Contacts of the helix formed by residues 422 - 437 (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 PRO 422 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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408A TRP* 3.6 29.2 - - + +
410A THR* 3.5 24.7 - - + +
412A ILE* 3.7 18.8 - - + -
420A GLU 3.7 4.4 - - - +
421A LEU* 1.4 86.9 - - + +
423A VAL* 1.3 66.6 + - - +
424A ASN 4.5 0.7 - - - +
425A ALA* 3.1 9.6 + - + -
426A GLN* 3.0 18.7 + - - +
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Residues in contact with VAL 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A LEU 3.7 0.8 + - - -
422A PRO* 1.3 71.9 - - - +
424A ASN* 1.3 63.8 + - - +
426A GLN* 3.3 16.4 + - - +
427A ASN* 2.8 48.3 + - - +
430A ARG* 5.3 1.8 - - - +
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Residues in contact with ASN 424 (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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406A PRO* 3.5 44.0 - - + +
407A GLY 2.9 27.7 + - - +
408A TRP* 3.5 11.1 - - - +
422A PRO* 3.3 2.6 - - - +
423A VAL* 1.3 83.3 - - - +
425A ALA* 1.3 60.0 + - - +
427A ASN* 3.5 13.4 + - - +
428A TYR* 3.0 26.7 + - - +
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Residues in contact with ALA 425 (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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363A LEU* 4.4 11.5 - - + +
408A TRP* 3.3 40.8 - - + +
412A ILE* 4.8 0.4 - - + -
421A LEU* 4.3 9.6 - - + -
422A PRO* 3.1 25.6 + - + +
424A ASN* 1.3 73.9 - - - +
426A GLN* 1.3 65.3 + - - +
428A TYR* 3.2 4.2 + - - +
429A VAL* 3.2 26.4 + - - +
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Residues in contact with GLN 426 (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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418A PHE* 2.9 58.5 + - + -
419A LYS* 3.8 10.1 + - - +
421A LEU* 3.5 23.3 + - + +
422A PRO 3.0 14.7 + - - +
423A VAL* 3.5 16.2 - - - +
425A ALA* 1.3 75.1 - - - +
427A ASN* 1.3 59.6 + - - +
429A VAL* 3.2 6.1 + - - +
430A ARG* 2.9 53.4 + - - +
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Residues in contact with ASN 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A LEU* 5.1 4.7 - - + +
406A PRO* 6.5 0.9 - - + -
423A VAL* 2.8 34.4 + - - +
424A ASN* 3.9 13.1 + - - +
425A ALA 3.2 0.4 - - - -
426A GLN* 1.3 73.3 - - - +
428A TYR* 1.3 59.5 + - - +
430A ARG* 3.0 34.4 + - - +
431A PHE* 2.9 30.8 + - - +
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Residues in contact with TYR 428 (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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299A ALA* 2.6 30.6 + - + -
341A LEU* 3.6 17.8 + - + +
360A LEU* 4.5 1.3 - - + -
363A LEU* 3.6 22.7 - - + -
366A LEU* 3.6 18.8 - - + +
372A ILE* 3.5 37.1 - - + +
374A VAL* 3.6 17.3 - - + +
405A LEU* 3.6 23.8 - - + -
408A TRP* 3.9 10.5 - + + -
424A ASN 3.0 14.9 + - - +
425A ALA 3.2 8.9 + - - +
427A ASN* 1.3 75.0 - - - +
429A VAL* 1.3 63.8 + - - +
431A PHE* 3.4 3.6 + - - +
432A ILE* 3.3 45.1 + - + +
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Residues in contact with VAL 429 (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 LEU* 3.9 23.1 - - + -
363A LEU* 4.0 11.4 - - + -
418A PHE* 4.0 19.7 - - + -
421A LEU* 5.0 0.2 - - + -
425A ALA 3.2 14.3 + - - +
426A GLN 3.4 7.0 - - - +
428A TYR* 1.3 77.2 - - - +
430A ARG* 1.3 60.9 + - - +
432A ILE* 3.3 6.9 + - - +
433A GLU* 3.1 27.0 + - - +
440A VAL* 4.0 29.5 - - + +
443A ILE* 3.9 23.6 - - + -
455A LEU* 5.2 2.2 - - + -
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Residues in contact with ARG 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A PHE* 3.9 24.2 - - + -
423A VAL* 5.0 3.0 + - - +
426A GLN* 2.9 43.1 + - - +
427A ASN* 3.0 30.5 + - - +
429A VAL* 1.3 72.5 - - - +
431A PHE* 1.3 60.6 + - - +
433A GLU* 3.5 18.0 - - - +
434A ASP* 2.8 46.1 + - - +
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Residues in contact with PHE 431 (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* 3.7 26.0 - - + -
374A VAL* 4.2 14.1 - - + -
376A VAL* 3.7 16.8 - - + -
403A LYS* 3.7 37.9 - - + -
405A LEU* 4.0 27.6 - - + -
427A ASN 2.9 17.6 + - - +
428A TYR 3.6 5.8 - - - +
429A VAL 3.3 0.2 - - - -
430A ARG* 1.3 77.2 - - - +
432A ILE* 1.3 60.6 + - + +
434A ASP* 3.7 6.5 - - + +
435A GLU* 2.8 58.8 + - + +
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Residues in contact with ILE 432 (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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297A VAL* 5.7 2.0 - - + -
341A LEU* 3.6 31.0 - - + -
343A LEU* 4.4 16.2 - - + -
346A LEU* 5.6 2.0 - - + -
358A LEU* 4.1 15.7 - - + -
360A LEU* 3.8 29.4 - - + -
374A VAL* 6.0 0.2 - - + -
428A TYR* 3.5 33.2 - - + +
429A VAL 3.3 7.0 + - - +
431A PHE* 1.3 78.4 - - + +
433A GLU* 1.3 63.5 + - - +
435A GLU* 3.9 0.3 - - - -
436A LEU* 3.0 46.6 + - + +
440A VAL* 4.9 5.4 - - + -
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Residues in contact with GLU 433 (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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418A PHE* 6.0 0.3 - - - -
429A VAL* 3.1 20.0 + - - +
430A ARG* 3.3 25.1 + - - +
432A ILE* 1.3 76.7 - - - +
434A ASP* 1.3 56.8 + - - +
437A GLN* 2.8 36.0 + - - -
438A ILE 3.5 18.6 + - - +
439A PRO* 3.5 8.9 - - + +
440A VAL* 2.8 47.1 + - + +
455A LEU* 5.0 4.8 - - - +
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Residues in contact with ASP 434 (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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430A ARG* 2.8 36.3 + - - +
431A PHE* 3.7 8.6 + - + +
433A GLU* 1.3 74.2 - - - +
435A GLU* 1.3 69.2 + - + +
437A GLN* 2.8 29.1 + - - +
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Residues in contact with GLU 435 (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* 3.7 20.3 - - + +
347A LYS* 5.2 6.9 + - - +
376A VAL* 4.2 18.3 - - - +
431A PHE* 2.8 54.8 + - + +
432A ILE 4.0 1.1 - - - +
434A ASP* 1.3 81.6 - - + +
436A LEU* 1.3 63.4 + - + +
437A GLN* 5.0 1.6 - - - +
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Residues in contact with LEU 436 (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* 3.8 24.0 - - + +
346A LEU* 4.1 20.6 - - + -
347A LYS* 3.8 44.1 + - + +
350A HIS* 4.2 9.5 + - - -
358A LEU* 3.8 17.7 - - + -
432A ILE* 3.0 36.6 + - + +
435A GLU* 1.3 79.4 - - + +
437A GLN* 1.3 69.9 + - - +
438A ILE* 3.4 30.0 + - + +
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Residues in contact with GLN 437 (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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350A HIS* 5.0 2.8 + - - -
433A GLU 2.8 13.2 + - - -
434A ASP* 2.8 36.7 + - - +
435A GLU 5.0 1.6 - - - +
436A LEU* 1.3 81.1 - - - +
438A ILE* 1.3 58.2 + - - +
439A PRO* 4.6 2.5 - - - +
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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