Contacts of the helix formed by residues 371 - 383 (chain B) in PDB entry 1V40
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 371 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325B PRO* 4.6 6.7 - - + -
328B MET* 3.7 22.2 - - + +
329B GLN* 3.7 30.1 + - + +
332B ASP* 2.9 39.0 - - + +
367B LEU 3.9 16.9 + - - -
368B LEU* 3.0 13.5 + - - +
370B ASN* 1.3 98.6 + - + +
372B PRO* 1.3 65.9 - - - +
373B ARG 3.1 3.1 - - - -
374B LEU* 3.0 32.0 + - + +
375B VAL* 3.4 10.6 + - - +
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Residues in contact with PRO 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B ASP* 5.2 0.9 - - - +
368B LEU 4.0 1.3 - - - +
369B ASP 4.5 6.7 - - - +
370B ASN 3.5 7.9 - - - +
371B HIS* 1.3 87.6 - - - +
373B ARG* 1.3 64.4 + - + +
375B VAL* 3.2 13.3 + - + +
376B THR* 2.9 32.0 + - - +
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Residues in contact with ARG 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329B GLN* 6.1 0.2 - - - +
332B ASP* 2.6 51.4 + - - +
333B THR* 4.5 4.0 - - - +
335B LEU* 3.8 16.3 - - + +
336B GLY* 3.4 35.6 + - - +
337B GLY* 3.9 7.9 - - - +
371B HIS 3.1 1.4 + - - -
372B PRO* 1.3 84.8 - - + +
374B LEU* 1.3 57.7 + - - +
376B THR* 3.3 9.5 + - - -
377B LEU* 3.1 25.5 + - - +
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Residues in contact with LEU 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B MET* 3.5 32.1 - - + +
331B LEU* 4.2 11.7 - - + +
332B ASP* 4.0 21.1 - - + +
335B LEU* 4.0 19.7 - - + -
341B LEU* 5.5 2.9 - - + -
353B TRP* 3.2 48.0 + - + +
368B LEU* 4.3 5.4 - - + -
371B HIS* 3.0 28.4 + - + +
373B ARG* 1.3 74.7 - - - +
375B VAL* 1.3 63.9 + - - +
377B LEU* 3.6 5.3 + - + +
378B ARG* 3.2 21.1 + - - +
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Residues in contact with VAL 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B LEU* 3.6 38.8 - - + +
371B HIS 3.7 7.4 - - - +
372B PRO* 3.2 12.7 + - + +
374B LEU* 1.3 77.5 - - - +
376B THR* 1.3 65.8 + - - +
378B ARG* 3.1 14.5 + - - +
379B LYS* 3.0 41.9 + - + +
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Residues in contact with THR 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B PRO* 2.9 18.1 + - - +
373B ARG* 3.6 12.4 - - - -
375B VAL* 1.3 77.3 - - - +
377B LEU* 1.3 56.3 + - - +
379B LYS* 3.3 10.7 + - + +
380B LYS* 2.9 41.7 + - + +
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Residues in contact with LEU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B LEU* 4.0 19.5 - - + -
339B GLU 3.6 23.1 - - - +
340B TRP* 3.9 15.0 - - + -
341B LEU* 3.6 29.8 - - + -
350B ASP* 3.7 19.5 - - + +
353B TRP* 3.5 25.4 - - + +
373B ARG 3.1 13.6 + - - +
374B LEU* 3.6 10.8 - - + +
375B VAL 3.2 0.2 - - - -
376B THR* 1.3 73.8 - - - +
378B ARG* 1.3 66.2 + - - +
380B LYS* 3.1 7.3 + - + +
381B VAL* 3.1 23.7 + - + +
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Residues in contact with ARG 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B TRP* 3.6 11.2 - - + +
354B GLU* 3.2 18.3 + - + +
357B SER* 2.7 39.4 + - - +
358B THR* 3.2 29.3 + - - +
361B LEU* 3.2 25.1 - - - +
368B LEU* 3.4 28.3 - - - +
374B LEU 3.2 12.1 + - - +
375B VAL* 3.1 13.7 + - + +
377B LEU* 1.3 78.0 - - - +
379B LYS* 1.3 57.6 + - + +
381B VAL* 3.2 5.3 + - - +
382B GLN* 2.9 53.1 + - - +
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Residues in contact with LYS 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375B VAL* 3.0 31.4 + - + +
376B THR* 3.6 12.3 - - + +
378B ARG* 1.3 74.7 - - + +
380B LYS* 1.3 66.3 + - + +
382B GLN* 3.2 17.1 + - - +
383B ALA* 2.9 26.2 + - - +
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Residues in contact with LYS 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B GLU* 3.3 56.9 + - + +
340B TRP* 3.5 32.6 - - + -
376B THR* 2.9 32.6 + - + +
377B LEU* 3.1 11.2 + - - +
379B LYS* 1.3 75.6 - - - +
381B VAL* 1.3 63.5 + - - +
383B ALA* 3.3 14.8 + - - +
384B ILE* 3.4 14.7 + - - +
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Residues in contact with VAL 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B TYR* 4.6 2.9 - - + -
340B TRP* 4.3 7.9 - - + -
350B ASP* 3.7 36.1 - - + +
351B PHE* 3.8 28.7 - - + +
353B TRP* 5.9 0.2 - - + -
354B GLU* 3.9 21.5 - - + -
377B LEU* 3.1 16.6 + - + +
378B ARG 3.5 6.5 - - - +
380B LYS* 1.3 77.0 - - - +
382B GLN* 1.3 61.7 + - - +
383B ALA 3.1 0.2 - - - -
384B ILE* 3.1 26.6 + - - +
387B VAL* 3.6 17.1 - - + +
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Residues in contact with GLN 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B GLU* 2.6 34.8 + - + +
358B THR* 4.5 0.8 + - - -
378B ARG* 2.9 41.7 + - - +
379B LYS* 3.6 20.2 - - - +
381B VAL* 1.3 75.1 - - - +
383B ALA* 1.3 57.1 + - - +
384B ILE 3.4 0.7 - - - -
387B VAL* 4.5 0.2 - - - -
388B ALA* 3.2 27.5 - - - +
391B ILE* 4.0 21.9 - - + +
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Residues in contact with ALA 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379B LYS 2.9 16.4 + - - +
380B LYS* 3.7 8.1 - - - +
381B VAL 3.1 0.6 - - - -
382B GLN* 1.3 76.4 - - - +
384B ILE* 1.3 65.2 + - - +
385B PRO* 3.1 11.6 - - - +
388B ALA* 4.5 4.3 - - - +
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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