Contacts of the strand formed by residues 370 - 379 (chain A) in PDB entry 5DST
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 370 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A TYR 4.9 1.8 - - - +
190A CYS* 5.0 2.2 - - + -
192A PHE* 4.0 13.9 - - + +
193A TYR* 3.6 40.2 - - + +
195A SER* 4.5 10.8 - - - +
360A MET* 3.9 22.9 - - + -
361A LYS 3.6 17.0 - - - +
362A PRO* 4.5 2.0 - - + -
368A ARG 4.6 0.4 - - - +
369A ASP* 1.3 80.9 - - - +
371A ASP* 1.3 66.0 - - - +
372A PHE* 3.7 32.2 - - + -
392A LYS* 3.4 4.7 - - - -
393A MET* 3.0 36.8 + - + +
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Residues in contact with ASP 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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360A MET* 3.1 27.5 - - - +
361A LYS* 3.0 35.4 + - + +
363A ASN* 3.3 43.1 + - - +
364A ALA 4.6 1.0 + - - -
369A ASP* 4.4 0.9 - - - +
370A LEU* 1.3 75.5 - - - +
372A PHE* 1.3 61.4 + - - +
391A TYR 3.7 4.3 - - - +
392A LYS* 3.6 21.3 + - + +
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Residues in contact with PHE 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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190A CYS* 3.9 24.5 - - + -
258A PRO* 4.9 0.2 - - + -
340A PHE* 3.9 30.1 - + + -
358A ILE* 4.3 16.4 - - + -
359A SER 3.2 8.5 - - - -
360A MET* 3.6 31.2 - - + -
370A LEU* 3.7 38.1 - - + -
371A ASP* 1.3 76.6 - - - +
373A THR* 1.3 70.4 + - - +
374A VAL* 5.0 2.2 - - + -
390A ASP* 3.5 5.2 - - - +
391A TYR* 2.9 48.4 + - + +
393A MET* 3.9 19.1 - - + -
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Residues in contact with THR 373 (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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357A THR* 3.7 2.1 + - - +
358A ILE* 3.4 3.1 - - - -
359A SER* 3.0 42.4 + - - +
372A PHE* 1.3 75.2 + - - +
374A VAL* 1.3 61.7 + - - +
375A ASP* 3.2 24.6 + - - +
388A SER* 3.8 8.3 - - - +
389A ASN 3.4 4.9 - - - +
390A ASP* 2.9 24.4 + - - +
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Residues in contact with VAL 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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294A PHE* 4.3 7.0 - - + -
307A LEU* 3.8 28.5 - - + -
340A PHE* 4.9 9.6 - - + -
342A LEU* 5.7 4.0 - - + -
357A THR 3.4 9.0 - - - +
358A ILE* 4.3 20.9 - - + -
372A PHE* 4.2 2.9 - - + -
373A THR* 1.3 76.3 - - - +
375A ASP* 1.3 70.4 + - - +
376A LEU* 4.0 9.0 + - + +
387A VAL 4.0 0.3 - - - +
388A SER* 3.6 0.7 - - - -
389A ASN* 3.0 32.5 + - + +
391A TYR* 3.8 30.5 - - + +
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Residues in contact with ASP 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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294A PHE* 3.8 2.9 - - - -
356A GLY* 3.0 6.4 - - - -
357A THR* 2.9 50.7 + - + +
373A THR* 3.2 16.3 + - - +
374A VAL* 1.3 73.2 - - - +
376A LEU* 1.3 58.3 - - - +
377A ASP* 5.0 3.6 - - - +
387A VAL 3.3 6.1 - - - +
388A SER* 2.7 30.9 + - - -
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Residues in contact with LEU 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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294A PHE* 4.6 2.0 - - + -
307A LEU* 4.4 22.4 - - + -
342A LEU* 4.3 29.4 - - + -
346A LEU* 4.0 22.9 - - + -
354A ILE* 3.6 27.6 - - + -
355A TYR 3.6 2.7 - - - +
356A GLY* 4.3 0.2 - - - -
374A VAL* 4.0 8.7 + - + +
375A ASP* 1.3 76.5 - - - +
377A ASP* 1.3 71.7 + - - +
378A PHE* 4.4 4.3 - - + +
385A THR* 4.4 10.5 - - - +
386A SER* 3.2 2.3 - - - -
387A VAL* 2.9 43.7 + - + +
389A ASN* 6.3 0.9 - - - +
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Residues in contact with ASP 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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353A GLU 4.4 0.7 - - - +
354A ILE* 3.9 1.0 - - - +
355A TYR* 2.7 48.5 + - + +
356A GLY* 4.6 1.8 - - - -
375A ASP* 4.3 3.7 - - - +
376A LEU* 1.3 81.3 + - - +
378A PHE* 1.3 62.9 + - - +
385A THR 3.6 3.1 - - - -
386A SER* 3.6 25.1 + - - -
387A VAL 4.6 1.2 + - - +
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Residues in contact with PHE 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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298A ILE* 4.1 3.4 - - + -
346A LEU* 4.4 12.3 - - + -
347A THR 3.9 13.9 - - - -
348A VAL* 3.7 22.7 - - + -
352A GLU* 3.5 35.0 - - + -
353A GLU 3.1 36.3 - - - -
354A ILE* 3.8 9.2 - - + -
355A TYR* 6.0 0.2 - - - -
376A LEU* 4.3 13.4 - - + -
377A ASP* 1.3 76.5 - - - +
379A LYS* 1.3 60.6 + - - +
380A GLY* 3.5 20.9 - - - -
383A CYS* 3.8 24.2 - - - -
384A GLU* 3.2 6.6 - - - +
385A THR* 2.9 34.9 + - - +
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Residues in contact with LYS 379 (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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352A GLU* 5.5 1.7 - - - +
353A GLU 4.8 2.2 + - - +
378A PHE* 1.3 77.0 - - - +
380A GLY* 1.3 62.8 + - - +
383A CYS 4.1 2.2 - - - -
384A GLU* 3.6 32.5 - - + +
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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