Contacts of the helix formed by residues 260 - 269 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119E ARG* 5.5 0.2 - - - -
123E ASP* 4.3 2.8 + - - -
210E ASN* 3.8 21.5 - - - +
212E ARG* 3.5 28.0 - - - +
213E LEU 3.4 14.2 + - - -
214E THR* 4.0 1.8 - - - +
259E GLN* 1.3 74.4 - - - +
261E ILE* 1.3 67.3 + - - +
262E ALA* 3.7 8.3 + - - +
263E GLN* 3.2 31.6 + - - +
264E VAL* 3.3 14.6 + - - +
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Residues in contact with ILE 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E SER* 4.5 0.4 - - - +
84E VAL* 6.1 0.9 - - + -
126E TYR* 3.6 37.5 - - + +
130E MET* 4.6 6.3 - - - -
213E LEU* 3.1 18.2 + - + +
214E THR 3.3 31.9 - - - +
215E LEU* 3.9 7.0 - - + +
218E LEU* 3.7 26.2 - - + -
236E LEU* 3.7 28.3 - - + -
259E GLN 3.4 0.9 + - - -
260E SER* 1.3 72.3 - - - +
262E ALA* 1.3 62.1 + - - +
263E GLN 3.2 0.2 + - - -
264E VAL* 3.2 7.5 - - - +
265E VAL* 3.1 31.4 + - + +
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Residues in contact with ALA 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119E ARG* 3.2 32.9 - - + +
122E LEU* 3.7 18.5 - - + +
123E ASP* 3.4 27.1 + - - +
126E TYR* 3.6 9.5 - - + -
213E LEU 4.8 0.2 + - - -
260E SER* 3.3 4.1 + - - +
261E ILE* 1.3 79.2 - - - +
263E GLN* 1.3 57.1 + - - +
265E VAL 4.1 0.4 - - - -
266E GLN* 3.2 27.2 + - - +
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Residues in contact with GLN 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E ARG* 4.1 19.2 - - + +
198E THR* 4.3 26.7 - - - +
212E ARG* 6.0 0.4 - - - +
259E GLN* 3.7 19.1 + - - -
260E SER* 3.2 27.3 + - - +
261E ILE 3.1 1.0 - - - -
262E ALA* 1.3 77.9 - - - +
264E VAL* 1.3 61.7 + - + +
266E GLN* 3.5 2.1 + - - +
267E TRP* 3.0 69.3 + - + +
279E ARG 4.9 4.8 + - - -
280E ASN* 5.9 0.4 - - - +
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Residues in contact with VAL 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215E LEU* 3.9 14.4 - - + -
238E VAL* 3.4 26.4 - - + +
240E VAL* 3.7 2.7 - - - +
251E TYR* 3.5 28.5 - - + -
259E GLN* 3.5 31.6 - - + -
260E SER 3.4 7.6 - - - +
261E ILE* 3.2 20.6 - - - +
263E GLN* 1.3 74.5 - - - +
265E VAL* 1.3 64.5 + - + +
267E TRP* 3.9 10.3 - - + -
268E SER* 3.1 28.1 + - - -
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Residues in contact with VAL 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E SER 4.7 0.9 - - - +
76E ALA* 3.4 23.5 - - + +
77E MET* 3.5 35.4 - - + +
80E SER* 3.9 5.8 - - - -
118E PHE* 4.6 4.9 - - + -
122E LEU* 3.6 23.1 - - + -
126E TYR* 3.4 14.1 - - - +
238E VAL* 4.3 11.2 - - + -
261E ILE* 3.1 23.3 + - + +
264E VAL* 1.3 75.4 - - + +
266E GLN* 1.3 66.0 + - - +
268E SER* 3.9 1.4 - - - -
269E GLY* 3.1 18.4 + - - -
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Residues in contact with GLN 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E ARG 5.0 3.0 + - - -
115E GLY* 3.2 30.3 + - - +
118E PHE* 4.2 17.5 - - + -
119E ARG* 4.1 18.5 - - + +
122E LEU* 4.2 0.8 - - + +
262E ALA 3.2 20.4 + - - +
263E GLN* 3.7 3.8 - - - +
265E VAL* 1.3 76.2 - - - +
267E TRP* 1.3 71.3 + - - +
269E GLY 3.1 4.2 + - - -
270E ALA* 2.7 46.1 + - - +
275E PHE* 3.7 19.9 - - - -
276E VAL 5.5 1.6 + - - +
278E GLY* 5.6 2.8 - - - -
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Residues in contact with TRP 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240E VAL* 3.7 5.4 - - + -
251E TYR* 3.7 17.0 - + - -
259E GLN* 3.7 26.5 - - - -
263E GLN* 3.0 49.6 + - + +
264E VAL* 3.9 12.3 - - + +
265E VAL 3.4 0.2 - - - -
266E GLN* 1.3 95.1 - - - +
268E SER* 1.3 57.2 + - - +
270E ALA* 2.9 20.0 + - + +
278E GLY* 4.0 21.6 - - - -
279E ARG 3.7 21.5 - - - +
280E ASN* 3.5 21.8 - - + -
286E ILE* 3.6 44.4 - - + -
287E ALA 2.9 22.6 - - - +
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Residues in contact with SER 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E GLY 4.1 0.5 + - - -
72E ALA* 3.2 6.6 - - - -
73E SER* 2.8 33.4 + - - -
76E ALA* 3.4 17.1 - - - +
238E VAL* 4.4 2.7 - - - -
239E VAL 3.0 20.2 + - - -
240E VAL* 3.5 9.8 - - - +
264E VAL 3.1 17.8 + - - -
265E VAL 3.9 0.7 - - - -
267E TRP* 1.3 77.9 - - - +
269E GLY* 1.3 56.7 + - - +
270E ALA 3.4 0.2 - - - -
288E ASP* 2.9 26.7 - - - +
289E GLY 3.1 7.4 + - - +
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Residues in contact with GLY 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E SER 3.9 16.3 + - - -
100E ILE* 5.7 1.6 - - - +
118E PHE* 5.4 9.3 - - - -
265E VAL 3.1 10.1 + - - -
266E GLN* 3.1 10.0 + - - -
268E SER* 1.3 76.1 - - - +
270E ALA* 1.3 58.4 + - - +
271E HIS* 3.3 7.7 + - - +
275E PHE* 3.7 16.5 - - - -
288E ASP* 4.2 7.4 - - - +
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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