Contacts of the strand formed by residues 368 - 372 (chain A) in PDB entry 5E3H
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 368 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277A ILE* 4.4 11.7 - - + -
278A CYS* 4.4 3.6 - - - -
281A HIS* 3.7 37.0 - - + +
292A LYS 3.3 2.6 + - - +
293A VAL* 3.5 28.8 - - + -
294A VAL* 3.1 29.0 + - - +
366A PHE* 3.4 1.7 - - - +
367A THR* 1.3 82.1 + - - +
369A MET* 1.3 67.2 + - - +
370A ILE* 4.1 15.0 - - + -
403A PRO* 3.9 0.4 - - - +
404A GLN* 3.4 33.9 - - + +
406A ILE* 3.7 26.2 - - + -
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Residues in contact with MET 369 (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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294A VAL* 3.5 20.2 - - + -
296A PHE* 3.9 25.1 - - + -
363A LEU* 4.3 18.4 - - + -
366A PHE* 4.3 9.6 - - + -
368A LEU* 1.3 75.9 - - - +
370A ILE* 1.3 58.0 + - - +
371A PHE* 3.8 21.8 - - + -
386A ILE* 4.4 4.0 - - + -
387A MET* 3.9 12.8 - - - -
390A TYR* 4.2 7.4 - - + -
403A PRO* 3.8 25.6 - - + -
404A GLN 2.8 11.4 + - - +
405A VAL* 3.4 19.6 - - + +
406A ILE* 2.8 33.8 + - - +
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Residues in contact with ILE 370 (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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274A SER* 4.1 28.7 - - - +
277A ILE* 5.0 4.3 - - + -
278A CYS* 4.5 4.3 - - + +
293A VAL* 4.1 21.5 - - + -
294A VAL 3.0 10.7 + - - +
295A PHE* 3.7 31.3 - - + -
296A PHE* 2.9 32.3 + - - +
310A PHE* 5.4 0.9 - - + -
368A LEU* 4.1 19.7 - - + -
369A MET* 1.3 76.2 - - - +
371A PHE* 1.3 60.9 + - - +
372A ASP 3.7 0.3 + - - -
406A ILE* 3.7 17.9 - - + -
408A LEU* 4.0 22.7 - - + -
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Residues in contact with PHE 371 (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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296A PHE* 3.9 24.9 - + - -
369A MET* 3.8 26.2 - - + -
370A ILE* 1.3 75.4 - - - +
372A ASP* 1.3 62.0 + - - +
374A CYS* 3.6 19.2 - - + +
377A THR* 4.4 2.9 - - - -
383A TYR* 3.5 56.1 - + + -
386A ILE* 4.2 11.7 - - + -
387A MET* 3.8 21.5 - - + -
405A VAL* 3.9 15.5 - - + -
406A ILE 3.0 22.0 + - - +
407A GLY* 3.3 1.4 - - - -
408A LEU* 2.9 27.4 + - - +
434A LEU* 4.1 6.5 - - + -
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Residues in contact with ASP 372 (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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270A LYS* 5.6 0.3 + - - -
295A PHE* 3.8 21.1 - - + -
296A PHE 3.3 23.6 + - - +
297A ALA* 4.8 3.1 - - - +
298A ASN* 4.7 1.9 - - - +
302A VAL* 3.9 20.2 - - - +
306A GLN* 6.1 0.9 - - - -
370A ILE* 3.7 1.8 + - - +
371A PHE* 1.3 68.8 - - - +
373A GLU* 1.3 91.8 + - - +
383A TYR* 2.7 25.0 + - - +
408A LEU* 3.8 21.2 - - - +
1003A MG 3.2 23.2 - - - -
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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