Contacts of the helix formed by residues 270 - 274 (chain A) in PDB entry 1KOJ
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 270 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A HIS* 5.6 2.2 + - - -
210A LYS* 4.4 5.4 - - - -
267A ASP 4.6 0.4 + - - -
268A TRP 3.8 4.2 + - - -
269A VAL* 1.3 73.7 - - - +
271A GLY* 1.3 67.0 + - - -
272A ARG* 3.3 6.1 - - - -
273A TYR* 2.9 30.5 + - - +
274A SER* 3.1 11.4 + - - -
509A PHE 5.8 3.6 - - - -
511A GLN* 6.1 0.4 - - - -
902A PAN 5.1 0.4 - - - -
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Residues in contact with GLY 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A GLY* 3.2 17.6 - - - +
159A SER* 6.0 0.2 - - - -
210A LYS* 4.8 10.0 - - - +
265A PHE* 6.0 1.3 - - - -
269A VAL 3.5 3.5 + - - -
270A GLY* 1.3 71.2 - - - -
272A ARG* 1.3 57.1 + - - +
273A TYR 3.0 3.6 + - - -
274A SER* 2.6 28.9 + - - -
275A LEU 4.9 0.2 + - - -
902A PAN 3.4 30.6 + - - -
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Residues in contact with ARG 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A GLY* 4.3 6.1 - - - -
270A GLY* 5.0 2.1 - - - -
271A GLY* 1.3 73.1 - - - +
273A TYR* 1.3 81.3 + - + +
274A SER 3.7 0.4 - - - -
350A TYR* 3.4 25.1 + - - -
353A GLN* 4.1 13.9 - - + +
354A GLY* 3.8 15.9 - - - -
357A GLU* 3.4 44.6 + - - +
358A SER* 2.8 27.4 + - - +
494A GLU* 4.6 0.2 - - - +
508A SER 3.1 19.0 + - - -
509A PHE* 3.2 14.8 + - - +
510A ASP 2.9 23.6 + - - -
511A GLN* 2.7 20.0 + - - -
902A PAN 2.6 36.0 + - - +
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Residues in contact with TYR 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A HIS* 3.5 49.9 - - + +
102A LEU* 4.1 4.9 - - - +
269A VAL* 4.2 1.9 - - - +
270A GLY* 2.9 21.9 + - - +
272A ARG* 1.3 111.1 - - + +
274A SER* 1.3 55.7 + - - +
275A LEU 3.8 1.6 - - - -
276A TRP* 3.6 11.2 - - - -
350A TYR* 4.8 2.0 - - - -
354A GLY* 4.3 4.1 + - - -
358A SER* 2.8 22.0 + - - -
494A GLU* 3.4 49.7 + - + +
497A ILE* 3.8 15.9 - - + +
498A PHE 5.4 0.3 + - - -
508A SER* 4.1 0.3 + - - -
509A PHE* 3.7 34.9 - + - -
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Residues in contact with SER 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A GLY 3.2 14.7 + - - -
265A PHE* 4.8 2.9 - - - -
269A VAL* 3.7 19.1 - - - -
270A GLY 3.4 8.7 - - - -
271A GLY* 2.6 27.3 + - - -
272A ARG 3.7 0.8 - - - -
273A TYR* 1.3 76.9 - - - +
275A LEU* 1.3 58.5 + - - +
276A TRP 2.9 6.5 - - - -
277A SER* 2.6 31.9 + - - +
279A ILE* 3.3 24.9 - - - +
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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
------------------------------------------------------------
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