Contacts of the helix formed by residues 420 - 434 (chain B) in PDB entry 4WIK
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 420 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371B ALA* 3.7 10.8 - - - +
396B PRO* 5.8 0.9 - - - +
418B PHE* 3.9 2.6 - - - +
419B ALA* 1.4 78.3 - - - +
421B LYS* 1.4 64.2 + - - +
422B PRO* 3.4 17.6 - - - +
423B ALA* 3.3 27.0 + - - +
424B ALA 3.5 4.7 + - - -
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Residues in contact with LYS 421 (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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370B ALA* 4.0 20.2 - - - -
371B ALA* 3.7 19.0 - - + +
420B SER* 1.4 67.9 - - - +
422B PRO* 1.4 66.3 - - + +
424B ALA* 3.3 5.1 + - + +
425B ARG* 2.9 47.2 + - - +
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Residues in contact with PRO 422 (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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420B SER* 3.4 18.4 - - - +
421B LYS* 1.4 93.7 - - + +
423B ALA* 1.4 53.5 + - - +
425B ARG* 3.3 35.2 + - + +
426B LYS* 3.1 28.6 + - - +
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Residues in contact with ALA 423 (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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394B PHE* 4.1 12.9 - - - +
395B GLY* 4.3 3.6 - - - -
396B PRO* 4.3 19.5 - - + -
418B PHE* 3.9 23.1 - - + -
420B SER* 3.3 22.9 + - - +
421B LYS 3.2 0.2 - - - -
422B PRO* 1.4 78.7 - - - +
424B ALA* 1.3 60.9 + - - +
426B LYS* 3.6 5.2 + - - +
427B ALA* 3.3 20.8 + - - +
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Residues in contact with ALA 424 (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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371B ALA* 4.3 14.6 - - + +
373B LEU* 3.4 23.1 - - + +
418B PHE* 3.7 29.8 - - + -
420B SER 3.5 6.4 + - - +
421B LYS* 3.3 10.4 + - + +
423B ALA* 1.3 76.4 - - - +
425B ARG* 1.4 59.0 + - - +
427B ALA 3.8 0.2 - - - -
428B PHE* 2.9 27.7 + - - +
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Residues in contact with ARG 425 (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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421B LYS* 2.9 38.0 + - - +
422B PRO* 3.4 36.3 - - + +
424B ALA* 1.4 74.5 - - - +
426B LYS* 1.4 53.6 + - - +
428B PHE* 3.2 7.3 + - + +
429B GLU* 2.9 59.0 + - - +
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Residues in contact with LYS 426 (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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393B GLN 5.1 4.2 + - - -
394B PHE* 4.1 29.1 - - + +
422B PRO 3.1 9.8 + - - +
423B ALA* 3.7 9.6 - - - +
425B ARG* 1.4 76.9 - - - +
427B ALA* 1.4 56.7 + - - +
429B GLU* 4.7 6.3 - - - -
430B ARG* 3.0 68.4 + - + +
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Residues in contact with ALA 427 (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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373B LEU* 3.8 9.6 - - + -
391B PHE* 4.7 4.3 - - + -
394B PHE* 3.6 26.4 - - + +
418B PHE* 3.6 30.5 - - + -
423B ALA 3.3 6.0 + - - +
424B ALA 3.6 7.9 - - - +
425B ARG 3.3 0.4 - - - -
426B LYS* 1.4 76.4 - - - +
428B PHE* 1.3 65.0 + - - +
431B CYS* 3.2 31.6 + - - +
447B VAL* 4.5 1.3 - - - +
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Residues in contact with PHE 428 (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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373B LEU* 4.0 13.0 - - + +
424B ALA 2.9 19.1 + - - +
425B ARG* 3.8 5.6 - - + +
427B ALA* 1.3 78.0 - - - +
429B GLU* 1.3 70.6 + - + +
431B CYS* 3.9 1.6 - - - +
432B SER* 2.6 48.0 + - - -
447B VAL* 3.6 28.3 - - - +
448B GLU* 4.1 4.9 - - + -
449B PRO* 3.7 37.7 - - + -
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Residues in contact with GLU 429 (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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425B ARG* 2.9 48.9 + - - +
426B LYS* 4.1 5.0 + - - +
428B PHE* 1.3 84.9 - - + +
430B ARG* 1.4 57.0 - - + +
432B SER* 3.3 7.7 + - - -
433B GLU* 3.0 32.5 + - - +
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Residues in contact with ARG 430 (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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480A PHE* 3.3 55.2 - - + +
394B PHE* 3.8 8.7 - - + -
426B LYS* 3.0 55.2 + - + +
429B GLU* 1.4 76.5 - - + +
431B CYS* 1.3 53.7 + - - +
433B GLU* 2.8 42.8 + - - +
434B GLY* 2.7 35.1 + - - +
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Residues in contact with CYS 431 (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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480A PHE* 4.2 5.4 - - - -
495A LYS* 3.3 11.8 + - - -
391B PHE* 4.2 1.1 - - - -
394B PHE* 3.7 26.7 - - - -
427B ALA 3.2 19.9 + - - +
428B PHE 4.0 0.9 - - - +
430B ARG* 1.3 72.6 - - - +
432B SER* 1.3 58.8 + - - +
434B GLY 3.2 14.8 - - - +
436B PHE* 3.7 27.2 + - + -
445B VAL 4.5 8.4 - - - +
446B ILE* 6.0 0.2 - - - -
447B VAL* 3.7 37.5 + - + +
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Residues in contact with SER 432 (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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495A LYS* 3.7 13.4 + - - +
428B PHE* 2.6 45.8 + - - -
429B GLU* 3.5 6.7 - - - -
431B CYS* 1.3 74.7 - - - +
433B GLU* 1.4 65.9 + - - +
447B VAL 4.5 3.7 + - - -
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Residues in contact with GLU 433 (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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495A LYS* 5.2 0.3 + - - -
429B GLU* 3.0 18.9 + - - +
430B ARG* 2.8 34.1 + - - +
432B SER* 1.4 78.9 - - - +
434B GLY* 1.3 59.5 + - - +
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Residues in contact with GLY 434 (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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480A PHE* 3.7 13.2 - - - -
488A TYR* 6.3 1.1 - - - -
495A LYS* 3.1 23.9 + - - -
430B ARG* 2.7 22.7 + - - +
431B CYS 3.2 8.2 - - - +
433B GLU* 1.3 75.8 - - - +
435B VAL* 1.3 62.8 + - - -
436B PHE 4.1 0.2 - - - -
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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