Contacts of the helix formed by residues 405 - 410 (chain A) in PDB entry 1SKW
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 ALA 405 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A GLY 3.6 7.2 - - - +
398A GLN 3.4 7.4 - - - -
399A SER 3.8 0.2 - - - +
400A ALA* 3.3 41.3 - - - +
402A GLY 3.1 18.6 + - - +
403A ASP 3.4 1.8 + - - -
404A LYS* 1.3 81.0 - - - +
406A TRP* 1.3 68.6 + - - +
407A LEU 4.4 0.7 - - - +
408A ARG* 3.0 18.0 + - + +
409A TYR* 3.2 10.9 + - - -
11T C 3.9 0.2 + - - -
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Residues in contact with TRP 406 (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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234A PHE* 3.5 26.0 - + + -
239A ILE* 4.4 9.0 - - + -
395A ARG 6.0 0.2 - - - -
398A GLN* 3.2 40.6 + - + +
399A SER* 3.5 27.5 + - - +
404A LYS 4.6 0.4 - - - -
405A ALA* 1.3 71.3 - - - +
407A LEU* 1.3 58.9 + - - +
409A TYR* 2.8 22.8 + - - +
410A VAL* 3.0 12.6 + - - +
416A ILE* 3.8 11.6 - - + +
435A PRO* 4.1 25.0 - - + +
436A ASN 5.4 1.0 + - - -
440A ILE* 3.5 38.4 - - + +
441A PRO* 3.9 6.5 - - + -
451A CYS* 3.6 42.4 - - + -
455A PHE* 3.8 23.3 - + - -
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Residues in contact with LEU 407 (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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234A PHE* 4.3 5.2 - - + -
236A THR* 4.0 19.7 - - + +
239A ILE* 3.9 23.1 - - + -
240A GLU* 3.8 33.0 - - + +
243A TYR* 4.4 13.2 - - + -
399A SER 3.2 11.7 + - - +
400A ALA* 3.4 33.9 - - + +
405A ALA 3.3 0.4 - - - -
406A TRP* 1.3 77.4 - - - +
408A ARG* 1.3 60.0 + - + +
410A VAL* 3.8 16.3 - - - +
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Residues in contact with ARG 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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400A ALA 3.6 10.6 + - - +
401A GLU* 2.8 31.1 + - - +
402A GLY 2.7 27.1 + - - -
403A ASP* 3.7 17.5 - - - +
405A ALA* 3.0 14.2 + - + +
407A LEU* 1.3 78.6 - - + +
409A TYR* 1.3 66.9 + - + +
410A VAL 3.7 3.0 - - - +
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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
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403A ASP 3.9 7.1 + - - -
404A LYS* 3.5 49.4 - - + +
405A ALA 3.2 17.8 + - - +
406A TRP 2.8 8.5 + - - +
408A ARG* 1.3 82.5 - - + +
410A VAL* 1.3 65.9 + - - +
411A ALA* 3.3 5.4 + - - +
415A LYS 4.1 3.6 - - - +
416A ILE* 4.2 11.2 - - + -
417A HIS* 4.8 5.5 + - - -
434A PHE* 3.3 37.2 - - + +
435A PRO* 3.7 19.1 - - + -
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Residues in contact with VAL 410 (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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234A PHE* 3.9 20.2 - - + -
236A THR* 3.5 32.3 - - + +
406A TRP 3.0 9.8 + - - +
407A LEU* 3.8 20.1 - - - +
408A ARG 4.6 3.1 - - - +
409A TYR* 1.3 77.3 - - - +
411A ALA* 1.3 71.9 + - - +
414A GLY* 3.9 21.1 - - - -
415A LYS 3.7 7.6 - - - +
416A ILE* 3.8 4.9 - - + +
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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