Contacts of the helix formed by residues 261 - 271 (chain A) in PDB entry 6EJ9
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 GLY 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259A ILE 3.8 0.4 - - - -
260A SER* 1.3 76.1 + - - +
262A LYS* 1.3 66.9 + - - -
263A GLU* 3.2 6.2 + - - -
264A ALA* 3.3 4.6 + - - +
265A ILE* 3.1 25.1 + - - +
284A TYR* 3.3 23.5 + - - -
478A LEU 5.8 1.1 - - - -
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Residues in contact with LYS 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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260A SER 3.4 6.1 + - - +
261A GLY* 1.3 72.4 - - - -
263A GLU* 1.3 70.6 + - + +
265A ILE* 3.6 7.3 + - + +
266A SER* 3.2 23.4 + - - -
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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
----------------------------------------------------------
261A GLY* 3.2 2.7 - - - -
262A LYS* 1.3 88.7 + - + +
264A ALA* 1.3 61.3 + - - +
266A SER* 3.4 7.8 + - - -
267A ALA* 3.1 17.7 + - - +
270A ARG* 5.0 1.2 + - - -
466A ARG* 4.8 3.6 + - - -
477A ARG* 3.6 55.4 + - + +
478A LEU 3.9 9.0 - - - +
479A GLY* 3.3 27.9 + - - +
480A ASP* 4.1 9.4 + - - +
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Residues in contact with ALA 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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259A ILE* 4.0 12.1 - - + -
261A GLY 3.3 8.0 + - - +
263A GLU* 1.3 75.6 - - - +
265A ILE* 1.3 61.1 + - - +
267A ALA* 3.2 7.3 + - - +
268A LEU* 2.9 34.8 + - + +
280A ILE* 4.5 4.4 - - + +
284A TYR* 3.6 36.6 - - + -
478A LEU* 4.1 18.5 + - + +
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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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259A ILE* 3.5 33.4 - - + +
260A SER* 3.6 15.5 - - - +
261A GLY 3.1 20.1 + - - +
262A LYS* 4.0 6.5 - - + +
264A ALA* 1.3 76.2 - - - +
266A SER* 1.3 63.5 + - - +
268A LEU* 3.3 9.1 + - + +
269A SER* 3.0 26.4 + - - -
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Residues in contact with SER 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 LYS 3.2 17.9 + - - -
263A GLU* 3.6 7.2 - - - -
264A ALA 3.3 0.2 - - - -
265A ILE* 1.3 79.3 - - - +
267A ALA* 1.3 60.8 + - - +
269A SER* 2.9 23.1 + - - -
270A ARG* 3.1 34.6 + - - +
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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 GLU 3.1 14.0 + - - +
264A ALA 3.2 7.2 + - - +
266A SER* 1.3 76.1 - - - +
268A LEU* 1.3 59.8 + - - +
270A ARG* 3.8 12.5 - - - +
271A ALA* 2.9 32.6 + - - +
280A ILE* 4.0 9.3 - - + +
476A TRP* 3.8 23.3 - - + -
477A ARG 4.5 1.6 - - - +
478A LEU* 4.0 22.4 - - + -
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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 ILE* 3.8 37.7 - - + -
264A ALA* 2.9 20.1 + - + +
265A ILE* 3.8 8.5 - - + +
266A SER 3.3 0.4 - - - -
267A ALA* 1.3 76.9 - - - +
269A SER* 1.3 61.6 + - - +
270A ARG 3.6 0.2 + - - -
271A ALA* 3.8 6.9 + - - +
277A ARG* 3.4 60.5 - - + +
280A ILE* 3.4 22.0 - - + -
281A GLY* 4.4 2.5 - - - +
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Residues in contact with SER 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 ILE* 3.0 16.1 + - - -
266A SER* 2.9 19.4 + - - -
267A ALA 3.3 0.2 - - - -
268A LEU* 1.3 78.1 - - - +
270A ARG* 1.3 65.3 + - - +
271A ALA 4.2 3.2 - - - +
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Residues in contact with ARG 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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263A GLU 5.0 1.4 + - - -
266A SER* 3.1 34.3 + - - +
267A ALA* 3.8 16.0 - - - +
269A SER* 1.3 83.8 + - - +
271A ALA* 1.3 66.7 + - - +
272A LYS* 3.6 10.2 + - - +
474A HIS* 4.2 5.1 + - - -
476A TRP* 3.8 30.7 - - + -
477A ARG 5.4 0.8 + - - -
570A ASP* 3.0 42.0 + - - -
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Residues in contact with ALA 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 ALA 2.9 18.3 + - - +
268A LEU 3.8 3.0 + - - +
269A SER 3.5 6.0 - - - +
270A ARG* 1.3 81.0 - - - +
272A LYS* 1.3 60.7 - - - +
276A CYS* 4.0 24.0 - - + -
277A ARG* 3.7 35.4 + - + -
280A ILE* 4.1 6.5 - - + -
476A TRP* 3.9 12.1 - - + -
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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