -
369A VAL* 3.6 22.9 - - + -
370A MET 2.8 9.5 + - - +
371A VAL* 3.8 6.1 - - + +
372A SER* 2.7 34.3 + - - +
386A LEU* 4.1 14.8 - - + -
390A LEU* 4.1 11.2 - - + -
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Residues in contact with LYS 345 (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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320A ASP* 2.8 30.2 + - - +
321A ASP* 4.8 1.6 + - - -
325A THR* 3.2 10.3 + - - +
343A LEU* 3.3 19.7 + - + +
344A LEU* 1.3 80.2 - - - +
346A VAL* 1.3 57.2 + - - +
347A ASN* 3.3 7.9 - - - +
348A GLN* 3.0 48.5 + - + +
372A SER* 4.3 10.5 - - - -
373A HIS 3.8 2.5 - - - +
374A ARG* 3.3 31.8 - - - +
439A 2PG 3.2 50.7 + - - -
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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