Contacts of the helix formed by residues 262 - 278 (chain C) in PDB entry 6PSI
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 THR 262 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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467B ALA 4.4 2.7 - - - -
468B LEU* 4.0 25.4 - - + -
469B GLY 5.0 0.9 - - - +
261C LEU* 1.3 77.4 - - - +
263C PRO* 1.4 74.4 - - - +
264C GLU* 3.7 9.3 + - - +
265C GLU* 3.2 30.2 + - + +
266C GLU* 3.0 24.4 + - - +
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Residues in contact with PRO 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466B ALA 4.8 5.8 - - - +
467B ALA* 3.1 31.6 - - - +
261C LEU 4.8 0.7 - - - +
262C THR* 1.4 85.6 - - - +
264C GLU* 1.3 56.1 + - - +
266C GLU* 4.3 4.0 - - + +
267C ALA* 3.0 32.9 + - - +
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Residues in contact with GLU 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A LEU* 6.2 0.4 - - + -
275A ALA* 5.7 6.1 - - + -
258B LEU* 5.9 3.1 - - - +
262C THR* 3.2 9.4 - - - +
263C PRO* 1.3 78.4 - - - +
265C GLU* 1.4 76.0 - - + +
267C ALA* 3.5 3.6 - - - +
268C LEU* 3.2 55.5 + - + +
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Residues in contact with GLU 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A LEU* 3.4 42.7 - - - +
275A ALA* 3.5 28.6 - - - +
276A TYR* 4.1 18.7 - - + -
261C LEU* 3.7 21.9 - - + +
262C THR* 3.2 27.6 + - + +
264C GLU* 1.4 82.4 - - + +
266C GLU* 1.3 63.6 + - - +
268C LEU 3.0 13.7 + - - -
269C TRP* 3.0 26.0 + - + -
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Residues in contact with GLU 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A VAL* 5.4 4.3 - - + -
206A VAL* 6.1 0.2 - - + -
226A ARG* 2.9 39.2 + - - +
261C LEU* 3.7 26.7 + - + +
262C THR 3.0 15.0 + - - +
263C PRO* 4.3 4.2 - - + +
265C GLU* 1.3 79.3 - - - +
267C ALA* 1.3 56.7 + - - +
269C TRP* 3.3 3.0 + - - +
270C LYS* 2.9 52.9 + - + +
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Residues in contact with ALA 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C PRO 3.0 22.8 + - - +
264C GLU* 3.5 6.1 - - - +
266C GLU* 1.3 76.3 - - - +
268C LEU* 1.4 67.5 + - + +
270C LYS* 3.3 11.5 + - - +
271C LYS* 3.1 28.1 + - + +
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Residues in contact with LEU 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A LEU* 3.7 45.6 - - + +
271A LYS* 4.2 14.8 - - + -
272A LEU* 3.6 25.4 - - + -
264C GLU* 3.3 34.8 - - + +
265C GLU 3.0 2.2 + - - -
267C ALA* 1.4 83.1 - - + +
269C TRP* 1.4 57.1 + - - +
271C LYS* 3.1 10.7 + - + +
272C LEU* 3.0 33.7 + - - +
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Residues in contact with TRP 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ALA* 3.6 33.4 - - + -
202A PRO* 3.9 8.9 - - + +
205A VAL* 3.8 28.5 - - + -
206A VAL* 3.6 6.2 - - + +
269A TRP* 3.6 22.7 - + - -
272A LEU* 3.7 21.8 - - + +
276A TYR* 5.8 0.9 - + - -
201C ALA* 3.7 8.5 - - + -
202C PRO* 3.6 39.9 - - + -
257C ILE* 3.9 9.2 - - + -
258C PRO* 5.2 5.8 - - + -
261C LEU* 3.5 25.0 - - + +
265C GLU* 3.0 39.0 + - - -
266C GLU* 3.3 9.2 + - - +
268C LEU* 1.4 74.8 - - - +
270C LYS* 1.3 56.5 + - - +
272C LEU* 3.5 9.8 + - + +
273C ALA* 3.0 25.5 + - - +
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Residues in contact with LYS 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A VAL* 3.7 34.3 - - + +
266C GLU* 2.9 42.2 + - + +
267C ALA* 3.5 9.2 - - - +
268C LEU 3.2 0.2 - - - -
269C TRP* 1.3 72.8 - - - +
271C LYS* 1.3 61.4 + - - +
273C ALA* 3.3 3.6 + - - +
274C GLU* 2.9 45.8 + - - +
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Residues in contact with LYS 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A GLU* 5.7 0.2 - - - +
268A LEU* 4.1 19.1 - - + -
267C ALA* 3.1 20.1 + - + +
268C LEU* 3.1 10.1 + - + +
270C LYS* 1.3 72.8 - - - +
272C LEU* 1.3 61.2 + - - +
274C GLU* 3.1 35.2 + - + +
275C ALA* 3.0 26.0 + - - +
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Residues in contact with LEU 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A PRO* 3.7 15.9 - - + -
265A GLU* 4.1 15.0 - - + +
268A LEU* 4.1 23.6 - - + -
269A TRP* 3.6 50.5 - - + +
272A LEU* 3.6 31.9 - - + -
268C LEU 3.0 16.3 + - - +
269C TRP* 3.5 13.7 - - + +
271C LYS* 1.3 73.9 - - - +
273C ALA* 1.3 57.4 + - - +
275C ALA* 3.2 7.5 + - - +
276C TYR* 3.0 34.3 + - + -
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Residues in contact with ALA 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A PRO* 3.5 19.2 - - + +
206A VAL* 3.7 20.6 - - + -
269C TRP 3.0 15.1 + - - +
270C LYS* 3.4 9.4 - - - +
272C LEU* 1.3 76.4 - - - +
274C GLU* 1.3 55.2 + - - +
276C TYR* 3.2 7.2 + - - +
277C TYR* 2.9 54.4 + - + +
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Residues in contact with GLU 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C LYS* 2.9 38.3 + - - +
271C LYS* 3.1 47.7 + - + +
272C LEU 3.3 0.2 - - - -
273C ALA* 1.3 72.9 - - - +
275C ALA* 1.3 59.3 + - - +
277C TYR* 3.4 16.8 + - + +
278C ALA* 3.0 30.1 + - - +
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Residues in contact with ALA 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A GLU* 4.5 26.0 - - + +
271C LYS 3.0 13.9 + - - +
272C LEU* 3.2 13.7 + - - +
274C GLU* 1.3 75.2 - - - +
276C TYR* 1.3 63.9 + - + +
278C ALA* 3.6 14.9 - - - +
279C ARG* 3.5 15.5 - - - +
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Residues in contact with TYR 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A PRO* 3.4 39.3 - - + +
202A PRO* 3.7 20.6 - - + +
203A ILE* 3.9 18.8 - - + -
257A ILE 4.1 0.2 - - - -
258A PRO* 3.1 48.8 - - + +
269A TRP* 5.1 2.5 - + - -
272C LEU* 3.0 25.3 + - + +
273C ALA* 3.2 10.7 + - - +
275C ALA* 1.3 77.3 - - + +
277C TYR* 1.3 65.7 + - - +
278C ALA 3.2 0.2 - - - -
279C ARG* 3.1 69.7 + - - +
280C ALA* 4.2 1.6 + - - +
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Residues in contact with TYR 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A ILE* 4.2 17.2 - - + -
206A VAL* 3.9 16.2 - - + +
207A GLY 4.0 1.6 + - - -
208A GLY* 3.3 38.0 + - - -
209A LYS 4.7 3.4 - - - -
273C ALA* 2.9 47.2 + - + +
274C GLU* 3.8 16.8 - - + +
276C TYR* 1.3 74.3 - - + +
278C ALA* 1.4 57.0 - - - +
280C ALA* 3.1 30.7 + - - +
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Residues in contact with ALA 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274C GLU 3.0 18.0 + - - +
275C ALA* 3.6 12.6 - - - +
276C TYR 3.2 0.2 - - - -
277C TYR* 1.4 75.8 - - - +
279C ARG* 1.4 59.1 + - - +
280C ALA* 3.3 4.5 + - - +
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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