Contacts of the strand formed by residues 373 - 378 (chain A) in PDB entry 1R5M
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 373 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A PHE* 3.4 4.3 - - - -
368A ASN 2.9 25.7 + - - -
371A ASN* 2.9 38.3 + - + +
372A LYS* 1.3 81.8 - - - +
374A LEU* 1.3 60.0 + - - +
385A ILE* 3.8 18.6 - - + -
386A TRP 3.5 15.5 - - - +
387A HIS* 3.7 27.8 - - + +
394A GLN* 3.9 20.9 - - - +
409A TRP* 3.5 16.0 - - + -
412A ASP 5.3 0.7 - - - +
429A LEU* 3.9 11.9 - - + -
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Residues in contact with LEU 374 (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 GLU* 4.3 2.7 - - + -
327A VAL* 4.4 5.2 - - + -
333A VAL* 4.1 33.0 - - + -
341A ILE* 4.6 0.9 - - + -
355A LEU* 3.8 28.7 - - + -
365A LEU* 4.2 13.5 - - + -
366A GLU 3.7 22.0 - - - +
367A PHE* 4.0 18.3 - - + +
372A LYS 4.4 0.2 + - - -
373A LEU* 1.3 72.3 - - - +
375A LEU* 1.3 70.1 + - - +
385A ILE* 3.3 5.4 - - - +
386A TRP* 2.8 54.4 + - + +
409A TRP* 4.2 2.0 - - - -
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Residues in contact with LEU 375 (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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364A VAL* 3.8 1.9 - - + +
365A LEU* 3.4 4.0 - - - -
366A GLU* 2.8 50.3 + - + +
374A LEU* 1.3 74.4 - - - +
376A SER* 1.3 74.6 + - - +
383A LEU* 4.3 18.4 - - + -
384A ARG 3.5 3.1 - - - +
385A ILE* 3.7 18.8 - - + -
407A ALA* 4.0 14.1 - - + +
408A SER* 3.8 41.5 - - - +
409A TRP* 3.5 16.5 - - + +
415A VAL* 4.0 15.7 - - + -
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Residues in contact with SER 376 (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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341A ILE* 3.7 17.3 - - - -
358A HIS* 2.7 28.2 + - - -
362A ILE* 4.9 0.7 - - - -
364A VAL 3.1 10.3 - - - -
365A LEU* 3.7 5.4 - - - -
374A LEU 4.0 0.2 + - - -
375A LEU* 1.3 78.3 - - - +
377A ALA* 1.3 63.5 + - - +
383A LEU* 3.2 7.8 - - - +
384A ARG* 2.9 33.1 + - - +
386A TRP* 2.8 26.4 + - - -
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Residues in contact with ALA 377 (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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358A HIS* 4.3 1.6 - - - -
362A ILE* 3.6 8.0 - - - +
363A SER* 2.9 34.4 + - - +
364A VAL* 3.0 28.6 + - + -
376A SER* 1.3 73.7 - - - +
378A SER* 1.3 63.4 + - - +
382A THR 3.6 6.3 - - - -
383A LEU* 3.5 20.6 - - + -
404A ILE* 3.7 11.4 - - + -
407A ALA* 4.2 2.0 - - + -
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Residues in contact with SER 378 (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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358A HIS* 3.2 31.4 - - - -
360A GLY 3.0 14.2 + - - -
361A PRO 2.9 15.0 + - - -
362A ILE* 4.4 0.7 - - - -
363A SER* 3.8 6.1 - - - -
377A ALA* 1.3 76.6 - - - +
379A ASP* 1.3 72.3 + - - +
380A ASP* 2.9 23.2 + - - -
381A GLY* 3.1 11.6 + - - -
382A THR 3.2 7.1 + - - -
404A ILE* 3.6 15.3 + - - +
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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