Contacts of the helix formed by residues 256 - 271 (chain A) in PDB entry 3EIJ
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 ARG 256 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A THR* 2.8 8.8 + - + +
255A PRO* 1.3 79.5 - - + +
257A ALA* 1.3 63.6 + - - +
258A PRO* 3.3 3.6 - - - -
259A GLN* 3.2 36.6 + - - +
260A LEU* 3.1 37.5 + - + +
263A GLN* 4.7 10.3 - - - +
346A GLU* 2.9 41.4 + - - -
349A HIS* 2.5 53.1 + - - +
350A CYS* 5.3 2.2 - - - +
353A GLU* 4.7 2.5 + - - -
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Residues in contact with ALA 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LEU* 4.3 19.1 - - + -
247A LEU* 4.2 6.1 - - + -
250A LEU* 4.0 15.5 - - + +
251A ALA* 4.0 17.9 - - - +
254A THR* 2.7 27.2 + - - +
256A ARG* 1.3 70.7 - - - +
258A PRO* 1.3 71.5 - - + +
260A LEU 3.2 0.3 + - - -
261A VAL* 2.8 30.0 + - - +
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Residues in contact with PRO 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A LEU* 3.4 26.0 - - + -
251A ALA* 4.5 4.9 - - + -
255A PRO 3.8 11.2 - - - +
256A ARG 3.4 3.8 - - - -
257A ALA* 1.3 93.6 - - + +
259A GLN* 1.3 65.9 + - - +
261A VAL 3.3 0.2 + - - -
262A GLY 2.9 23.7 + - - -
290A GLN* 3.8 32.3 - - + +
293A ALA* 3.9 15.5 - - + -
294A ALA* 3.3 17.2 - - + +
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Residues in contact with GLN 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A PRO 4.4 1.8 + - - -
256A ARG* 3.2 63.7 + - - +
258A PRO* 1.3 92.6 - - - +
260A LEU* 1.3 57.7 + - + +
262A GLY* 3.1 3.8 + - - -
263A GLN* 2.9 28.6 + - - +
293A ALA* 4.7 9.2 - - - +
297A LYS* 3.7 30.0 - - + +
346A GLU* 3.9 14.9 - - - +
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Residues in contact with LEU 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LEU* 3.6 31.0 - - + +
216A ARG* 3.5 46.4 - - - +
254A THR* 4.2 15.7 - - + -
256A ARG* 3.1 33.6 + - + +
259A GLN* 1.3 72.9 - - - +
261A VAL* 1.3 61.0 + - - +
263A GLN* 3.3 32.8 + - - +
264A PHE* 3.0 33.9 + - + -
353A GLU* 5.2 3.1 - - - +
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Residues in contact with VAL 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A VAL* 4.7 11.2 - - + -
209A LEU* 4.5 18.2 - - + -
240A PHE* 5.2 0.9 - - + -
243A LEU* 4.8 21.3 - - + -
244A LEU* 4.2 11.0 - - + -
247A LEU* 3.7 21.5 - - + -
250A LEU* 4.9 1.1 - - + -
257A ALA 2.8 20.5 + - - +
258A PRO 3.7 3.1 - - - +
260A LEU* 1.3 75.2 - - - +
262A GLY* 1.3 61.6 + - - +
264A PHE* 3.2 6.5 + - + +
265A ILE* 2.9 46.4 + - + +
294A ALA* 4.2 8.7 - - + -
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Residues in contact with GLY 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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258A PRO 2.9 11.6 + - - -
259A GLN 3.1 6.0 + - - -
261A VAL* 1.3 75.6 - - - +
263A GLN* 1.3 59.9 + - - +
265A ILE* 3.2 2.1 + - - -
266A ALA* 3.0 26.0 + - - +
294A ALA* 3.2 26.4 + - - +
297A LYS* 4.1 2.5 - - - -
298A ALA* 3.7 14.9 - - - +
301A LEU* 4.4 2.7 - - - -
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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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216A ARG* 4.4 8.7 + - - +
256A ARG* 4.7 7.5 - - - +
259A GLN 2.9 18.4 + - - +
260A LEU* 3.5 35.1 - - - +
261A VAL 3.3 0.2 - - - -
262A GLY* 1.3 74.2 - - - +
264A PHE* 1.3 62.1 + - + +
266A ALA* 4.0 1.2 - - - +
267A ARG* 3.1 26.0 + - - +
297A LYS* 4.0 17.5 - - - +
301A LEU* 3.7 25.5 - - + +
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Residues in contact with PHE 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A VAL* 3.7 40.2 - - + -
208A ALA* 4.2 5.8 - - + -
209A LEU* 4.5 10.8 - - + -
216A ARG* 3.2 52.0 - - + -
219A THR* 3.8 22.0 - - + -
220A SER* 3.4 18.5 + - - -
223A LEU* 4.8 6.0 - - + +
240A PHE* 3.8 17.1 - - + -
260A LEU 3.0 28.3 + - - -
261A VAL* 3.2 10.0 + - + +
263A GLN* 1.3 77.2 - - + +
265A ILE* 1.3 55.7 + - - +
267A ARG* 3.8 2.1 - - - +
268A ALA* 2.9 29.3 + - - +
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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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240A PHE* 3.6 26.0 - - + -
244A LEU* 4.1 27.1 - - + -
261A VAL* 2.9 35.5 + - + +
262A GLY* 3.7 7.4 - - - +
264A PHE* 1.3 72.6 - - - +
266A ALA* 1.3 67.3 + - - +
268A ALA* 2.9 15.7 + - - +
269A VAL* 2.9 13.7 + - + +
274A LEU* 4.0 12.8 - - + -
278A TYR* 4.6 5.6 - - + -
279A ILE* 4.0 21.5 - - + -
294A ALA 4.7 5.2 - - - +
295A LEU* 4.4 10.8 - - + -
298A ALA* 3.8 14.4 - - + -
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Residues in contact with ALA 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A GLY 3.0 16.7 + - - +
263A GLN 4.0 3.4 - - - +
265A ILE* 1.3 76.1 - - - +
267A ARG* 1.3 58.4 + - - +
269A VAL 3.3 0.5 + - - -
270A GLY* 3.0 23.6 + - - -
298A ALA* 3.9 21.0 - - - +
301A LEU* 3.9 20.4 - - + -
302A LEU* 3.4 30.4 - - + +
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Residues in contact with ARG 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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217A GLU* 2.8 42.8 + - - -
220A SER* 3.3 27.7 - - - +
221A LYS* 3.7 23.4 - - - +
224A SER* 5.7 0.2 - - - -
263A GLN 3.1 17.0 + - - +
264A PHE 3.9 2.2 - - - +
266A ALA* 1.3 77.4 - - - +
268A ALA* 1.3 61.1 + - - +
270A GLY* 3.8 2.2 - - - +
271A ASP* 2.9 54.5 + - - +
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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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223A LEU* 5.8 1.1 - - + -
240A PHE* 3.8 13.0 - - + -
264A PHE 2.9 17.3 + - - +
265A ILE 2.9 5.7 + - - +
267A ARG* 1.3 72.9 - - - +
269A VAL* 1.3 65.3 + - - +
271A ASP* 3.4 2.7 + - - -
272A GLY 3.1 3.6 + - - -
273A ILE* 3.0 52.2 + - + +
274A LEU* 3.2 22.3 + - + -
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Residues in contact with VAL 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* 2.9 18.2 + - + +
266A ALA 3.5 7.6 - - - +
268A ALA* 1.3 77.0 - - - +
270A GLY* 1.3 57.5 + - - +
272A GLY* 3.0 18.5 + - - -
274A LEU* 3.6 17.6 - - + +
275A CYS 3.5 19.1 - - - +
276A ASN* 3.4 40.2 - - + +
279A ILE* 4.1 11.9 - - + -
302A LEU* 3.8 24.5 - - + -
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Residues in contact with GLY 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 ALA 3.0 14.9 + - - -
267A ARG* 3.8 5.2 - - - -
269A VAL* 1.3 78.7 - - - +
271A ASP* 1.3 61.9 + - - +
272A GLY 3.4 0.7 + - - -
302A LEU* 4.5 5.1 - - - +
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Residues in contact with ASP 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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220A SER 4.0 4.2 - - - +
224A SER* 3.4 35.3 + - - +
267A ARG* 2.9 49.7 + - - +
268A ALA* 3.9 6.5 - - - +
269A VAL 3.3 0.4 - - - -
270A GLY* 1.3 78.6 - - - +
272A GLY* 1.3 61.5 + - - +
273A ILE* 3.3 12.2 + - + +
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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