Contacts of the helix formed by residues 426 - 432 (chain A) in PDB entry 1WCP
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 VAL 426 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A PRO* 5.5 0.2 - - - -
350A SER* 3.8 30.4 - - - +
351A VAL* 4.5 10.3 - - + -
362A TRP* 3.7 30.7 - - + -
384A VAL* 4.6 17.3 - - + -
394A TYR* 5.0 7.6 - - + -
409A LEU* 5.1 7.9 - - + -
415A VAL* 5.2 0.2 - - - +
416A VAL* 3.5 34.5 - - + +
425A SER* 1.3 70.2 - - - +
427A SER* 1.3 64.1 + - - +
429A LEU* 2.9 28.2 + - + +
430A ILE* 3.9 2.9 + - + +
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Residues in contact with SER 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A SER 5.8 0.8 + - - -
360A GLU* 5.8 1.8 - - - -
362A TRP* 4.6 13.8 - - - -
425A SER* 3.2 20.3 + - - -
426A VAL* 1.3 75.6 - - - +
428A HIS* 1.3 69.2 + - - +
430A ILE* 2.9 39.2 + - - +
431A SER* 3.8 6.3 + - - -
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Residues in contact with HIS 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A PRO* 5.2 10.8 - - + +
290A CYS* 3.2 18.3 - - - -
291A PRO* 5.6 2.5 - - + -
344A VAL* 5.7 2.0 - - + -
424A GLU* 3.9 31.1 + - + +
425A SER* 3.0 41.3 + - - +
427A SER* 1.3 84.7 + - - +
429A LEU* 1.3 55.9 + - - +
431A SER* 4.2 5.1 + - - -
432A TYR* 3.1 25.3 + - - +
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Residues in contact with LEU 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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290A CYS* 4.1 9.8 - - + -
291A PRO* 3.8 39.8 - - + +
292A GLY* 5.5 1.1 - - - -
384A VAL* 4.7 3.6 - - + -
396A LEU* 3.7 25.4 - - + -
409A LEU* 3.6 36.6 - - + -
425A SER 4.5 0.4 + - - -
426A VAL* 2.9 17.5 + - + +
428A HIS* 1.3 75.3 - - - +
430A ILE* 1.3 66.1 + - + +
432A TYR* 3.0 17.3 + - + +
433A HIS* 3.2 40.1 - - + +
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Residues in contact with ILE 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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362A TRP* 3.8 55.6 - - + +
382A PHE* 3.3 39.7 - - + -
383A LEU 5.2 0.2 - - - -
384A VAL* 3.6 33.7 - - + +
396A LEU* 4.5 6.7 - - + -
426A VAL* 4.5 3.4 - - + +
427A SER* 2.9 22.3 + - - +
429A LEU* 1.3 72.2 - - + +
431A SER* 1.3 65.2 + - - +
433A HIS* 3.3 4.2 + - - -
434A MET* 3.9 4.1 + - + +
452A PRO* 4.3 14.1 - - + -
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Residues in contact with SER 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A SER 3.8 8.0 + - - -
428A HIS* 4.9 4.0 - - - -
429A LEU 3.4 0.4 - - - -
430A ILE* 1.3 72.8 - - - +
432A TYR* 1.3 58.7 + - - +
433A HIS 3.0 10.5 + - - -
434A MET* 3.1 33.1 + - - +
435A ASP* 3.5 13.0 + - - +
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Residues in contact with TYR 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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288A PRO* 3.5 21.3 - - + -
289A PRO* 3.5 19.1 - - + +
290A CYS* 3.6 35.8 + - + -
291A PRO 5.8 0.7 - - - -
314A VAL* 4.6 9.5 - - - +
428A HIS 3.1 20.9 + - - +
429A LEU* 3.0 9.5 + - + +
431A SER* 1.3 79.4 - - - +
433A HIS* 1.3 66.4 + + - +
435A ASP 4.1 5.6 - - - -
436A ASN* 3.3 54.7 + - + +
440A ILE* 4.4 17.8 - - + +
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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