Contacts of the helix formed by residues 406 - 411 (chain A) in PDB entry 1KSW
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 GLY 406 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A GLU* 4.3 6.5 - - - -
382A TYR* 3.4 16.8 + - - -
383A VAL 3.9 8.6 + - - -
384A HIS 3.1 18.3 + - - +
385A ARG* 4.7 1.9 - - - +
404A ASP 3.5 0.8 + - - -
405A PHE* 1.3 71.1 - - - +
407A LEU* 1.3 50.0 + - - -
408A ALA* 2.5 22.4 + - - +
409A ARG* 2.7 21.8 + - - +
410A LEU* 4.1 5.8 - - - -
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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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295A LYS* 4.3 11.2 - - + +
297A LEU* 5.5 4.3 - - + -
302A MET* 3.2 33.7 - - + +
307A PHE* 4.2 5.2 - - + -
314A MET* 3.8 29.7 - - + -
336A ILE* 3.4 32.5 - - + -
404A ASP* 4.3 29.4 - - + +
405A PHE 3.2 7.7 + - - +
406A GLY* 1.3 66.6 - - - +
408A ALA* 1.3 64.8 + - - +
409A ARG 3.1 0.7 - - - -
410A LEU* 2.9 22.0 + - + +
411A ILE* 3.5 5.1 + - + +
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Residues in contact with ALA 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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385A ARG* 3.5 29.6 + - + +
386A ASP* 4.1 24.5 - - + +
404A ASP 4.9 2.2 + - - -
406A GLY 2.5 9.2 + - - +
407A LEU* 1.3 74.0 - - - +
409A ARG* 1.3 57.0 + - - +
410A LEU 3.0 5.7 + - - -
411A ILE* 3.0 29.6 + - - +
416A TYR* 3.4 23.2 - - - +
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Residues in contact with ARG 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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306A ALA* 5.2 3.2 + - - +
309A GLN* 5.4 6.9 + - - +
310A GLU* 3.0 39.8 + - - +
385A ARG* 3.6 35.0 + - - +
406A GLY* 2.7 20.5 + - - +
408A ALA* 1.3 72.4 - - - +
410A LEU* 1.3 69.5 + - + +
411A ILE 5.1 1.6 - - - +
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Residues in contact with LEU 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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302A MET* 3.1 36.2 - - + +
303A SER 4.3 1.1 + - - +
306A ALA* 3.5 42.8 - - + +
307A PHE* 3.8 7.4 - - - +
310A GLU* 3.5 32.5 - - + -
406A GLY 4.1 1.6 - - - -
407A LEU* 2.9 37.0 + - + +
409A ARG* 1.3 94.4 - - + +
411A ILE* 1.3 65.5 + - - +
412A GLU* 3.1 10.7 + - - +
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Residues in contact with ILE 411 (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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278A PHE* 3.2 42.8 - - + -
301A THR* 3.7 19.1 - - + +
302A MET* 3.8 20.2 - - + -
407A LEU* 3.8 2.9 - - + +
408A ALA* 3.0 31.1 + - - +
409A ARG 5.1 1.6 - - - +
410A LEU* 1.3 76.5 - - - +
412A GLU* 1.3 62.5 + - - +
413A ASP 3.7 8.0 + - - +
416A TYR* 3.4 31.9 - - + +
417A THR* 4.0 13.0 + - - +
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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