Contacts of the helix formed by residues 260 - 269 (chain A) in PDB entry 4KYI
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 SER 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A ASP* 4.5 0.9 + - - -
210A ASN* 4.3 9.5 + - - +
212A ARG* 3.8 30.3 - - - +
213A LEU 3.5 15.7 + - - -
214A THR* 3.8 3.9 - - - +
258A GLN 3.9 3.0 + - - -
259A GLN* 1.3 82.8 + - - +
261A ILE* 1.3 64.7 + - - +
262A ALA* 3.6 10.7 + - - +
263A GLN* 3.8 23.3 + - - +
264A VAL* 3.2 20.1 + - - +
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Residues in contact with ILE 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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80A SER* 4.6 1.1 - - - +
84A VAL* 6.4 0.2 - - + -
126A TYR* 3.5 35.9 - - + +
130A MET* 4.6 9.6 - - - -
213A LEU* 3.3 10.8 + - + +
214A THR 3.3 30.5 - - - +
215A LEU* 3.8 10.8 - - + -
218A LEU* 3.7 26.7 - - + -
236A LEU* 3.7 28.7 - - + -
260A SER* 1.3 70.0 + - - +
262A ALA* 1.3 66.8 + - - +
263A GLN 3.1 1.9 + - - -
264A VAL* 3.3 7.0 - - + +
265A VAL* 3.1 30.8 + - + +
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Residues in contact with ALA 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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119A ARG* 3.3 39.1 - - + +
122A LEU* 3.6 16.2 - - + +
123A ASP* 3.4 30.0 + - - +
126A TYR* 3.6 9.9 - - + -
260A SER* 3.6 3.0 + - - +
261A ILE* 1.3 78.8 - - - +
263A GLN* 1.3 62.1 + - - +
265A VAL 4.1 0.2 - - - -
266A GLN* 3.4 17.5 + - - +
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Residues in contact with GLN 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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119A ARG* 4.1 15.6 - - + +
198A THR* 4.8 22.1 - - - +
210A ASN* 5.5 2.3 + - - -
212A ARG* 6.3 0.9 - - - -
259A GLN* 2.8 26.0 + - - +
260A SER* 3.7 19.5 + - - +
261A ILE 3.1 0.6 - - - -
262A ALA* 1.3 80.0 - - - +
264A VAL* 1.3 59.4 + - - +
266A GLN* 3.9 2.5 - - - +
267A TRP* 2.9 70.7 + - + +
279A ARG 4.3 4.8 + - - -
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Residues in contact with VAL 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A LEU* 4.1 14.1 - - + -
238A VAL* 3.5 23.1 - - + +
240A VAL* 4.0 1.2 - - + +
251A TYR* 3.6 24.0 - - + -
259A GLN* 3.4 24.7 - - + -
260A SER 3.2 15.5 - - - +
261A ILE* 3.3 14.4 - - + +
263A GLN* 1.3 74.0 - - - +
265A VAL* 1.3 61.9 + - + +
267A TRP* 3.3 24.4 - - + +
268A SER* 2.8 31.9 + - - -
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Residues in contact with VAL 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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73A SER 4.6 1.0 - - - +
76A ALA* 3.6 23.2 - - - +
77A MET* 3.5 34.7 - - + +
80A SER* 3.9 5.8 - - - -
118A PHE* 4.6 3.9 - - + -
122A LEU* 3.6 18.4 - - + -
126A TYR* 3.5 18.4 - - - +
236A LEU* 4.9 0.2 - - + -
238A VAL* 4.4 11.7 - - + -
261A ILE* 3.1 24.0 + - + +
264A VAL* 1.3 75.9 - - + +
266A GLN* 1.3 65.1 + - - +
268A SER* 3.5 2.8 + - - -
269A GLY* 3.1 18.7 + - - -
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Residues in contact with GLN 266 (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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114A ARG 4.7 1.6 + - - -
115A GLY* 3.2 42.8 - - - +
118A PHE* 3.7 34.2 - - + -
119A ARG* 4.1 10.7 + - + +
122A LEU* 3.8 3.1 - - + +
262A ALA 3.4 18.6 + - - +
263A GLN* 3.9 2.6 - - - +
265A VAL* 1.3 75.0 - - - +
267A TRP* 1.3 81.8 + - - +
269A GLY 3.2 3.5 + - - -
270A ALA* 2.8 45.6 + - - +
275A PHE* 4.1 8.3 - - + +
276A VAL 5.1 3.4 + - - -
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Residues in contact with TRP 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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240A VAL* 4.0 3.4 - - + -
251A TYR* 3.8 24.5 - + - -
259A GLN* 3.9 10.5 - - - -
263A GLN* 2.9 57.3 + - + +
264A VAL* 3.3 32.8 - - + +
266A GLN* 1.3 93.1 + - - +
268A SER* 1.3 57.8 + - - +
270A ALA* 2.9 21.8 + - + +
278A GLY* 3.8 24.1 - - - -
279A ARG 3.2 26.6 - - - +
280A ASN* 4.2 7.9 - - - -
281A ALA 5.0 1.3 - - - -
286A ILE* 3.7 34.8 - - + -
287A ALA 3.0 21.2 - - - +
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Residues in contact with SER 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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72A ALA* 3.3 5.5 - - - -
73A SER* 3.1 20.8 + - - -
76A ALA* 3.6 16.7 - - - +
238A VAL* 4.6 2.9 - - - -
239A VAL 2.6 26.2 + - - -
240A VAL* 3.8 10.5 - - - -
264A VAL 2.8 20.9 + - - -
265A VAL 3.9 0.4 - - - -
266A GLN 3.4 0.4 - - - -
267A TRP* 1.3 73.4 - - - +
269A GLY* 1.3 57.0 + - - +
270A ALA 3.4 0.4 - - - -
288A ASP* 2.8 24.4 - - - +
289A GLY 3.0 9.5 + - - +
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Residues in contact with GLY 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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73A SER* 4.0 17.9 + - - -
118A PHE* 5.6 6.8 - - - -
265A VAL 3.1 13.0 + - - -
266A GLN* 3.3 6.5 - - - -
267A TRP 3.0 1.2 - - - -
268A SER* 1.3 78.3 - - - +
270A ALA* 1.3 57.9 + - - +
271A HIS* 3.2 8.3 + - - +
275A PHE* 4.1 13.9 - - - -
288A ASP* 4.3 5.6 - - - +
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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