Contacts of the helix formed by residues 261 - 273 (chain A) in PDB entry 2EIT
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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258A PHE* 3.6 3.3 - - - -
260A GLY* 1.3 75.7 - - - +
262A LEU* 1.3 58.7 + - - +
263A GLU* 3.6 9.0 + - - +
264A VAL* 3.2 19.1 + - - +
265A GLY* 2.9 23.7 + - - -
289A THR* 3.9 1.0 - - - +
1518A NAD 2.8 53.5 + - - -
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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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261A SER* 1.3 70.1 - - - +
263A GLU* 1.3 66.9 + - - +
266A LEU* 2.8 50.1 + - + +
289A THR* 3.6 18.6 + - - +
417A GLU* 5.4 0.4 + - - -
442A PRO* 5.7 0.2 - - + -
443A TYR* 3.6 34.5 + - + +
490A LEU* 3.5 41.3 - - + +
1518A NAD 4.4 1.2 + - - -
282B PHE* 3.9 16.6 - - + -
2533B MPD 4.3 15.5 - - + -
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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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261A SER* 3.2 9.2 + - - +
262A LEU* 1.3 81.0 - - - +
264A VAL* 1.3 70.8 + - + +
266A LEU* 3.6 9.4 + - - +
267A LYS* 3.4 42.3 + - - +
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Residues in contact with VAL 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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258A PHE* 3.5 24.7 - - + -
261A SER* 3.2 13.2 + - - +
263A GLU* 1.3 84.6 - - + +
265A GLY* 1.3 66.1 + - - +
267A LYS* 3.1 12.0 + - + +
268A ILE* 2.9 27.7 + - + +
1518A NAD 3.4 68.0 - - + +
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Residues in contact with GLY 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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258A PHE* 3.5 24.7 - - - -
261A SER 2.9 12.5 + - - -
262A LEU 3.6 2.9 - - - -
264A VAL* 1.3 76.0 - - - +
266A LEU* 1.3 55.2 + - - +
268A ILE* 3.4 2.6 + - - +
269A TYR* 2.9 31.7 + - - +
287A VAL* 4.0 6.3 - - - +
289A THR* 3.8 9.9 - - - -
282B PHE* 4.4 6.1 - - - -
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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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262A LEU* 2.8 46.9 + - + +
263A GLU* 3.8 8.5 - - - +
265A GLY* 1.3 71.3 - - - +
267A LYS* 1.3 64.6 + - + +
269A TYR* 3.9 1.9 - - - +
270A GLU* 3.0 26.5 + - - +
490A LEU* 4.5 2.0 - - + -
273B GLY 4.6 1.2 - - - +
275B LEU* 4.0 47.1 - - + -
282B PHE* 3.8 27.8 - - + -
2533B MPD 4.5 6.1 - - + -
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Residues in contact with LYS 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* 3.4 34.8 + - + +
264A VAL* 3.1 12.7 + - + +
266A LEU* 1.3 79.6 - - + +
268A ILE* 1.3 57.3 + - - +
270A GLU* 3.4 6.7 + - - +
271A ALA* 2.9 30.3 + - - +
274A ARG* 5.2 0.7 + - - -
1518A NAD 4.7 8.9 + - - +
1519A ACT 3.8 25.4 - - + +
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Residues in contact with ILE 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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180A ILE* 4.3 8.3 - - + -
248A VAL* 4.1 15.4 - - + +
256A ILE* 3.7 28.0 - - + -
258A PHE* 3.4 37.5 - - + -
264A VAL* 2.9 28.2 + - + +
265A GLY* 3.7 4.7 - - - +
267A LYS* 1.3 73.9 - - - +
269A TYR* 1.3 60.4 + - - +
271A ALA* 3.3 2.4 + - - +
272A ALA* 2.8 28.8 + - - +
285A ALA* 4.6 2.9 - - + -
287A VAL* 4.1 13.2 - - + -
1518A NAD 4.1 11.0 - - + -
1519A ACT 3.6 17.5 - - - +
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Residues in contact with TYR 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 GLY 2.9 20.1 + - - +
266A LEU* 3.9 3.4 - - - +
268A ILE* 1.3 75.5 - - - +
270A GLU* 1.3 62.7 + - - +
272A ALA* 3.4 5.7 + - + +
273A GLY* 3.3 15.2 + - - -
285A ALA* 3.7 26.7 - - + -
287A VAL* 4.3 5.8 - - + -
493A THR* 3.6 25.4 - - + +
272B ALA 4.0 12.1 - - - -
273B GLY* 3.7 27.1 - - - +
282B PHE* 3.6 36.9 + + + +
283B LYS 2.6 30.4 + - - -
284B ARG* 4.5 5.2 - - - +
285B ALA 5.4 0.5 + - - -
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Residues in contact with GLU 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 LEU 3.0 19.1 + - - +
267A LYS* 3.7 6.9 - - - +
269A TYR* 1.3 76.0 - - - +
271A ALA* 1.3 64.4 + - - +
273A GLY* 3.0 14.7 + - - -
274A ARG* 3.7 24.1 + - + +
270B GLU* 5.1 2.6 - - + +
273B GLY* 3.2 14.7 + - - +
274B ARG* 3.9 38.1 - - + +
275B LEU 4.9 2.8 + - - -
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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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248A VAL* 3.8 13.0 - - + +
249A GLU* 4.4 5.4 - - + -
267A LYS 2.9 18.3 + - - +
268A ILE 3.8 3.1 - - - +
270A GLU* 1.3 77.8 - - - +
272A ALA* 1.3 61.4 + - - +
274A ARG* 3.1 53.7 + - - +
283A LYS* 5.0 4.7 + - - -
1519A ACT 3.7 20.0 - - + -
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Residues in contact with ALA 272 (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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248A VAL* 4.8 1.0 - - - +
256A ILE* 4.0 14.1 - - + -
268A ILE 2.8 17.2 + - - +
269A TYR* 3.8 4.9 - - + +
270A GLU 3.3 0.2 - - - -
271A ALA* 1.3 75.6 - - - +
273A GLY* 1.3 60.2 + - - +
274A ARG 3.4 5.0 + - - +
279A GLN* 5.0 0.2 + - - -
283A LYS* 3.5 35.7 + - + +
285A ALA* 3.5 29.2 - - + +
269B TYR* 3.9 9.5 - - - -
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Residues in contact with GLY 273 (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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269A TYR 3.3 8.1 + - - -
270A GLU 3.0 11.2 + - - -
272A ALA* 1.3 77.3 - - - +
274A ARG* 1.3 59.9 + - - +
275A LEU 4.0 0.3 + - - -
266B LEU 4.6 1.7 - - - +
269B TYR* 3.7 33.4 - - - +
270B GLU* 3.3 29.0 + - - +
273B GLY* 4.9 2.7 - - - -
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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