Contacts of the helix formed by residues 423 - 436 (chain A) in PDB entry 3VP1
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 THR 423 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A THR 3.4 13.0 - - - -
279A LYS* 3.8 28.7 - - + +
280A VAL 4.2 5.8 - - - -
281A PRO* 4.1 7.2 - - + -
282A PHE* 4.1 5.2 - - - -
370A TYR* 3.9 28.4 - - + +
422A VAL* 1.3 79.0 - - - +
424A CYS* 1.3 65.6 + - - +
425A GLU* 3.5 6.1 + - - +
426A SER* 3.1 25.7 + - - -
427A ALA* 3.0 23.9 + - - +
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Residues in contact with CYS 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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262A GLY 3.8 21.1 - - - -
264A SER* 3.2 26.6 - - - +
277A ASP 4.2 12.8 - - - -
278A THR* 3.4 13.5 + - + -
280A VAL 5.0 0.4 + - - -
282A PHE* 3.9 6.9 - - - -
423A THR* 1.3 73.0 - - - +
425A GLU* 1.3 57.1 + - - +
428A SER* 2.9 25.3 + - - -
499A MET* 3.5 21.8 - - - +
501A TRP* 3.5 31.9 - - - -
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Residues in contact with GLU 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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264A SER* 3.4 18.8 - - - +
272A ARG* 3.3 23.7 + - - +
274A SER* 3.5 14.4 + - - +
278A THR* 2.9 28.8 + - - +
279A LYS* 3.0 42.7 + - - +
369A GLU* 3.9 7.7 - - - +
423A THR* 3.0 6.0 + - - +
424A CYS* 1.3 77.5 - - - +
426A SER* 1.3 60.9 + - - +
428A SER* 2.8 18.7 + - - -
429A VAL* 3.4 2.8 - - - +
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Residues in contact with SER 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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366A ALA* 3.8 6.2 - - - +
369A GLU* 3.7 18.1 + - - -
370A TYR 2.7 45.2 + - - -
371A VAL* 5.2 0.2 - - - -
422A VAL* 3.5 3.8 - - - +
423A THR* 3.1 26.1 + - - -
425A GLU* 1.3 73.6 - - - +
427A ALA* 1.3 67.7 + - - +
429A VAL* 3.0 16.3 + - - +
430A MET* 3.2 15.8 + - - +
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Residues in contact with ALA 427 (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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284A LEU* 5.3 1.1 - - + -
422A VAL* 4.0 12.6 - - + -
423A THR 3.0 18.0 + - - +
426A SER* 1.3 78.1 + - - +
428A SER* 1.3 64.6 + - - +
430A MET* 2.9 28.3 + - - +
431A ALA 2.9 10.6 + - - -
489A LEU* 3.8 7.4 - - + +
499A MET* 3.5 38.8 - - + -
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Residues in contact with SER 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A SER* 3.5 31.8 - - - -
265A VAL 4.1 3.0 + - - -
266A CYS* 3.7 13.3 - - - +
272A ARG* 4.4 2.6 + - - -
424A CYS 2.9 18.1 + - - -
425A GLU* 2.8 17.3 + - - -
427A ALA* 1.3 76.2 - - - +
429A VAL* 1.3 57.2 + - - +
431A ALA* 3.4 2.8 + - - +
432A ALA* 2.9 27.7 + - - +
497A GLY 3.7 9.7 - - - -
498A MET 4.2 6.5 - - - -
499A MET* 3.8 9.1 - - - +
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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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266A CYS* 4.1 10.8 - - - -
272A ARG* 3.4 31.4 - - - +
365A MET 3.6 3.8 - - - +
366A ALA* 3.5 27.4 - - - +
367A GLY 4.1 0.9 - - - +
369A GLU* 4.2 9.2 - - - +
425A GLU 3.4 15.9 - - - +
426A SER 3.0 8.4 + - - +
428A SER* 1.3 76.3 - - - +
430A MET* 1.3 64.7 + - - +
432A ALA* 3.2 7.3 + - - +
433A THR* 3.0 25.6 + - - -
440A CYS* 4.1 8.5 - - - -
441A PRO* 4.3 2.2 - - + +
442A ILE* 4.0 14.1 - - + -
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Residues in contact with MET 430 (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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284A LEU* 5.0 2.9 - - + -
291A LEU* 4.0 31.4 - - + +
362A LEU* 3.7 35.4 - - + +
365A MET* 3.5 19.4 - - + +
366A ALA* 3.8 16.2 - - + +
370A TYR 5.0 0.4 - - - +
371A VAL* 3.8 23.6 - - + -
422A VAL* 3.9 19.7 - - + -
426A SER 3.2 10.1 + - - +
427A ALA* 2.9 18.7 + - - +
429A VAL* 1.3 79.0 - - - +
431A ALA* 1.3 61.7 + - - +
433A THR* 3.1 18.2 + - - -
434A LEU* 3.3 12.8 + - - +
489A LEU* 5.0 4.5 - - + -
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Residues in contact with ALA 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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427A ALA 2.9 6.0 + - - +
428A SER 3.6 4.0 - - - +
430A MET* 1.3 78.0 - - - +
432A ALA* 1.3 56.5 + - - +
434A LEU* 3.0 10.9 + - - +
435A ALA* 2.9 26.7 + - - +
489A LEU* 3.6 25.7 - - + +
490A LEU 3.5 10.3 - - - +
491A VAL* 3.7 11.3 - - + +
497A GLY* 3.6 2.0 - - - -
498A MET 3.5 27.8 - - - +
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Residues in contact with ALA 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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266A CYS* 3.1 34.5 - - - +
267A THR 4.2 1.3 - - - +
268A VAL* 4.9 0.9 - - - +
428A SER 2.9 14.5 + - - +
429A VAL 3.2 4.9 + - - +
431A ALA* 1.3 75.8 - - - +
433A THR* 1.3 58.4 + - - +
435A ALA* 3.2 4.5 + - - +
436A ASN* 2.8 31.9 + - - +
441A PRO* 3.5 21.6 - - + +
496A MET 4.4 0.2 - - - -
497A GLY* 3.4 10.3 - - - +
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Residues in contact with THR 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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365A MET* 2.8 34.6 + - + +
429A VAL 3.0 6.3 + - - -
430A MET* 3.1 10.5 + - - -
432A ALA* 1.3 78.5 - - - +
434A LEU* 1.3 58.9 + - + +
436A ASN 3.3 5.4 + - - -
438A GLY* 2.9 48.8 + - - +
439A PHE 3.7 14.3 + - - -
440A CYS* 3.5 16.2 - - - +
441A PRO* 3.6 1.5 - - - +
447A VAL* 4.3 14.4 - - + -
448A LEU* 5.0 6.3 - - + -
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Residues in contact with LEU 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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290A PRO* 5.6 0.2 - - + -
291A LEU* 4.3 23.1 - - + -
294A ALA* 5.0 2.0 - - + -
365A MET* 5.7 1.8 - - - -
430A MET 3.3 10.7 + - - +
431A ALA* 3.0 10.6 + - - +
433A THR* 1.3 77.4 - - + +
435A ALA* 1.3 63.9 + - - +
436A ASN 3.3 0.5 + - - -
437A GLY 3.7 2.3 + - - -
448A LEU* 3.8 28.7 - - + -
453A VAL* 3.1 37.7 - - + +
456A THR* 4.5 18.2 - - + -
457A LEU* 4.0 13.3 - - + +
460A MET* 4.3 23.8 - - - -
489A LEU* 4.7 4.9 - - + -
491A VAL* 4.1 17.3 - - + -
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Residues in contact with ALA 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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268A VAL* 4.2 3.4 - - + -
431A ALA 2.9 8.4 + - - +
432A ALA 3.2 8.3 + - - +
434A LEU* 1.3 75.8 - - - +
436A ASN* 1.3 56.3 + - - +
437A GLY 3.4 3.5 + - - -
457A LEU* 5.4 0.7 - - - -
491A VAL* 3.5 18.1 - - + +
492A VAL 3.6 9.6 - - - +
493A PRO* 4.2 2.4 - - - +
494A ASN* 2.9 34.0 + - - +
496A MET* 3.3 34.1 - - - +
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Residues in contact with ASN 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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268A VAL* 2.7 39.5 + - + +
432A ALA 2.8 16.5 + - - +
433A THR 3.3 0.4 + - - +
434A LEU 3.1 0.8 - - - -
435A ALA* 1.3 77.3 - - - +
437A GLY* 1.3 62.0 + - - +
438A GLY 3.0 4.0 + - - -
439A PHE* 2.8 50.6 + - - +
440A CYS 4.5 0.6 + - - -
441A PRO* 4.2 13.7 - - + +
494A ASN* 5.5 1.1 - - - +
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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