Contacts of the helix formed by residues 343 - 354 (chain A) in PDB entry 2V40
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 343 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341A LEU* 3.6 15.9 - - + -
342A ASP* 1.3 71.4 - - - +
344A VAL* 1.3 60.0 + - - +
346A LEU* 3.4 26.0 - - + -
347A LYS* 3.0 28.9 + - - +
374A VAL* 3.4 24.9 - - + -
375A GLY 2.8 15.2 + - - +
376A VAL* 4.5 6.7 - - + -
431A PHE* 3.7 24.0 - - + -
432A ILE* 4.4 11.2 - - + -
435A GLU* 3.7 24.7 - - + +
436A LEU* 3.8 22.7 - - + +
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Residues in contact with VAL 344 (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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342A ASP* 2.9 7.4 + - - +
343A LEU* 1.3 77.1 - - - +
345A LEU* 1.3 58.9 + - - +
347A LYS* 3.4 6.2 + - - +
348A TYR* 3.1 26.0 + - - +
375A GLY 4.1 1.1 - - - +
376A VAL* 3.4 12.3 - - - +
377A ALA* 3.4 34.8 - - - +
378A TYR* 3.7 32.5 - - + +
385A ILE 5.9 2.0 - - - +
386A PRO 5.8 3.8 - - - +
387A HIS 5.1 3.1 - - - +
388A ILE* 3.6 21.0 - - + +
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Residues in contact with LEU 345 (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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36A ALA 5.0 0.6 - - - +
38A TRP* 3.6 34.5 - - + -
258A LEU* 3.9 29.7 - - + +
265A THR* 6.0 2.0 - - + -
310A PRO* 4.1 8.5 - - + -
342A ASP* 3.0 24.3 + - + +
344A VAL* 1.3 76.1 - - - +
346A LEU* 1.3 59.0 + - - +
348A TYR* 3.4 8.0 - - + +
349A ALA* 3.0 27.9 + - - +
378A TYR* 3.2 24.7 - - - +
388A ILE* 3.6 35.9 - - + -
395A LEU* 5.3 5.2 - - + -
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Residues in contact with LEU 346 (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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36A ALA* 3.8 19.7 - - + +
37A GLN* 4.0 14.4 - - + +
297A VAL* 3.6 36.3 - - + -
341A LEU* 3.3 34.5 - - + -
342A ASP 3.1 15.9 + - - +
343A LEU* 3.4 24.5 - - + +
344A VAL 3.3 0.2 - - - -
345A LEU* 1.3 75.0 - - - +
347A LYS* 1.3 65.0 + - - +
349A ALA* 3.2 5.4 + - - +
350A HIS* 2.9 22.7 + - - +
355A PHE* 4.5 4.7 - - + -
432A ILE* 5.6 0.2 - - + -
436A LEU* 4.1 17.6 - - + +
438A ILE* 5.6 0.2 - - - +
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Residues in contact with LYS 347 (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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343A LEU 3.0 17.7 + - - +
344A VAL* 3.7 6.3 - - - +
346A LEU* 1.3 75.7 - - - +
348A TYR* 1.3 58.1 + - - +
350A HIS* 3.2 23.0 + - + +
351A MET* 2.9 56.0 + - + +
435A GLU 5.2 6.3 + - - +
436A LEU* 3.8 24.9 + - + +
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Residues in contact with TYR 348 (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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257A ALA 5.8 0.2 - - - -
258A LEU* 4.0 23.8 - - + -
263A PHE* 2.7 45.7 + + + +
344A VAL 3.1 9.2 + - - +
345A LEU* 3.4 9.9 - - + +
347A LYS* 1.3 76.9 - - - +
349A ALA* 1.3 64.5 + - - +
351A MET* 3.1 31.8 + - + +
352A ILE* 3.3 35.6 + - + +
388A ILE* 3.4 47.6 - - + -
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Residues in contact with ALA 349 (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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36A ALA* 3.7 23.8 - - + +
257A ALA* 3.8 18.4 - - + -
258A LEU* 4.9 2.5 - - + -
345A LEU 3.0 13.6 + - - +
346A LEU* 3.7 8.3 - - - +
348A TYR* 1.3 80.1 - - - +
350A HIS* 1.3 56.8 + - - +
352A ILE* 3.4 6.7 + - - +
353A ASN* 2.8 34.2 + - - +
355A PHE* 3.9 14.1 - - + -
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Residues in contact with HIS 350 (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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346A LEU 2.9 13.0 + - - +
347A LYS* 3.4 25.1 - - + +
349A ALA* 1.3 76.0 - - - +
351A MET* 1.3 61.9 + - - +
352A ILE 3.2 0.4 - - - -
353A ASN 4.3 0.7 - - - +
354A GLY* 2.9 33.5 + - - -
355A PHE* 3.0 59.3 + - + -
436A LEU 4.2 9.9 + - - -
437A GLN 5.0 2.8 + - - -
438A ILE* 3.4 34.4 - - + +
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Residues in contact with MET 351 (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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347A LYS* 2.9 53.5 + - + +
348A TYR* 3.1 22.0 + - + +
350A HIS* 1.3 75.2 - - - +
352A ILE* 1.3 63.3 + - + +
354A GLY* 4.6 1.0 + - - -
386A PRO 5.1 9.9 - - - +
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Residues in contact with ILE 352 (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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257A ALA* 6.1 1.6 - - + +
263A PHE* 3.6 43.3 - - + -
275A THR* 3.7 35.0 - - + +
276A VAL* 3.6 12.3 - - + +
277A GLY 6.2 0.2 - - - +
348A TYR* 3.3 51.4 + - + +
349A ALA* 3.7 7.6 - - - +
350A HIS 3.2 0.4 - - - -
351A MET* 1.3 83.9 - - + +
353A ASN* 1.3 61.6 + - - +
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Residues in contact with ASN 353 (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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34A LEU* 3.7 17.9 - - + +
35A GLY 5.0 0.2 + - - -
257A ALA* 3.9 21.0 - - - +
274A CYS 5.3 0.4 + - - -
275A THR* 3.2 16.5 - - - +
276A VAL* 2.8 49.5 + - - +
293A VAL* 3.9 7.3 - - - +
349A ALA 2.8 20.4 + - - +
352A ILE* 1.3 74.5 - - - +
354A GLY* 1.3 65.8 + - - +
355A PHE* 3.4 37.8 - - + -
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Residues in contact with GLY 354 (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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293A VAL* 4.1 5.7 - - - +
350A HIS* 2.9 24.5 + - - -
351A MET 4.6 1.0 + - - -
352A ILE 3.6 1.4 + - - -
353A ASN* 1.3 78.2 - - - +
355A PHE* 1.3 67.4 + - - +
356A THR* 3.4 10.4 + - - +
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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