Contacts of the helix formed by residues 8 - 18 (chain C) in PDB entry 3CUQ
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 PRO 8 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C GLU 3.8 2.6 - - - +
7C TRP* 1.3 89.3 - - + +
9C TRP* 1.3 67.2 + - + +
10C GLN* 3.6 17.3 - - + +
11C TYR* 2.9 34.8 + - + +
12C ARG* 3.7 6.1 + - - -
16C PHE* 5.7 0.7 - - + -
32C ALA* 5.4 3.4 - - + +
36C LEU* 3.4 38.6 - - + -
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Residues in contact with TRP 9 (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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113A HIS* 5.4 2.0 - - - -
114A ARG* 3.8 71.0 - - + +
223A TRP* 4.2 19.3 - + - -
237A PRO* 4.7 10.1 - - + -
240A PHE* 4.4 5.0 - + - -
242A ASP* 4.0 35.4 - - + +
7C TRP 4.0 1.4 + - - -
8C PRO* 1.3 69.2 - - + +
10C GLN* 1.3 110.1 + - + +
12C ARG* 3.1 28.9 + - - +
13C PHE* 3.7 32.0 + + + +
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Residues in contact with GLN 10 (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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223A TRP* 4.8 6.2 - - + -
8C PRO* 3.6 19.3 - - + +
9C TRP* 1.3 129.5 + - + +
11C TYR* 1.3 66.0 + - - +
13C PHE* 2.7 21.3 + - + +
16C PHE* 3.3 46.4 - - + +
28C LYS 5.3 0.5 - - - +
32C ALA* 3.5 22.1 - - + +
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Residues in contact with TYR 11 (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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7C TRP* 3.6 52.5 - + + -
8C PRO* 2.9 29.8 + - + +
10C GLN* 1.3 78.3 - - - +
12C ARG* 1.3 62.6 + - - +
16C PHE* 4.0 9.2 - - - -
17C PHE* 3.1 39.0 - + - -
33C TRP* 5.1 1.3 - + - -
36C LEU* 4.1 11.7 - - + -
58C PRO* 2.5 32.4 + - - +
59C LEU 3.8 11.2 - - - -
61C ASN 3.6 12.0 + - - -
62C ASN* 3.2 35.3 + - + -
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Residues in contact with ARG 12 (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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240A PHE* 3.2 24.1 - - + -
242A ASP* 5.3 10.3 - - + -
7C TRP* 3.4 48.5 + - - +
8C PRO 3.7 9.7 + - - -
9C TRP* 3.2 21.1 - - - +
10C GLN 3.0 0.2 - - - -
11C TYR* 1.3 82.1 - - - +
13C PHE* 1.3 57.5 + - - +
14C PRO* 3.5 0.9 - - - +
62C ASN* 4.4 6.6 - - - +
65C LEU* 3.3 26.0 - - + +
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Residues in contact with PHE 13 (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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223A TRP* 3.8 25.8 - + - -
235A TRP* 3.6 29.6 - + + -
236A LEU 4.5 0.4 - - - -
237A PRO* 3.5 36.6 - - + -
240A PHE* 3.7 43.7 - + + -
9C TRP* 3.7 23.3 + + + +
10C GLN* 2.7 20.5 + - - +
11C TYR 3.3 0.4 - - - -
12C ARG* 1.3 70.7 - - - +
14C PRO* 1.3 71.5 - - + +
15C PRO* 3.6 27.1 - - + -
16C PHE* 2.9 22.3 + - + +
17C PHE* 4.0 2.3 - - - -
65C LEU* 3.9 1.8 - - - -
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Residues in contact with PRO 14 (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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225A ASP* 3.7 22.8 - - - +
235A TRP* 3.8 26.2 - - + -
240A PHE* 4.4 7.4 - - + -
12C ARG 3.5 9.4 - - - +
13C PHE* 1.3 86.2 - - + -
15C PRO* 1.3 71.3 - - + +
16C PHE 3.0 1.9 + - - -
17C PHE* 3.2 20.1 + - - +
18C THR* 4.5 0.9 + - - -
65C LEU* 3.7 27.3 - - + -
67C ARG* 3.8 22.6 + - + +
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Residues in contact with PRO 15 (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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223A TRP* 3.4 31.6 - - + +
224A LEU 3.5 13.5 - - - +
225A ASP* 4.1 5.2 - - + -
235A TRP* 3.5 38.1 - - + -
13C PHE* 3.4 21.8 - - + -
14C PRO* 1.3 93.2 - - + +
16C PHE* 1.3 52.3 + - - +
17C PHE 2.9 5.6 - - - -
18C THR* 2.8 25.6 + - - +
20C GLN* 3.3 13.1 + - - -
29C GLN* 3.7 0.2 + - - -
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Residues in contact with PHE 16 (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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223A TRP* 4.1 12.0 - + + -
8C PRO* 5.7 1.1 - - + -
10C GLN* 3.3 46.9 - - + +
11C TYR* 4.0 9.2 - - - -
13C PHE* 2.9 18.7 + - + +
15C PRO* 1.3 78.7 - - - +
17C PHE* 1.3 60.9 + + + +
18C THR 3.3 0.4 + - - -
29C GLN* 2.7 51.1 + - + +
32C ALA* 3.8 10.8 - - + -
33C TRP* 3.1 86.6 + + - -
36C LEU* 4.5 8.5 - - + -
69C LEU* 5.1 0.2 - - - +
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Residues in contact with PHE 17 (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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227A GLN* 2.9 22.7 + - - +
11C TYR* 3.1 44.6 - + - -
13C PHE 4.0 6.7 - - - -
14C PRO 3.5 16.4 - - - +
15C PRO 2.8 0.6 + - - -
16C PHE* 1.3 82.1 - + + +
18C THR* 1.3 57.4 + - - +
33C TRP* 3.9 28.3 - + - -
60C PHE 4.4 6.5 - - - -
62C ASN* 3.7 21.3 - - + -
65C LEU* 3.6 14.4 - - + -
67C ARG* 3.6 33.7 - - + -
68C LYS 4.3 1.6 - - - +
69C LEU* 3.8 24.1 - - - +
70C PRO* 3.5 14.9 - - - +
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Residues in contact with THR 18 (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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224A LEU* 3.8 20.2 - - + +
225A ASP* 4.0 2.5 + - - -
226A LEU* 3.2 47.0 + - + +
227A GLN* 3.9 10.1 + - - +
14C PRO 5.3 0.7 + - - -
15C PRO* 2.8 16.7 + - - +
16C PHE 3.3 0.6 - - - -
17C PHE* 1.3 75.0 + - - +
19C LEU* 1.3 77.2 + - - +
20C GLN* 2.9 9.6 + - - +
29C GLN* 2.5 27.2 + - - -
69C LEU* 5.6 0.9 - - - -
70C PRO* 5.4 2.0 - - - -
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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