Contacts of the strand formed by residues 372 - 379 (chain A) in PDB entry 3CL0
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 SER 372 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365A THR* 3.5 1.8 - - - -
366A LYS 3.0 20.4 + - - -
367A SER* 3.1 24.9 + - - -
370A SER* 2.9 19.7 + - - -
371A ARG* 1.3 70.3 - - - +
373A GLY* 1.3 62.4 + - - +
400A ILE* 3.4 21.7 + - - -
402A ASP 3.4 7.7 + - - -
403A TRP* 3.4 21.3 - - - -
404A SER* 3.6 0.4 + - - -
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Residues in contact with GLY 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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365A THR* 3.4 7.1 - - - -
366A LYS* 3.6 7.6 - - - -
372A SER* 1.3 75.4 - - - +
374A PHE* 1.3 63.4 + - - +
398A VAL* 3.2 19.3 - - - -
399A ALA 3.3 15.4 + - - -
400A ILE 4.0 2.0 - - - -
402A ASP 2.8 14.2 + - - -
404A SER* 2.7 26.3 + - - -
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Residues in contact with PHE 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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352A PHE* 3.7 2.2 - + - -
363A GLY* 3.6 19.5 - - - -
364A ARG* 3.4 35.7 - - - -
365A THR* 4.0 5.2 - - + -
366A LYS* 3.6 7.3 - - - +
373A GLY* 1.3 77.8 - - - +
375A GLU* 1.3 73.7 + - - +
376A MET* 4.1 2.0 - - - -
396A ASP* 4.1 0.2 - - - -
397A ILE* 2.9 38.6 + - + -
398A VAL* 2.7 31.3 + - + +
404A SER* 4.6 5.8 - - - -
405A GLY 5.0 4.5 - - - -
407A SER* 3.3 37.2 - - - -
422A PHE* 3.8 21.3 - + - -
424A VAL* 3.9 21.8 - - + -
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Residues in contact with GLU 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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327A ARG* 4.7 0.3 + - - -
362A ILE 3.5 3.1 - - - +
363A GLY* 3.6 2.9 - - - -
364A ARG* 2.9 74.2 + - + +
365A THR 4.1 3.6 - - - +
366A LYS* 2.8 45.0 + - + +
374A PHE* 1.3 81.5 - - - +
376A MET* 1.3 61.5 + - - +
377A ILE* 3.4 13.6 - - + +
394A LYS* 2.8 30.2 - - + -
395A GLN 3.4 11.2 - - - +
397A ILE* 4.3 1.1 - - - -
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Residues in contact with MET 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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97A TRP* 3.7 50.3 - - + +
352A PHE* 3.7 23.6 - - + -
361A TRP* 3.9 16.3 - - + -
362A ILE 3.5 3.6 - - - +
363A GLY* 3.6 27.8 - - - +
374A PHE* 4.1 2.9 - - - -
375A GLU* 1.3 73.2 - - - +
377A ILE* 1.3 60.5 + - - +
392A VAL 3.9 1.2 - - - +
394A LYS* 3.4 6.2 - - - +
395A GLN* 2.8 35.9 + - + +
397A ILE* 3.5 21.1 - - + -
422A PHE* 3.6 24.2 - - + -
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Residues in contact with ILE 377 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321A VAL* 3.9 15.7 - - + -
360A VAL 3.4 2.1 - - - +
361A TRP* 3.2 8.3 - - - -
362A ILE* 2.8 46.0 + - + +
364A ARG* 3.5 27.4 - - + +
375A GLU* 3.4 31.0 - - + +
376A MET* 1.3 79.7 - - - +
378A TRP* 1.3 62.2 + - - +
379A ASP* 4.4 4.9 - - + +
390A PHE* 3.7 36.1 - - + -
392A VAL 3.2 4.9 - - - +
394A LYS* 4.2 19.7 - - + +
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Residues in contact with TRP 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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356A TYR* 3.9 29.8 - + + -
359A GLY* 4.0 12.8 - - - -
360A VAL 3.5 29.4 - - - -
361A TRP* 3.6 48.0 - + + -
377A ILE* 1.3 71.8 - - - +
379A ASP* 1.3 59.5 + - - +
380A PRO* 3.5 28.7 - - + +
390A PHE* 3.4 3.5 - - - +
391A SER* 3.0 51.4 + - - -
392A VAL* 2.8 25.4 + - + -
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Residues in contact with ASP 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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319A SER* 2.7 26.9 + - - +
321A VAL* 4.1 2.5 - - + +
360A VAL* 2.8 47.2 + - + +
362A ILE* 4.6 7.0 - - + -
377A ILE* 3.8 2.6 + - + -
378A TRP* 1.3 75.1 - - - +
380A PRO* 1.3 60.7 - - - +
381A ASN* 2.7 33.4 + - - -
382A GLY* 3.1 14.9 + - - -
387A ASP 4.3 3.5 - - - +
389A SER 3.1 23.0 - - - +
390A PHE* 4.2 7.0 - - + -
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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