Contacts of the helix formed by residues 407 - 416 (chain A) in PDB entry 2VWK
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 407 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A PHE 3.3 1.6 + - - -
406A ARG* 1.3 78.8 - - - +
408A LEU* 1.3 66.0 + - - +
409A TYR 3.2 2.8 + - - -
410A PRO* 3.5 21.2 - - - +
411A SER* 2.9 22.5 + - - -
457A LEU* 4.4 18.7 - - - +
460A ARG* 4.9 4.2 + - - -
490A ALA* 6.0 0.2 - - - +
491A ASN* 4.4 3.3 + - - -
1776A SO4 2.7 39.9 + - - -
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Residues in contact with LEU 408 (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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404A ASP* 5.7 0.7 - - - +
405A PHE* 3.8 40.9 + - + +
406A ARG 3.5 1.9 + - - -
407A SER* 1.3 74.7 - - - +
409A TYR* 1.3 86.6 + - + +
411A SER* 3.3 5.7 - - - -
412A ILE* 3.1 42.8 + - + +
517A GLY* 4.4 9.4 - - - +
520A TYR* 4.8 1.6 - - + -
521A ILE* 3.9 23.8 - - + -
541A THR 3.8 23.1 - - - +
575A LEU* 4.1 9.6 - - + -
1776A SO4 4.9 0.2 + - - -
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Residues in contact with TYR 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A LEU* 1.3 98.0 - - + +
410A PRO* 1.4 75.6 - - + +
412A ILE* 2.9 16.1 + - + +
413A ILE* 2.9 20.5 + - - +
494A TYR* 3.5 48.5 + + + -
513A VAL* 3.5 39.5 - - + -
514A THR* 4.5 10.6 + - - +
517A GLY* 4.2 8.2 - - - -
541A THR* 3.5 33.5 + - - +
1781A SO4 4.7 4.5 + - - -
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Residues in contact with PRO 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A SER* 3.5 15.0 - - - +
409A TYR* 1.4 91.0 - - + +
411A SER* 1.3 63.1 + - - +
413A ILE* 3.1 4.3 + - + +
414A ILE* 3.0 29.4 + - - +
453A LEU* 3.7 20.9 - - + -
457A LEU* 3.9 22.7 - - + -
490A ALA* 3.8 22.9 - - + +
491A ASN* 3.6 24.7 - - - +
493A PHE* 5.9 0.4 - - + -
494A TYR* 5.8 1.8 - - + +
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Residues in contact with SER 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ARG* 3.2 11.9 + - - -
407A SER* 2.9 25.7 + - - -
408A LEU* 3.3 6.5 - - - -
410A PRO* 1.3 71.8 - - - +
412A ILE* 1.3 58.0 + - - +
414A ILE* 4.0 3.5 - - - -
415A THR* 2.8 36.7 + - - -
457A LEU* 4.5 4.6 - - - +
574A LEU* 3.0 39.3 + - - +
575A LEU* 4.0 12.5 - - - -
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Residues in contact with ILE 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A LEU* 3.1 23.5 + - + +
409A TYR* 2.9 13.2 + - + +
411A SER* 1.3 74.2 - - - +
413A ILE* 1.3 60.5 + - - +
416A HIS* 2.8 36.3 + - + +
418A VAL* 4.7 0.7 - - + -
513A VAL* 4.3 24.2 - - + +
516A TRP* 3.6 41.3 - - + -
517A GLY 3.9 6.5 - - - +
520A TYR* 3.4 35.9 - - + -
575A LEU* 3.8 15.9 - - + -
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Residues in contact with ILE 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A TYR 2.9 15.8 + - - +
410A PRO* 3.6 6.5 - - + +
412A ILE* 1.3 76.5 - - - +
414A ILE* 1.3 57.3 + - - +
417A ASN* 3.1 8.0 + - - -
418A VAL* 2.9 51.0 + - + +
449A ILE* 4.7 2.0 - - + -
450A PRO* 3.8 14.9 - - + +
453A LEU* 3.9 26.2 - - + -
493A PHE* 4.4 12.3 - - + -
494A TYR* 4.5 9.9 - - + +
497A TYR* 3.8 26.5 - - + +
513A VAL* 3.8 22.7 - - + -
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Residues in contact with ILE 414 (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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410A PRO 3.0 16.7 + - - +
411A SER 4.1 0.2 - - - +
413A ILE* 1.3 75.9 - - - +
415A THR* 1.3 67.2 + - - +
417A ASN* 3.1 14.9 + - - +
450A PRO* 3.8 26.7 - - + +
453A LEU* 3.9 12.3 - - + -
454A GLY* 3.7 24.7 - - - +
457A LEU* 3.6 21.1 - - + -
574A LEU* 3.6 35.9 - - + -
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Residues in contact with THR 415 (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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411A SER 2.8 22.1 + - - -
412A ILE 4.0 1.1 - - - -
414A ILE* 1.3 79.4 - - - +
416A HIS* 1.3 65.4 + - + +
432A ASP* 3.9 0.7 - - - +
443A LYS* 3.2 25.9 + - - +
572A PRO* 4.0 16.6 - - + +
573A GLY* 3.8 24.5 - - - +
574A LEU* 2.9 27.8 + - - +
575A LEU* 4.0 11.1 - - + +
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Residues in contact with HIS 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ILE* 2.8 30.6 + - + +
415A THR* 1.3 87.0 + - + +
417A ASN* 1.3 70.2 + - - +
418A VAL* 3.2 3.8 + - + +
432A ASP* 2.7 34.3 + - + +
441A PHE* 3.7 18.5 - - - +
443A LYS* 4.7 2.5 - - - +
516A TRP* 3.2 56.0 + + + -
520A TYR* 2.6 33.1 + + - -
572A PRO* 4.8 5.2 - - + -
575A LEU* 4.6 0.4 - - - +
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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