Contacts of the helix formed by residues 267 - 271 (chain C) in PDB entry 1KYZ
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 ILE 267 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C VAL 3.9 15.3 - - - +
208C GLY* 4.1 3.1 - - - +
252C MET* 4.0 14.8 - - + -
264C MET* 3.7 37.0 - - + +
265C LYS 3.4 1.2 - - - +
266C TRP* 1.3 80.4 - - - +
268C CYS* 1.3 67.6 + - - +
269C HIS 3.4 0.2 - - - -
270C ASP* 3.3 5.5 + - - +
271C TRP* 2.9 47.9 - - + -
279C PHE* 3.9 18.8 - - + -
297C GLU* 3.2 0.6 + - - -
1699C SAH 3.8 46.2 - - + +
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Residues in contact with CYS 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C MET* 3.5 32.5 - - - +
267C ILE* 1.3 74.4 - - - +
269C HIS* 1.3 53.7 + - - +
270C ASP 2.5 18.2 + - - -
271C TRP 2.8 23.7 + - - +
276C CYS* 3.7 19.2 - - - -
279C PHE* 4.2 13.2 - - - -
280C LEU* 4.8 9.6 - - - -
295C VAL* 4.4 10.8 - - - -
297C GLU* 3.1 7.0 + - - +
330C ARG* 3.1 6.5 + - - +
335C PHE* 4.1 20.6 - - + -
338C LEU* 5.3 1.8 - - + -
361C PHE* 5.5 1.8 - - - -
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Residues in contact with HIS 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C MET* 6.3 0.6 - - + +
266C TRP* 3.4 49.9 + + + +
267C ILE 3.4 0.2 - - - -
268C CYS* 1.3 68.9 - - - +
270C ASP* 1.3 59.2 + - + +
297C GLU* 2.9 29.6 + - + +
298C CYS* 5.5 1.0 + - - +
316C ILE* 4.4 15.3 - - + -
320C MET* 3.9 13.7 - - - +
328C LYS 3.4 31.1 + - - +
329C GLU* 2.8 40.6 + - - +
330C ARG* 3.9 3.5 - - - +
335C PHE* 5.4 4.2 - - + -
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Residues in contact with ASP 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C PHE* 4.6 17.3 - - - -
266C TRP 4.3 6.1 - - - +
267C ILE 3.4 13.2 - - - +
268C CYS 2.5 8.3 + - - -
269C HIS* 1.3 86.4 + - + +
271C TRP* 1.3 76.5 + - + -
320C MET* 4.8 9.8 - - - +
325C PRO* 4.5 21.0 - - - +
327C GLY* 3.9 18.4 + - - -
366C FER 4.5 18.6 - - - -
1699C SAH 5.3 7.6 - - - -
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Residues in contact with TRP 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C PHE* 5.5 9.4 - + - -
252C MET* 4.6 3.4 - - + -
253C PHE* 3.7 18.8 - + - -
266C TRP 5.6 0.2 - - - -
267C ILE* 2.9 54.7 - - + -
268C CYS 2.8 10.6 + - - +
270C ASP* 1.3 97.2 - - + +
272C SER* 1.3 60.8 + - - +
275C HIS* 3.5 32.4 + - + -
276C CYS* 3.7 11.6 - - - -
279C PHE* 4.2 12.1 - + + -
326C GLY 4.1 9.0 - - - +
327C GLY* 4.9 1.6 - - - -
328C LYS* 5.2 0.7 + - - +
330C ARG* 2.8 21.0 + - - -
1699C SAH 3.4 51.6 - + - -
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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
------------------------------------------------------------
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