Contacts of the helix formed by residues 261 - 271 (chain A) in PDB entry 7EHI
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 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A THR 3.8 2.2 - - - -
219A GLN* 3.6 20.9 - - - +
257A ILE* 3.6 24.1 - - - +
258A GLY 2.9 21.6 + - - -
260A LYS* 1.3 81.1 - - - +
262A VAL* 1.3 65.8 + - - +
263A GLN* 3.6 12.2 + - - -
264A TRP* 3.1 19.6 + - - +
265A GLN* 2.9 22.7 + - - +
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Residues in contact with VAL 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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219A GLN* 4.3 6.7 + - + +
260A LYS 3.8 1.0 + - - -
261A SER* 1.3 72.2 - - - +
263A GLN* 1.3 71.4 + - - +
265A GLN* 3.4 5.8 + - - +
266A ASP* 2.9 29.4 + - + +
276A TYR* 4.8 15.9 - - + +
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Residues in contact with GLN 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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219A GLN 4.7 2.8 - - - +
257A ILE* 3.6 10.5 - - + +
261A SER* 3.1 17.8 - - - +
262A VAL* 1.3 87.1 + - - +
264A TRP* 1.3 62.9 + - - +
266A ASP* 3.3 4.9 + - - +
267A VAL* 3.1 23.9 + - - +
276A TYR* 3.6 46.0 + - + +
279A TRP* 4.0 12.9 - - + -
280A PHE* 3.9 19.3 - - + -
325A TYR* 3.4 35.6 + - - -
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Residues in contact with TRP 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ILE* 4.8 0.2 - - + -
258A GLY 4.0 5.2 - - - +
259A ASP* 3.3 41.0 - - + +
261A SER* 3.1 16.9 + - - +
263A GLN* 1.3 76.4 - - - +
265A GLN* 1.3 66.3 + - - +
267A VAL* 3.0 8.5 + - + +
268A LEU* 2.9 47.5 + - + +
280A PHE* 3.6 44.8 - + + -
282A ILE* 4.1 7.9 - - + -
287A ALA* 3.7 21.8 - - + -
303A TYR* 3.6 54.4 + + + -
313A PRO* 3.7 22.2 - - + -
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Residues in contact with GLN 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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259A ASP* 2.7 25.6 + - - +
260A LYS* 3.9 29.6 - - - +
261A SER 2.9 21.4 + - - +
262A VAL* 3.8 5.4 - - - +
264A TRP* 1.3 75.4 - - - +
266A ASP* 1.3 58.0 + - - +
268A LEU* 3.2 24.7 + - - +
269A LYS* 3.0 27.7 + - - +
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Residues in contact with ASP 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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262A VAL* 2.9 20.2 + - + +
263A GLN 3.5 5.4 - - - +
264A TRP 3.1 0.2 - - - -
265A GLN* 1.3 73.7 - - - +
267A VAL* 1.3 58.3 + - - +
269A LYS* 3.2 4.5 + - - +
270A ASN* 2.8 56.3 + - - +
274A SER* 2.6 23.8 + - - -
275A PRO* 3.3 11.7 - - - +
276A TYR* 3.7 21.4 - - + -
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Residues in contact with VAL 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 GLN 3.1 13.4 + - - +
264A TRP* 3.0 22.3 + - + +
266A ASP* 1.3 76.8 - - - +
268A LEU* 1.3 58.3 + - - +
271A GLU* 2.9 28.3 + - - +
274A SER* 3.8 19.5 - - - +
276A TYR 3.9 9.9 - - - +
277A ALA* 4.1 4.3 - - - +
280A PHE* 3.8 25.1 - - + -
282A ILE* 3.6 24.0 - - + -
285A PHE* 4.6 8.7 - - + -
287A ALA* 4.2 14.8 + - + -
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Residues in contact with LEU 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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259A ASP* 5.8 0.7 - - + -
264A TRP* 2.9 49.4 + - + +
265A GLN* 3.6 28.7 - - - +
267A VAL* 1.3 77.7 - - - +
269A LYS* 1.3 62.2 + - - +
271A GLU* 4.6 6.8 + - - +
286A PRO* 6.0 1.2 - - - +
287A ALA* 3.6 32.1 - - + +
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Residues in contact with LYS 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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265A GLN 3.0 15.9 + - - +
266A ASP* 3.2 5.8 + - - +
268A LEU* 1.3 78.8 - - - +
270A ASN* 1.3 89.1 + - - +
271A GLU* 4.9 3.3 - - - +
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Residues in contact with ASN 270 (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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266A ASP* 2.8 44.1 + - - +
269A LYS* 1.3 107.9 + - - +
271A GLU* 1.3 71.0 + - - +
273A ALA* 3.1 23.8 + - + +
274A SER* 3.7 17.6 - - - +
275A PRO* 4.9 2.4 - - - +
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Residues in contact with GLU 271 (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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267A VAL* 2.9 19.6 + - - +
268A LEU 4.7 8.1 - - - +
269A LYS 4.9 2.2 - - - +
270A ASN* 1.3 79.0 - - - +
272A GLN* 1.3 60.9 + - - +
274A SER* 2.9 25.5 + - - -
277A ALA* 4.2 1.2 - - - +
285A PHE* 3.6 24.7 - - + +
286A PRO* 3.8 43.1 - - + +
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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