Contacts of the helix formed by residues 15 - 26 (chain C) in PDB entry 2CVD
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 15 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C LEU* 4.3 8.5 - - + -
8C TYR* 3.4 41.0 - - + -
12C ARG 3.2 1.6 + - - -
14C ARG* 1.3 77.0 - - - +
16C GLU* 1.3 66.4 + - - +
17C ILE 3.2 3.1 - - - -
18C ILE* 2.9 19.8 + - - +
19C ARG* 3.1 26.5 + - - +
52C PRO* 4.1 12.8 - - + -
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Residues in contact with GLU 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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12C ARG* 3.0 35.9 + - + +
13C GLY 3.8 8.1 - - - +
14C ARG 3.4 1.2 - - - -
15C ALA* 1.3 76.7 - - - +
17C ILE* 1.3 57.1 + - - +
19C ARG* 2.9 32.2 + - - +
20C TYR* 2.9 43.6 + - + -
33C ARG* 4.7 1.4 + - - -
155C ILE* 3.7 16.8 - - + -
190C TRP* 2.8 30.3 + - - -
194C ARG* 2.8 25.1 + - - +
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Residues in contact with ILE 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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13C GLY 4.9 0.2 + - - -
14C ARG 3.8 17.9 - - - +
16C GLU* 1.3 77.0 - - - +
18C ILE* 1.3 73.1 + - + +
20C TYR* 3.4 0.9 + - - +
21C ILE* 3.2 27.6 + - + +
64C SER* 4.4 3.4 - - - +
65C LEU* 4.4 9.0 - - + -
68C ALA* 4.1 11.7 - - + -
148C TRP* 3.8 34.1 - - + +
151C PHE* 3.6 31.6 - - + -
152C TYR* 3.9 34.3 - - + +
155C ILE* 3.4 10.6 - - + +
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Residues in contact with ILE 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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6C LEU* 3.9 29.6 - - + -
15C ALA* 2.9 10.1 + - - +
17C ILE* 1.3 78.7 - - + +
19C ARG* 1.3 65.1 + - - +
21C ILE* 3.2 10.4 + - - +
22C PHE* 3.0 48.8 + - + -
52C PRO* 4.3 9.6 - - + -
54C LEU* 5.0 0.7 - - + -
64C SER* 4.0 23.3 - - - +
67C ILE* 3.7 38.6 - - + -
68C ALA* 4.4 4.7 - - - +
71C LEU* 3.7 11.9 - - + -
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Residues in contact with ARG 19 (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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6C LEU* 3.7 11.2 - - + +
8C TYR* 3.9 5.9 - - - +
9C PHE 3.6 14.6 + - - -
11C MET 2.9 27.9 + - - -
12C ARG* 3.4 9.1 + - - +
15C ALA* 3.1 28.0 + - - +
16C GLU* 2.9 26.2 + - - +
18C ILE* 1.3 77.1 - - - +
20C TYR* 1.3 62.3 + - - +
22C PHE* 3.4 3.0 + - - +
23C ALA* 3.0 23.4 + - - +
29C TYR* 3.4 26.8 + - - +
31C ASP* 2.8 21.9 + - - -
32C HIS 5.4 0.6 + - - -
33C ARG* 3.3 21.3 - - - +
190C TRP* 3.5 36.6 - - + +
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Residues in contact with TYR 20 (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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16C GLU* 2.9 47.1 + - + +
17C ILE 3.7 5.6 - - - +
19C ARG* 1.3 76.0 - - - +
21C ILE* 1.3 59.2 + - - +
23C ALA* 3.2 6.5 + - - +
24C TYR* 2.9 30.7 + - - +
151C PHE* 3.8 32.3 - + + -
154C GLU* 2.6 34.6 + - - -
155C ILE* 3.6 22.7 - - + +
158C THR* 5.3 0.7 + - - +
181C VAL* 4.5 4.3 - - + -
187C VAL* 4.0 25.8 - - + +
190C TRP* 3.7 17.0 - + - -
191C ILE* 3.9 10.2 - - + +
194C ARG* 3.2 19.5 + - - -
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Residues in contact with ILE 21 (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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17C ILE* 3.2 22.6 + - + +
18C ILE* 3.2 7.6 + - - +
20C TYR* 1.3 75.3 - - - +
22C PHE* 1.3 66.4 + - + +
24C TYR* 3.3 0.7 + - - -
25C LEU* 3.0 46.1 + - + +
68C ALA* 3.6 33.4 - - + +
71C LEU* 3.8 21.3 - - + -
72C THR* 3.7 26.9 - - + -
77C LEU* 4.3 4.5 - - + -
148C TRP* 4.2 6.1 - - + -
151C PHE* 4.3 19.5 - - + -
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Residues in contact with PHE 22 (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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4C TYR* 3.8 37.5 - + + -
6C LEU* 4.9 0.4 - - + -
18C ILE* 3.0 39.1 + - + +
19C ARG 3.8 1.3 - - - +
21C ILE* 1.3 76.4 - - + +
23C ALA* 1.3 63.7 + - - +
25C LEU* 3.5 0.6 + - - -
26C ASP* 3.0 4.0 + - - -
27C ILE* 3.0 54.4 + - + +
29C TYR* 3.4 55.0 - + + -
54C LEU* 4.0 15.3 - - + -
71C LEU* 3.7 31.6 - - + -
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Residues in contact with ALA 23 (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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19C ARG 3.0 17.8 + - - +
20C TYR* 3.5 6.5 - - - +
21C ILE 3.2 0.2 - - - -
22C PHE* 1.3 77.6 - - - +
24C TYR* 1.3 63.9 + - - +
26C ASP* 3.1 14.3 + - - +
29C TYR* 5.2 1.5 - - + -
186C ALA* 3.5 22.5 - - - +
187C VAL* 5.1 1.8 - - - -
190C TRP* 3.9 31.0 - - + -
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Residues in contact with TYR 24 (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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20C TYR 2.9 21.2 + - - +
21C ILE 3.3 3.1 + - - +
23C ALA* 1.3 73.5 - - - +
25C LEU* 1.3 66.6 + - + +
26C ASP* 3.4 2.4 + - - +
76C ASP* 2.7 36.4 + - - -
77C LEU* 3.5 31.0 - - + -
146C VAL* 3.9 20.4 - - + +
151C PHE* 3.7 23.8 - + + -
184C ILE* 4.0 27.8 - - + -
186C ALA* 3.9 13.8 - - + +
187C VAL* 4.5 4.0 - - + +
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Residues in contact with LEU 25 (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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21C ILE* 3.0 34.9 + - + +
24C TYR* 1.3 95.7 - - + +
26C ASP* 1.3 71.2 + - - +
27C ILE* 3.5 31.3 + - + +
71C LEU* 3.6 24.9 - - + +
75C THR* 4.1 29.8 - - + +
76C ASP* 4.6 3.8 - - - +
77C LEU* 4.3 4.3 - - + -
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Residues in contact with ASP 26 (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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22C PHE 3.0 6.0 + - - -
23C ALA* 3.1 12.9 + - - +
24C TYR 3.2 2.4 - - - +
25C LEU* 1.3 82.0 - - - +
27C ILE* 1.3 60.4 + - - +
28C GLN* 4.2 14.4 + - - +
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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