Contacts of the helix formed by residues 256 - 269 (chain A) in PDB entry 2HCT
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 ASP 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A SER 4.9 5.8 - - - +
215A ILE* 3.9 26.0 + - + +
252A ASP 4.3 1.0 + - - -
253A LEU* 3.1 26.7 + - + +
254A CYS 3.4 0.2 - - - -
255A GLN* 1.3 80.1 - - - +
257A PRO* 1.3 78.6 - - - +
258A THR* 2.7 41.0 + - - +
259A ILE* 2.9 17.3 + - + +
260A LYS* 3.1 9.2 + - - +
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Residues in contact with PRO 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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255A GLN 3.5 4.7 - - - +
256A ASP* 1.3 94.7 - - - +
258A THR* 1.3 59.5 + - + +
260A LYS* 3.2 11.9 + - + +
261A GLU* 3.0 24.3 + - - +
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Residues in contact with THR 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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213A SER 4.5 4.9 - - - +
214A LYS* 4.3 22.7 - - + +
215A ILE* 3.6 3.5 + - - +
216A PHE* 2.9 53.4 + - - +
256A ASP* 2.7 22.4 + - - +
257A PRO* 1.3 77.3 - - + +
259A ILE* 1.3 60.3 + - - +
261A GLU* 3.2 18.7 - - - +
262A LEU 3.0 21.0 + - - -
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Residues in contact with ILE 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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208A LEU* 3.8 29.4 - - + -
215A ILE* 3.8 17.5 - - + -
216A PHE* 4.3 7.9 - - + -
240A ALA* 5.2 1.1 - - + -
242A VAL* 4.0 8.7 - - + -
253A LEU 3.4 19.7 - - - +
254A CYS 3.4 22.7 - - - +
256A ASP* 2.9 16.6 + - + +
258A THR* 1.3 77.0 + - - +
260A LYS* 1.3 61.9 + - - +
261A GLU 3.2 0.2 - - - -
262A LEU* 3.3 7.3 + - + +
263A GLU* 2.9 27.5 + - - +
273A PHE* 3.9 23.2 - - + -
275A CYS* 4.1 8.1 - - - -
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Residues in contact with LYS 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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254A CYS 3.4 21.6 + - - -
255A GLN* 3.4 33.5 + - - +
256A ASP 3.1 13.4 + - - +
257A PRO* 3.5 10.3 - - + +
259A ILE* 1.3 75.9 - - - +
261A GLU* 1.3 60.9 + - - +
263A GLU* 3.3 32.2 + - - +
264A SER* 3.0 29.3 + - - -
273A PHE* 6.0 0.6 - - - -
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Residues in contact with GLU 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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216A PHE* 3.6 17.7 - - + +
218A LYS* 3.4 45.9 + - + +
257A PRO 3.0 12.3 + - - +
258A THR* 3.2 18.1 - - - +
260A LYS* 1.3 73.4 - - - +
262A LEU* 1.3 65.7 + - - +
264A SER* 3.0 8.0 + - - -
265A ILE* 3.0 27.7 + - + +
163B PHE* 3.6 23.6 - - + -
164B ASP* 5.2 2.4 - - - +
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Residues in contact with LEU 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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208A LEU* 4.2 17.7 - - + -
216A PHE* 3.7 39.4 - - + -
222A PHE* 4.0 20.0 - - + -
227A VAL* 3.8 22.9 - - + -
238A LEU* 4.3 2.7 - - + -
240A ALA* 4.5 2.2 - - + -
258A THR 3.0 14.4 + - - +
259A ILE* 3.3 10.1 + - + +
261A GLU* 1.3 75.9 - - - +
263A GLU* 1.3 63.3 + - - +
265A ILE* 3.4 2.5 + - + +
266A ILE* 3.0 32.8 + - + +
273A PHE* 3.6 29.6 - - + -
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Residues in contact with GLU 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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259A ILE 2.9 17.7 + - - +
260A LYS* 3.5 38.0 + - - +
261A GLU 3.1 0.2 - - - -
262A LEU* 1.3 77.0 - - - +
264A SER* 1.3 55.7 + - - +
266A ILE* 3.9 0.7 - - - +
267A SER* 2.6 46.0 + - - +
273A PHE* 3.5 40.1 - - + +
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Residues in contact with SER 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 LYS 3.0 15.6 + - - -
261A GLU* 3.0 5.8 + - - -
263A GLU* 1.3 77.0 - - - +
265A ILE* 1.3 65.7 + - - +
267A SER* 3.4 4.6 + - - -
268A LYS* 3.0 26.2 + - - +
163B PHE* 3.5 23.5 - - - -
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Residues in contact with ILE 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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216A PHE* 4.0 28.7 - - + -
218A LYS* 4.6 6.7 - - + -
227A VAL* 3.6 27.4 - - + -
228A HIS* 3.8 18.6 - - + +
261A GLU* 3.0 21.9 + - + +
262A LEU* 3.8 4.3 - - + +
264A SER* 1.3 76.2 - - - +
266A ILE* 1.3 64.8 + - - +
268A LYS* 3.3 6.6 + - - +
269A ARG* 3.2 26.0 + - + +
97B HIS* 4.4 13.2 - - + +
100B ASP* 3.9 7.7 - - - +
163B PHE* 3.6 37.7 - - + -
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Residues in contact with ILE 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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227A VAL* 4.0 26.5 - - + +
230A LEU* 4.2 17.5 - - + -
238A LEU* 3.9 32.8 - - + -
262A LEU* 3.0 28.0 + - + +
263A GLU 4.1 2.5 - - - +
265A ILE* 1.3 78.2 - - - +
267A SER* 1.3 55.7 + - - +
269A ARG* 3.0 24.8 + - - +
271A ILE* 3.3 48.2 + - + +
272A GLN 3.9 10.8 - - - +
273A PHE* 4.4 6.7 - - + -
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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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263A GLU* 2.6 32.9 + - - +
264A SER* 3.9 5.2 - - - -
266A ILE* 1.3 76.4 - - - +
268A LYS* 1.3 59.4 + - - +
270A ASN* 2.9 23.6 + - - -
271A ILE 3.4 13.3 + - - -
273A PHE* 4.5 6.9 + - - +
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Residues in contact with LYS 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 SER* 3.0 18.3 + - - +
265A ILE* 4.2 7.0 - - - +
266A ILE 3.2 0.2 - - - -
267A SER* 1.3 77.8 - - - +
269A ARG* 1.3 59.2 + - + +
270A ASN* 3.2 6.8 + - - +
95B SER 5.2 3.4 - - - +
96B LYS* 3.9 38.5 - - + +
97B HIS* 4.7 9.6 - - + +
100B ASP* 3.7 33.4 + - - +
102B THR* 5.5 2.6 - - - +
105B ASP* 3.8 19.4 + - - -
163B PHE* 5.7 4.5 - - + -
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Residues in contact with ARG 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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227A VAL* 3.0 27.9 + - - -
228A HIS* 3.7 15.5 + - - -
230A LEU* 2.7 34.3 + - - +
231A GLN* 5.5 1.8 - - - +
232A PRO* 3.3 38.1 - - - +
265A ILE* 3.2 19.7 - - - +
266A ILE* 3.0 12.9 + - - +
268A LYS* 1.3 79.8 - - + +
270A ASN* 1.3 70.8 + - - +
271A ILE* 4.3 10.8 - - + +
100B ASP* 3.0 48.0 + - + +
182B ASN* 5.6 4.8 - - - +
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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