Contacts of the helix formed by residues 262 - 269 (chain A) in PDB entry 2HTE
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 ASN 262 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A TYR 3.4 4.2 + - - -
261A TYR* 1.3 86.9 - - - +
263A TYR* 1.3 64.3 + - - +
264A GLU* 3.2 8.6 + - - +
265A ASN* 2.9 51.1 + - - +
266A HIS* 3.1 22.5 + - - +
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Residues in contact with TYR 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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246A PRO* 3.6 42.9 + - + +
247A ASN 5.9 0.2 - - - -
248A LYS 4.2 7.2 - - - -
249A LYS* 3.6 53.3 - - + +
261A TYR* 4.0 11.5 - - - -
262A ASN* 1.3 75.5 - - - +
264A GLU* 1.3 74.8 + - + +
266A HIS* 3.5 13.7 - - - +
267A SER* 4.0 6.7 + - - -
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Residues in contact with GLU 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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262A ASN* 3.2 7.6 + - - +
263A TYR* 1.3 88.8 - - + +
265A ASN* 1.3 67.0 + - - +
266A HIS 3.2 2.2 + - - -
267A SER* 3.4 7.2 + - - -
268A ALA* 3.2 20.6 + - - +
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Residues in contact with ASN 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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67A MET* 3.9 12.1 - - + +
260A TYR* 2.9 33.9 + - + +
262A ASN* 2.9 35.6 + - - +
264A GLU* 1.3 74.6 - - - +
266A HIS* 1.3 67.8 + - - +
268A ALA* 3.7 10.0 - - - +
269A ALA* 3.2 23.0 + - - +
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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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67A MET* 4.4 6.6 - - - +
71A VAL* 3.2 36.4 - - + +
74A THR* 3.2 7.6 + - - -
75A VAL* 3.7 8.7 - - + -
243A LEU 2.6 26.5 + - - -
244A THR 3.5 17.9 - - - -
246A PRO* 3.6 12.2 - - + +
261A TYR* 2.8 42.0 + + + +
262A ASN 3.1 5.6 + - - +
263A TYR 3.5 13.5 - - - +
265A ASN* 1.3 80.6 - - - +
267A SER* 1.3 61.2 + - - +
269A ALA* 3.4 5.9 + - - +
270A PHE* 3.3 24.8 - + - -
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Residues in contact with SER 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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244A THR* 3.0 25.3 + - - -
245A LYS* 4.3 6.8 - - - +
246A PRO* 4.0 12.0 - - - +
263A TYR* 4.0 4.7 + - - -
264A GLU* 3.4 7.4 + - - -
266A HIS* 1.3 77.2 - - - +
268A ALA* 1.3 63.0 + - - +
269A ALA 3.1 1.2 + - - -
270A PHE* 3.2 19.3 + - - +
271A LYS* 4.0 18.0 + - - +
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Residues in contact with ALA 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 GLU 3.2 16.2 + - - +
265A ASN* 3.8 11.9 - - - +
266A HIS 3.3 0.4 - - - -
267A SER* 1.3 78.5 - - - +
269A ALA* 1.3 57.4 + - - +
270A PHE 3.1 0.2 - - - -
271A LYS* 3.1 34.7 + - - +
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Residues in contact with ALA 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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67A MET* 3.8 17.3 - - + -
219A ALA* 3.3 12.2 - - + -
220A ASN* 2.9 46.1 + - - +
233A ILE* 6.0 0.2 - - + -
265A ASN 3.2 16.7 + - - +
266A HIS 3.6 7.4 - - - +
267A SER 3.1 0.8 - - - -
268A ALA* 1.3 76.8 - - - +
270A PHE* 1.3 61.0 + - + +
271A LYS 3.3 2.0 + - - +
272A LEU* 4.0 5.2 - - - +
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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