Contacts of the helix formed by residues 265 - 269 (chain D) in PDB entry 1XSK
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 PRO 265 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263D LEU 3.7 1.5 - - - +
264D PRO* 1.3 85.1 - - + +
266D ALA* 1.3 65.2 + - - +
267D TRP* 3.6 38.4 - - + +
268D SER* 2.8 25.7 + - - -
269D PHE* 3.3 2.4 - - - -
459D GLU 3.2 24.2 - - - +
460D GLU* 3.6 16.8 - - - +
461D ALA 3.3 19.7 - - - +
462D VAL* 4.1 4.0 - - + -
574D TYR* 3.7 5.4 - - - +
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Residues in contact with ALA 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264D PRO 3.6 1.0 + - - -
265D PRO* 1.3 71.8 - - - +
267D TRP* 1.3 65.5 + - - +
269D PHE* 2.9 24.3 + - - +
570D MET* 4.2 2.2 - - + +
574D TYR* 3.7 17.4 + - + -
678D PRO* 3.5 9.2 - - - +
679D ASP* 3.8 15.7 - - + -
682D TRP* 3.8 35.9 - - + -
706D ALA* 5.7 2.2 + - + +
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Residues in contact with TRP 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D PRO* 3.6 12.9 - - + +
266D ALA* 1.3 77.8 - - - +
268D SER* 1.3 84.2 + - - +
269D PHE 2.8 6.2 + - - -
270D GLY* 2.9 15.1 + - - -
272D TRP* 4.2 7.6 - + - -
301D HIS* 4.6 6.0 - - + +
302D VAL* 3.8 19.4 - - + +
341D LYS* 3.5 55.7 - - + +
411D ASP* 4.3 16.4 - - + -
412D CYS* 4.0 14.8 - - + -
460D GLU* 2.8 46.8 + - + -
462D VAL* 3.5 19.5 - - + -
678D PRO* 3.8 11.5 - - + +
679D ASP* 4.0 20.1 - - - +
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Residues in contact with SER 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D PRO* 3.4 9.4 - - - +
265D PRO* 2.8 21.4 + - - -
266D ALA 3.2 0.2 - - - -
267D TRP* 1.3 97.8 - - - +
269D PHE* 1.3 59.0 + - - +
270D GLY 3.2 0.8 - - - +
272D TRP* 2.9 28.2 + - - +
462D VAL* 4.1 21.3 - - - -
536D HIS* 2.9 35.2 + - - +
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Residues in contact with PHE 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264D PRO* 3.4 26.0 - - + -
265D PRO 3.3 11.7 - - - -
266D ALA* 2.9 16.7 + - - +
267D TRP 2.8 1.6 + - - -
268D SER* 1.3 81.7 - - - +
270D GLY* 1.3 66.2 + - - +
507D PHE* 4.2 7.0 - + - -
535D SER* 3.3 22.7 - - - -
536D HIS* 3.6 20.0 - + - -
566D LYS* 2.9 34.8 + - - +
570D MET* 3.7 26.9 - - + -
573D LEU* 5.2 3.8 - - + -
574D TYR* 3.5 13.2 - + - -
577D ALA* 3.8 21.8 - - + -
587D MET* 3.9 24.7 - - + -
678D PRO* 4.2 3.6 - - + +
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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