Contacts of the helix formed by residues 260 - 271 (chain A) in PDB entry 5KFU
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 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257A SER 4.8 0.4 + - - -
258A LEU 3.2 2.0 - - - -
259A GLY* 1.3 79.7 - - - +
261A LYS* 1.3 67.4 + - - -
262A LEU 3.4 2.2 - - - -
263A GLY 3.3 2.0 + - - -
264A ALA* 3.1 21.8 + - - +
6P C 3.6 18.4 + - - -
7P A 3.8 4.8 + - - -
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Residues in contact with LYS 261 (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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260A GLY* 1.3 70.0 - - - -
262A LEU* 1.3 55.6 + - - +
264A ALA* 3.2 8.6 + - - +
265A SER* 2.5 39.1 + - - +
5P T 3.2 43.4 + - - +
6P C 2.8 23.2 + - - +
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Residues in contact with LEU 262 (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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257A SER* 4.6 10.3 - - - +
258A LEU* 3.8 22.2 - - + -
261A LYS* 1.3 75.5 - - - +
263A GLY* 1.3 65.0 + - - +
265A SER* 3.0 9.5 + - - -
266A VAL* 2.9 24.7 + - + +
290A PHE* 3.9 30.1 - - + -
294A ASN* 3.7 39.7 - - + +
297A TRP* 6.0 2.0 - - + -
298A LEU* 5.4 3.8 - - + -
6P C 2.9 17.6 + - - +
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Residues in contact with GLY 263 (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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252A ILE* 4.1 7.6 - - - +
253A ARG* 6.2 0.4 - - - -
258A LEU* 3.2 36.7 + - - +
260A GLY 3.3 4.2 + - - -
261A LYS 3.3 0.6 - - - -
262A LEU* 1.3 78.6 - - - +
264A ALA* 1.3 60.6 + - - +
266A VAL* 3.3 6.7 + - - +
267A ILE* 3.2 31.9 + - - +
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Residues in contact with ALA 264 (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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258A LEU 4.7 0.2 + - - -
260A GLY 3.1 14.0 + - - +
261A LYS* 3.6 11.0 - - - +
263A GLY* 1.3 76.5 - - - +
265A SER* 1.3 58.1 + - - +
267A ILE* 3.4 12.3 + - - +
268A GLU* 3.0 31.0 + - - +
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Residues in contact with SER 265 (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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261A LYS* 2.5 24.3 + - - +
262A LEU* 3.0 10.8 + - - -
264A ALA* 1.3 75.8 - - - +
266A VAL* 1.3 59.4 + - - +
268A GLU* 4.4 6.3 - - - +
269A ILE* 2.8 46.4 + - - +
290A PHE* 4.0 13.0 - - - -
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Residues in contact with VAL 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ILE* 3.8 26.9 - - + -
258A LEU* 5.0 2.5 - - + -
262A LEU* 2.9 26.5 + - + +
263A GLY* 3.3 11.2 + - - +
265A SER* 1.3 74.5 - - - +
267A ILE* 1.3 62.9 + - - +
270A LEU* 3.1 37.2 + - + +
272A ILE* 4.2 1.0 - - + +
278A LEU* 3.9 25.4 - - + -
290A PHE* 3.6 23.3 - - + -
298A LEU* 4.2 22.4 - - + -
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Residues in contact with ILE 267 (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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252A ILE* 4.0 25.8 - - + +
253A ARG* 5.1 14.6 - - + +
263A GLY 3.2 19.0 + - - +
264A ALA* 3.5 11.0 - - - +
265A SER 3.2 0.2 - - - -
266A VAL* 1.3 77.5 - - - +
268A GLU* 1.3 58.4 - - + +
271A GLY* 2.9 29.6 + - - -
272A ILE* 3.3 25.1 + - - +
273A GLU* 4.9 9.6 - - + +
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Residues in contact with GLU 268 (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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264A ALA* 3.0 19.4 + - - +
265A SER* 3.3 6.4 + - - +
267A ILE* 1.3 81.5 - - + +
269A ILE* 1.3 68.0 + - + +
271A GLY* 3.6 6.1 + - - -
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Residues in contact with ILE 269 (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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265A SER* 2.8 33.4 + - - +
268A GLU* 1.3 81.0 - - + +
270A LEU* 1.3 64.3 + - + +
289A HIS* 3.4 50.6 - - + +
290A PHE* 4.1 17.3 - - + -
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Residues in contact with LEU 270 (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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266A VAL* 3.1 20.0 + - + +
269A ILE* 1.3 82.4 - - + +
271A GLY* 1.3 63.9 + - - +
272A ILE* 3.7 14.1 - - + +
278A LEU* 3.7 29.8 - - + -
281A PHE* 3.7 41.3 - - + -
286A LEU* 3.9 14.8 - - + -
289A HIS* 3.8 32.1 - - + +
290A PHE* 3.9 14.1 - - + -
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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
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267A ILE 2.9 13.8 + - - -
268A GLU 3.6 5.3 + - - -
269A ILE 3.4 2.4 - - - -
270A LEU* 1.3 80.7 - - - +
272A ILE* 1.3 61.2 + - - +
277A GLU* 4.7 1.6 - - - +
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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