Contacts of the helix formed by residues 260 - 272 (chain C) in PDB entry 3CQ6
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 260 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A ASN* 5.6 3.3 + - - -
234A GLY 3.3 12.6 - - - -
235A GLY* 4.2 8.5 - - - -
236A ARG* 3.5 26.9 - - - +
263A SER* 4.1 9.7 + - - -
64C PRO* 4.0 1.6 - - - -
96C ASN* 5.3 1.2 + - - -
258C HIS 4.1 1.4 + - - -
259C LEU* 1.3 76.1 - - - +
261C ALA* 1.3 59.4 + - - +
262C LEU* 3.7 6.3 + - - +
263C SER* 2.9 32.5 + - - -
264C GLN* 3.0 28.2 + - - +
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Residues in contact with ALA 261 (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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234A GLY* 3.0 21.9 + - - +
56C ILE* 3.9 9.8 - - + +
59C GLU 5.8 1.6 - - - +
60C LEU* 3.9 17.7 - - + -
62C ARG 5.7 0.2 - - - +
64C PRO* 3.7 18.2 - - + +
260C SER* 1.3 70.8 - - - +
262C LEU* 1.3 57.5 + - - +
264C GLN* 3.4 5.7 + - - +
265C ALA* 3.0 30.3 + - - +
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Residues in contact with LEU 262 (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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49A LEU* 4.8 6.3 - - + -
53A VAL* 6.0 1.8 - - + -
232A PHE* 5.4 1.1 - - + -
234A GLY 4.6 0.6 + - - +
235A GLY* 5.8 5.2 - - - -
262A LEU* 4.1 27.7 - - + +
263A SER* 5.4 2.2 - - - +
266A ALA* 3.7 30.7 - - + -
53C VAL* 4.4 23.6 - - + -
56C ILE* 3.5 28.5 - - + -
57C ALA 5.7 0.2 - - - +
60C LEU* 4.0 28.0 - - + -
260C SER* 3.4 5.4 + - - +
261C ALA* 1.3 72.8 - - - +
263C SER* 1.3 58.2 + - - +
265C ALA* 4.0 1.5 - - - +
266C ALA* 2.7 38.3 + - - +
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Residues in contact with SER 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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260A SER* 3.9 17.7 + - - -
262A LEU* 5.2 3.0 - - - +
263A SER* 4.4 1.0 + - - -
96C ASN* 4.6 7.5 + - - -
232C PHE* 5.6 0.2 - - - -
235C GLY* 4.4 16.5 + - - +
236C ARG 5.3 0.2 - - - -
237C LEU* 4.6 6.5 - - - +
259C LEU* 4.8 13.5 - - - -
260C SER* 2.9 28.3 + - - -
262C LEU* 1.3 75.7 - - - +
264C GLN* 1.3 65.2 + - - +
266C ALA* 4.0 4.3 - - - +
267C ALA* 3.0 25.6 + - - +
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Residues in contact with GLN 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C PRO* 3.7 8.0 - - - +
65C GLU* 3.0 30.1 + - - +
66C ARG 5.4 0.2 - - - +
68C ALA* 3.4 34.1 - - + +
70C GLU* 5.8 1.8 - - - +
71C LEU* 4.3 16.9 - - + +
259C LEU* 3.0 36.1 - - + +
260C SER 3.0 19.2 + - - +
261C ALA* 3.8 5.2 - - - +
263C SER* 1.3 75.6 - - - +
265C ALA* 1.3 63.6 + - - +
267C ALA* 3.4 1.9 + - - +
268C ILE* 3.1 34.6 + - + +
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Residues in contact with ALA 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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49C LEU* 5.1 0.2 - - - -
52C THR* 3.9 18.5 - - + +
53C VAL* 6.5 0.7 - - + -
56C ILE* 3.9 23.8 - - + -
261C ALA 3.0 18.8 + - - +
262C LEU* 4.0 2.5 - - - +
264C GLN* 1.3 72.9 - - - +
266C ALA* 1.3 65.8 + - - +
268C ILE* 3.4 10.5 + - - +
269C VAL* 3.0 28.9 + - - +
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Residues in contact with ALA 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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262A LEU* 3.6 24.9 - - + -
49C LEU* 3.6 20.5 - - + +
232C PHE* 3.7 19.6 - - + -
235C GLY* 5.9 1.1 - - - -
262C LEU 2.7 23.1 + - - +
263C SER* 4.0 4.5 - - - +
265C ALA* 1.3 74.5 - - - +
267C ALA* 1.3 57.1 + - - +
269C VAL* 3.3 4.0 + - - +
270C ALA* 3.0 27.5 + - - +
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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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71C LEU* 3.5 22.7 - - + -
226C MET* 4.0 7.6 - - - +
232C PHE* 4.1 10.4 - - + -
237C LEU* 3.8 24.2 - - + -
263C SER 3.0 19.1 + - - +
264C GLN 3.8 0.4 - - - +
266C ALA* 1.3 75.4 - - - +
268C ILE* 1.3 58.6 + - - +
270C ALA* 3.2 5.1 + - - +
271C LEU* 2.9 34.6 + - - +
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Residues in contact with ILE 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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70C GLU* 3.9 29.8 - - + +
71C LEU* 3.8 35.9 - - + +
74C GLU* 4.5 19.1 - - + +
264C GLN* 3.1 32.6 + - + +
265C ALA* 3.6 8.3 - - - +
267C ALA* 1.3 73.4 - - - +
269C VAL* 1.3 68.3 + - + +
271C LEU* 3.1 9.0 + - - +
272C ARG* 3.1 43.4 + - + +
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Residues in contact with VAL 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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45C LEU* 3.8 16.4 - - + +
48C ASP* 3.6 30.1 - - + +
49C LEU* 3.8 17.5 - - + +
52C THR* 3.5 32.1 - - + +
265C ALA 3.0 15.8 + - - +
266C ALA 3.6 6.7 - - - +
268C ILE* 1.3 74.8 - - + +
270C ALA* 1.3 64.1 + - - +
272C ARG* 3.2 24.4 + - - +
273C HIS* 3.2 19.8 + - - +
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Residues in contact with ALA 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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45C LEU* 4.1 18.0 - - + +
226C MET* 3.6 19.5 - - + -
230C PHE* 4.0 11.4 - - + +
232C PHE* 4.2 23.1 - - + -
266C ALA 3.0 14.6 + - - +
267C ALA* 3.4 9.9 - - - +
268C ILE 3.2 0.4 - - - -
269C VAL* 1.3 75.6 - - - +
271C LEU* 1.3 59.1 + - - +
273C HIS* 3.0 19.6 + - - +
274C SER 3.5 7.3 + - - -
277C THR* 4.8 1.2 + - - -
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Residues in contact with LEU 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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71C LEU* 3.9 14.6 - - + -
74C GLU* 3.8 32.3 - - + +
75C LEU* 3.7 33.4 - - + +
78C TYR* 4.3 15.6 - - + +
226C MET* 3.9 10.8 - - + -
230C PHE* 3.4 33.2 - - + -
267C ALA 2.9 20.6 + - - +
268C ILE* 3.1 5.1 + - - +
270C ALA* 1.3 76.2 - - - +
272C ARG* 1.3 58.0 + - - +
273C HIS 3.1 0.2 - - - -
274C SER* 3.1 24.6 + - - -
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Residues in contact with ARG 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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48C ASP* 2.9 38.5 + - - +
52C THR* 3.5 16.4 + - - +
70C GLU* 5.6 1.2 + - - -
74C GLU* 5.8 4.3 - - - +
268C ILE* 3.1 36.1 + - + +
269C VAL* 3.3 23.3 - - - +
271C LEU* 1.3 75.9 - - - +
273C HIS* 1.3 63.8 + - + +
274C SER* 3.5 0.9 - - - -
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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