Contacts of the helix formed by residues 333 - 342 (chain A) in PDB entry 3CVW
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 HIS 333 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331A GLN* 3.7 3.5 + - + +
332A GLU* 1.3 79.9 + - - +
334A PRO* 1.4 65.5 - - + +
335A ASP* 3.2 19.6 - - + +
336A HIS* 3.1 57.3 + + + +
337A LEU* 2.9 27.7 + - - +
380A LEU 5.5 2.5 - - - +
382A ILE* 4.0 14.9 - - + +
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Residues in contact with PRO 334 (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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332A GLU* 4.1 17.7 - - + +
333A HIS* 1.4 87.0 - - + +
335A ASP* 1.3 59.5 - - - +
337A LEU* 3.6 13.9 - - + +
338A GLU* 2.9 32.7 + - - +
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Residues in contact with ASP 335 (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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333A HIS* 3.2 18.9 - - + +
334A PRO* 1.3 81.5 - - - +
336A HIS* 1.3 63.9 + - + +
338A GLU* 4.0 5.2 - - - +
339A ALA* 3.4 22.7 + - - +
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Residues in contact with HIS 336 (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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333A HIS* 3.1 44.4 + + + +
335A ASP* 1.3 81.1 - - + +
337A LEU* 1.3 61.9 + - - +
339A ALA* 4.0 2.3 - - - +
340A TRP* 3.4 14.9 + - - +
380A LEU* 3.6 36.7 + - + +
382A ILE* 3.9 9.6 - - + -
480A ILE* 3.5 48.9 + - + +
481A VAL* 3.8 19.5 - - + +
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Residues in contact with LEU 337 (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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333A HIS 2.9 15.2 + - - +
334A PRO* 3.6 12.6 - - + +
335A ASP 3.2 0.4 - - - -
336A HIS* 1.3 76.1 - - - +
338A GLU* 1.3 56.8 + - - +
339A ALA 3.2 0.4 - - - -
340A TRP* 3.3 6.9 + - + +
341A THR* 2.6 45.4 + - - +
375A LEU* 4.2 11.2 - - + -
382A ILE* 3.9 19.5 - - + +
386A GLU* 3.3 50.9 - - + +
390A VAL* 5.5 2.0 - - + -
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Residues in contact with GLU 338 (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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334A PRO 2.9 17.5 + - - +
335A ASP* 4.0 5.2 - - - +
337A LEU* 1.3 76.3 - - - +
339A ALA* 1.3 61.4 + - - +
341A THR* 4.3 4.4 - - - -
342A HIS* 3.1 57.7 + - - +
344A ARG* 3.7 18.5 + - - +
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Residues in contact with ALA 339 (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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335A ASP 3.4 15.2 + - - +
336A HIS 4.0 5.2 - - - +
337A LEU 3.2 0.6 - - - -
338A GLU* 1.3 76.9 - - - +
340A TRP* 1.3 59.1 + - - +
342A HIS 3.5 0.9 + - - -
343A GLY 3.0 8.7 + - - -
344A ARG* 2.8 55.5 + - + +
345A THR* 3.8 2.4 + - - -
480A ILE* 4.1 22.9 - - + -
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Residues in contact with TRP 340 (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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336A HIS 3.4 15.0 + - - +
337A LEU* 3.3 6.2 + - + +
339A ALA* 1.3 76.0 - - - +
341A THR* 1.3 75.9 + - - +
342A HIS 3.3 0.7 + - - -
343A GLY* 3.3 8.3 + - - -
345A THR* 3.7 9.4 - - + +
350A ILE* 4.3 9.4 - - + +
354A MET* 3.4 34.1 - - + +
371A VAL* 3.2 39.2 + - + +
374A PHE* 4.0 23.8 - + - -
375A LEU* 3.6 24.6 - - + +
380A LEU* 4.0 8.5 - - + -
387A GLY* 3.7 11.9 - - - -
390A VAL* 3.6 30.5 - - + -
391A PHE* 3.8 15.7 - + - -
407A TRP* 3.7 28.5 - + - -
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Residues in contact with THR 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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337A LEU* 2.6 30.0 + - - +
338A GLU* 3.9 3.2 - - - -
339A ALA 3.4 0.2 - - - -
340A TRP* 1.3 85.5 - - - +
342A HIS* 1.3 74.3 + - + +
354A MET* 3.9 15.1 - - - +
358A ARG* 3.5 31.5 + - - +
390A VAL* 3.8 32.6 - - + +
393A GLN* 6.1 2.0 - - - +
394A LEU* 4.8 1.7 - - - +
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Residues in contact with HIS 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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338A GLU* 3.1 53.1 + - - +
340A TRP 3.2 0.2 - - - -
341A THR* 1.3 91.4 - - + +
343A GLY* 1.3 64.8 + - - +
344A ARG* 3.6 24.7 - - - +
354A MET* 4.9 2.7 - - - -
355A ARG* 4.2 13.1 + - - +
358A ARG* 3.7 37.4 + - - +
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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