Contacts of the helix formed by residues 201 - 207 (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 ALA 201 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A ALA* 3.7 24.9 - - + -
257A ILE* 4.0 3.8 - - + -
269A TRP* 4.5 1.1 - - + -
199C VAL 3.6 1.0 + - - -
200C PRO* 1.3 69.5 - - - +
202C PRO* 1.4 67.9 - - + +
204C ALA* 3.2 3.7 + - - +
205C VAL* 3.0 29.5 + - - +
255C ILE* 3.6 28.5 - - + -
256C THR 2.9 8.5 + - - -
257C ILE* 3.8 8.3 - - + -
269C TRP* 3.7 9.2 - - + -
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Residues in contact with PRO 202 (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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269A TRP* 4.3 13.3 - - + +
272A LEU* 4.2 12.3 - - + -
273A ALA* 3.3 36.2 - - + +
276A TYR* 3.7 34.5 - - + -
200C PRO* 3.5 7.9 - - + -
201C ALA* 1.4 92.8 - - + +
203C ILE* 1.4 57.4 + - - +
205C VAL* 3.3 2.9 + - - +
206C VAL 3.1 23.9 + - - -
256C THR 4.8 1.1 - - - +
257C ILE* 5.2 1.1 - - + -
258C PRO* 5.5 1.1 - - + -
269C TRP* 3.6 18.8 - - + -
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Residues in contact with ILE 203 (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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273A ALA* 4.7 4.0 - - + +
276A TYR* 4.2 19.7 - - + -
277A TYR* 3.8 33.0 - - + -
199C VAL* 4.7 0.2 - - + -
200C PRO* 3.2 35.5 + - + +
202C PRO* 1.4 76.3 - - + +
204C ALA* 1.3 57.9 + - - +
206C VAL* 3.7 7.2 - - + -
207C GLY* 3.0 24.9 + - - -
208C GLY* 3.1 13.4 + - - -
209C LYS 3.6 31.2 - - - +
210C VAL* 3.7 18.8 - - + -
223C VAL* 4.1 5.0 - - + +
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Residues in contact with ALA 204 (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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257A ILE* 4.9 2.2 - - + -
199C VAL* 3.7 6.7 - - + -
200C PRO 2.9 13.5 + - - +
201C ALA* 3.2 11.0 + - - +
203C ILE* 1.3 78.4 - - - +
205C VAL* 1.3 56.6 + - - +
223C VAL* 3.8 10.5 - - - -
224C PRO 3.2 9.4 - - - +
226C ARG 3.0 7.6 + - - -
227C THR* 2.9 31.7 + - - +
255C ILE* 3.5 30.5 - - + -
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Residues in contact with VAL 205 (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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257A ILE* 3.8 31.4 - - + -
258A PRO* 5.0 0.9 - - + -
261A LEU* 3.5 31.2 - - + -
266A GLU* 3.8 7.2 - - - +
269A TRP* 3.5 41.1 - - + -
270A LYS* 4.9 0.2 + - - -
201C ALA 3.0 17.3 + - - +
202C PRO 3.3 4.2 + - - +
204C ALA* 1.3 75.6 - - - +
206C VAL* 1.3 62.3 + - - +
225C PRO* 3.4 4.7 - - - +
226C ARG* 2.9 30.4 + - + +
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Residues in contact with VAL 206 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A GLU* 4.5 0.2 - - - -
269A TRP 5.6 0.2 + - - -
270A LYS* 3.6 45.2 - - + +
273A ALA* 3.5 20.6 - - + -
274A GLU* 5.4 0.9 - - + -
248B ARG* 5.9 0.7 - - - +
250B GLN* 3.6 32.9 - - + +
251B ALA* 4.5 11.0 - - + +
202C PRO 3.1 18.4 + - - +
203C ILE* 3.4 11.9 - - + +
205C VAL* 1.3 77.4 - - - +
207C GLY* 1.3 62.5 + - - +
208C GLY* 3.4 13.0 - - - +
225C PRO* 4.0 14.9 - - - +
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Residues in contact with GLY 207 (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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245B LYS* 2.8 24.8 + - - -
248B ARG* 3.6 6.6 - - - +
249B GLU 3.7 4.4 - - - +
250B GLN* 4.8 0.7 - - - +
203C ILE 3.0 8.6 + - - -
205C VAL 3.3 2.6 - - - -
206C VAL* 1.3 81.3 - - - +
208C GLY* 1.3 64.2 + - - +
223C VAL 3.0 19.7 - - - -
224C PRO 3.6 14.8 + - - -
225C PRO* 4.0 1.1 - - - -
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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