Contacts of the helix formed by residues 259 - 268 (chain A) in PDB entry 1X79
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 MET 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A ALA* 3.6 28.0 - - + +
220A GLU* 3.7 28.0 - - + +
221A VAL* 3.5 29.6 - - + -
255A ARG* 3.2 14.9 + - + +
256A CYS* 3.6 19.7 - - - +
257A GLU 3.1 0.2 - - - -
258A ARG* 1.3 79.8 - - - +
260A ARG* 1.3 65.3 + - - +
261A PRO 3.4 0.2 - - - -
262A THR* 3.0 29.1 + - + -
263A LEU* 3.0 17.6 + - + +
287A LEU* 4.3 10.3 - - + -
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Residues in contact with ARG 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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256A CYS 4.1 8.7 - - - +
257A GLU* 3.3 16.2 - - - +
259A MET* 1.3 73.2 - - - +
261A PRO* 1.3 74.4 - - + +
262A THR 2.9 0.3 + - - -
263A LEU* 3.0 11.8 + - - +
264A PHE* 2.7 39.9 + - + -
284A ASN* 3.6 12.9 + - - -
287A LEU* 4.3 7.3 - - + +
288A THR* 2.7 39.6 + - - +
291A ILE* 4.1 33.7 - - - +
295A LYS* 5.7 1.6 - - - +
566B GLN* 2.8 36.8 + - - +
570B GLN* 3.8 17.7 - - - +
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Residues in contact with PRO 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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257A GLU 3.8 4.5 - - - +
258A ARG* 3.1 20.0 - - - +
260A ARG* 1.3 94.7 - - + +
262A THR* 1.3 55.4 + - - +
264A PHE* 3.1 4.4 + - + -
265A ARG* 2.9 26.3 + - - +
570B GLN* 4.0 3.4 - - - +
568C ASN* 3.0 26.8 + - - +
571C LEU* 3.9 12.1 - - + -
572C GLU* 4.2 11.4 - - + +
575C MET* 3.4 40.6 - - + -
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Residues in contact with THR 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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217A ALA* 4.2 24.2 - - + -
258A ARG 3.8 10.6 + - - -
259A MET* 3.0 27.4 + - + -
260A ARG 2.9 0.6 - - - -
261A PRO* 1.3 79.9 - - - +
263A LEU* 1.3 62.9 + - - +
265A ARG* 3.3 4.9 + - - +
266A LEU* 3.0 32.5 + - + +
572C GLU* 5.5 1.3 - - - -
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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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217A ALA* 4.5 9.6 - - + -
218A ILE* 5.3 2.9 - - + -
221A VAL* 4.1 22.7 - - + -
259A MET* 3.0 26.0 + - + +
260A ARG* 3.0 7.0 + - - +
262A THR* 1.3 74.2 - - - +
264A PHE* 1.3 65.3 + - + +
266A LEU* 3.4 16.8 + - + -
267A ALA* 2.9 26.2 + - - +
280A ILE* 3.7 14.7 - - + +
283A ALA* 4.9 7.0 - - + -
284A ASN* 4.4 20.2 - - - +
287A LEU* 3.5 29.8 - - + -
563B MET* 4.0 15.5 - - + -
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Residues in contact with PHE 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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260A ARG* 2.7 43.9 + - + -
261A PRO* 3.4 3.6 - - + +
263A LEU* 1.3 71.5 - - + +
265A ARG* 1.3 65.8 + - - +
268A SER* 2.9 22.2 + - - -
284A ASN* 4.5 5.2 - - - -
563B MET* 3.8 39.7 - - + -
566B GLN* 3.8 17.5 - - + -
567B ALA* 3.6 39.0 - - + -
570B GLN* 4.3 3.1 - - - -
564C LEU* 3.3 26.2 - - + +
568C ASN* 3.3 24.9 - - + +
571C LEU* 3.9 14.1 - - + -
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Residues in contact with ARG 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 PRO 2.9 11.3 + - - +
262A THR* 3.7 4.9 - - - +
264A PHE* 1.3 77.8 - - - +
266A LEU* 1.3 65.0 + - + +
268A SER* 2.6 20.1 + - - -
269A ASP* 2.8 33.8 + - - +
565C ARG* 2.8 57.1 - - - +
568C ASN* 3.0 24.4 - - - +
569C ASP* 4.7 3.6 + - - -
572C GLU* 4.8 11.3 + - - +
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Residues in contact with LEU 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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213A LYS* 4.7 4.9 - - + -
214A ARG* 3.9 31.2 - - + +
217A ALA* 3.5 32.3 - - + -
218A ILE* 5.4 0.2 - - + -
262A THR* 3.0 25.9 + - + +
263A LEU* 3.7 13.0 - - + +
265A ARG* 1.3 77.7 - - + +
267A ALA* 1.3 55.1 + - - +
269A ASP* 2.7 35.0 + - + +
270A THR* 3.4 8.7 + - - -
280A ILE* 3.8 21.3 - - + -
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Residues in contact with ALA 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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263A LEU 2.9 17.5 + - - +
264A PHE 3.7 2.9 - - - +
266A LEU* 1.3 77.1 - - - +
268A SER* 1.3 57.4 + - - +
269A ASP 3.0 1.9 + - - -
270A THR* 3.5 3.7 + - - -
277A LEU* 4.0 22.8 - - + +
280A ILE* 3.9 14.3 - - + +
281A LEU* 4.4 0.7 - - + -
560B LEU* 4.4 4.7 - - + +
563B MET* 3.8 23.1 - - + -
561C GLN* 2.8 26.5 + - - +
564C LEU* 4.3 4.3 - - + -
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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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264A PHE 2.9 14.0 + - - -
265A ARG* 2.6 34.3 + - - -
266A LEU 3.1 0.2 + - - -
267A ALA* 1.3 76.5 - - - +
269A ASP* 1.3 60.1 + - - +
270A THR 3.6 0.4 - - - -
561C GLN* 3.5 43.7 + - - +
562C LEU* 5.8 1.7 - - - +
564C LEU* 4.2 5.6 - - - +
565C ARG* 3.8 24.8 - - - +
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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