Contacts of the helix formed by residues 255 - 268 (chain A) in PDB entry 3ZG6
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 TYR 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A PHE* 3.5 34.5 - + - -
239A LEU* 3.8 13.5 - - + -
254A GLY* 1.3 71.2 - - - -
256A VAL* 1.3 66.0 + - - +
257A ASP* 4.4 4.3 - - + +
258A GLU* 3.0 31.9 + - + +
259A VAL* 2.9 19.5 + - - +
1296A APR 3.4 21.8 - - - +
1299A GOL 4.4 17.1 + - - -
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Residues in contact with VAL 256 (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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52A GLY 3.9 16.8 - - - +
53A ILE* 4.0 9.9 - - + -
92A THR* 3.5 20.6 - - + +
211A LEU* 4.1 28.7 - - + -
212A GLY 4.1 9.6 - - - +
237A VAL* 4.1 14.4 - - + -
254A GLY 4.5 0.2 - - - -
255A TYR* 1.3 72.8 - - - +
257A ASP* 1.3 68.3 + - - +
259A VAL* 3.1 6.1 + - - +
260A MET* 2.9 29.4 + - + +
1296A APR 3.0 36.6 + - + +
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Residues in contact with ASP 257 (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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53A ILE 5.3 0.2 - - - +
56A ALA* 3.3 28.4 - - - +
90A THR* 3.7 10.4 + - - -
91A GLN* 4.2 16.5 + - + +
92A THR* 2.6 45.6 + - - +
255A TYR* 3.2 4.8 - - + +
256A VAL* 1.3 80.4 - - - +
258A GLU* 1.3 56.7 + - - +
260A MET* 3.9 0.5 - - - +
261A THR* 2.9 35.4 + - - +
1296A APR 5.3 1.3 + - - +
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Residues in contact with GLU 258 (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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28A LEU* 3.5 13.9 - - + +
254A GLY* 5.9 1.7 - - - -
255A TYR* 3.0 34.0 + - + +
257A ASP* 1.3 81.0 - - - +
259A VAL* 1.3 61.2 + - + +
261A THR* 3.6 5.9 + - + -
262A ARG* 2.7 69.9 + - + +
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Residues in contact with VAL 259 (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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28A LEU* 4.2 10.1 - - + -
32A VAL* 3.7 27.8 - - + +
35A LEU* 4.0 21.8 - - + -
211A LEU* 5.6 0.4 - - + -
237A VAL* 4.1 20.2 - - + -
252A ILE* 3.6 30.5 - - + -
254A GLY 4.6 3.6 - - - -
255A TYR 2.9 16.6 + - - +
256A VAL* 3.8 8.7 - - - +
258A GLU* 1.3 80.5 - - + +
260A MET* 1.3 67.4 + - + +
262A ARG* 3.5 0.4 + - - -
263A LEU* 2.9 26.3 + - - +
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Residues in contact with MET 260 (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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35A LEU* 5.6 1.8 - - - -
47A PHE* 3.9 23.1 - - + -
91A GLN 5.2 0.9 - - - +
92A THR* 3.6 25.4 - - + +
95A ALA* 4.2 19.3 - - + -
96A LEU* 4.0 13.9 - - + -
99A LEU* 3.9 20.6 - - + -
209A ILE* 6.2 0.2 - - - -
211A LEU* 4.1 23.3 - - + -
256A VAL* 2.9 20.7 + - + +
257A ASP 4.2 2.0 - - - +
259A VAL* 1.3 80.5 - - + +
261A THR* 1.3 66.3 + - - +
263A LEU* 3.7 18.5 - - + +
264A MET* 3.0 31.2 + - - +
271A ILE* 4.8 0.9 - - - -
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Residues in contact with THR 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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91A GLN* 4.6 9.4 + - - +
257A ASP 2.9 20.6 + - - -
258A GLU* 3.7 7.9 - - + +
260A MET* 1.3 77.3 - - - +
262A ARG* 1.3 69.7 + - + +
264A MET* 3.3 2.6 + - - +
265A LYS* 3.1 23.0 + - + +
271A ILE* 4.0 22.1 - - + +
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Residues in contact with ARG 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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25A PRO* 4.9 8.3 + - - +
28A LEU* 3.5 14.5 - - + +
29A GLU* 3.2 39.8 + - - +
32A VAL* 3.5 23.7 - - + +
258A GLU* 2.7 52.6 + - - +
259A VAL* 4.1 2.5 - - - +
261A THR* 1.3 81.9 - - - +
263A LEU* 1.3 64.7 + - - +
265A LYS* 3.2 14.3 + - + +
266A HIS* 2.9 31.4 + - + +
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Residues in contact with LEU 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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32A VAL* 3.5 10.7 - - + +
35A LEU* 4.2 21.3 - - + +
36A ALA* 3.6 37.0 - - + +
39A VAL* 4.6 11.4 - - + -
47A PHE* 5.0 4.0 - - + -
99A LEU* 4.6 9.0 - - + -
259A VAL 2.9 18.6 + - - +
260A MET* 3.3 32.7 + - + +
262A ARG* 1.3 77.9 - - - +
264A MET* 1.3 64.5 + - - +
266A HIS* 3.3 4.9 + - - +
267A LEU* 3.0 42.3 + - + +
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Residues in contact with MET 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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95A ALA* 3.7 32.1 - - + +
98A GLN* 3.8 17.9 - - + -
99A LEU* 3.6 28.3 - - + -
260A MET* 3.0 20.5 + - - +
261A THR 3.6 3.1 - - - +
263A LEU* 1.3 78.0 - - - +
265A LYS* 1.3 53.5 + - - +
267A LEU* 2.7 27.2 + - - +
268A GLY 2.8 15.6 + - - -
269A LEU* 3.3 48.1 + - + +
270A GLU 4.3 5.8 - - - +
271A ILE* 3.9 20.6 - - + -
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Residues in contact with LYS 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 THR* 3.1 15.0 + - + +
262A ARG* 3.3 17.0 - - + +
264A MET* 1.3 74.3 - - - +
266A HIS* 1.3 70.0 + - + +
267A LEU 3.2 0.9 + - - -
268A GLY* 3.3 11.2 + - - +
269A LEU 4.5 2.4 + - - -
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Residues in contact with HIS 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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29A GLU* 4.9 3.8 + - - -
32A VAL* 4.0 17.2 - - + +
33A TRP* 4.0 53.9 + + + +
36A ALA* 3.8 15.2 - - + +
262A ARG* 2.9 31.8 + - - +
263A LEU* 3.7 5.6 - - - +
264A MET 3.3 0.2 - - - -
265A LYS* 1.3 81.4 - - + +
267A LEU* 1.3 60.0 + - - +
293A PRO* 3.4 25.5 - - - +
294A LYS* 5.5 2.1 - - - -
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Residues in contact with LEU 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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36A ALA* 4.1 27.1 - - + +
39A VAL* 4.2 11.2 - - + -
40A TRP* 4.7 15.7 - - + -
99A LEU* 3.8 30.1 - - + -
104A LEU* 4.0 18.6 - - + -
263A LEU* 3.0 36.9 + - + +
264A MET* 2.7 19.0 + - - +
266A HIS* 1.3 76.1 - - - +
268A GLY* 1.3 56.1 + - - -
269A LEU* 3.5 13.0 - - + -
290A PRO* 3.3 26.2 - - - +
291A PRO 4.9 2.1 - - - +
293A PRO* 4.7 12.2 - - + +
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Residues in contact with GLY 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 MET 2.8 7.8 + - - -
265A LYS* 3.3 10.7 + - - -
266A HIS 3.4 0.4 - - - -
267A LEU* 1.3 79.0 - - - +
269A LEU* 1.3 61.3 + - - +
270A GLU* 4.3 1.7 + - - -
290A PRO* 4.2 8.3 - - - +
291A PRO* 5.6 3.4 - - - +
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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