Contacts of the helix formed by residues 12 - 25 (chain C) in PDB entry 2V5Q
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 12 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C ASP* 1.3 63.0 + - - +
14C LEU* 3.4 7.7 - - - +
15C GLY* 3.7 10.8 - - - +
16C LYS* 3.1 45.6 + - - +
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Residues in contact with ASP 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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12C SER* 1.3 76.3 - - - +
14C LEU* 1.3 62.5 + - + +
16C LYS* 3.4 16.2 + - - +
17C LYS* 3.0 49.0 + - - +
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Residues in contact with LEU 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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12C SER 3.4 4.6 - - - +
13C ASP* 1.3 76.6 - - + +
15C GLY* 1.3 54.6 + - - +
17C LYS* 3.2 17.2 + - + +
18C LEU* 2.7 36.2 + - - +
33C LEU* 3.8 22.6 - - + +
36C ASN* 3.5 36.8 - - + +
37C GLY 4.2 2.9 - - - +
38C ALA* 3.9 27.1 - - + +
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Residues in contact with GLY 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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12C SER* 3.6 13.7 + - - +
13C ASP 3.3 0.4 - - - -
14C LEU* 1.3 78.7 - - - +
16C LYS* 1.3 55.7 + - - +
18C LEU* 3.1 7.2 + - - +
19C LEU* 2.8 34.7 + - - +
38C ALA* 4.5 1.6 - - - +
39C ASP* 4.7 9.6 - - - +
42C ALA* 3.8 24.4 - - - +
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Residues in contact with LYS 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 SER* 3.1 38.5 + - - +
13C ASP* 3.6 19.0 + - - +
14C LEU 3.2 0.4 - - - -
15C GLY* 1.3 74.8 - - - +
17C LYS* 1.3 57.7 + - + +
19C LEU* 3.4 17.5 + - + +
20C GLU* 3.1 41.0 + - - +
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Residues in contact with LYS 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 ASP* 3.0 38.0 + - - +
14C LEU* 3.2 17.5 + - + +
16C LYS* 1.3 73.9 - - + +
18C LEU* 1.3 58.8 + - - +
20C GLU* 3.3 16.2 + - - +
21C ALA* 2.8 31.0 + - - +
29C GLU* 5.3 2.7 - - - +
33C LEU* 3.5 25.9 - - + +
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Residues in contact with LEU 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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14C LEU 2.7 19.6 + - - +
15C GLY 3.5 5.4 - - - +
17C LYS* 1.3 69.0 - - - +
19C LEU* 1.3 60.3 + - - +
21C ALA 3.7 0.2 - - - -
22C ALA* 2.8 33.6 + - + +
30C VAL* 4.1 42.6 - - + +
33C LEU* 3.6 10.9 - - + +
34C ILE* 4.2 5.6 - - + -
38C ALA* 3.9 15.7 - - + +
39C ASP 3.4 27.8 - - - +
40C VAL* 3.7 21.1 - - + +
50C PRO* 3.8 15.5 - - + -
66C LEU* 4.5 6.5 - - + -
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Residues in contact with LEU 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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15C GLY 2.8 21.1 + - - +
16C LYS* 3.4 20.0 - - + +
18C LEU* 1.3 76.8 - - - +
20C GLU* 1.3 62.4 + - + +
22C ALA* 3.4 1.3 + - - +
23C ARG* 3.1 19.6 + - - +
42C ALA* 3.9 6.5 - - + +
43C VAL 3.9 10.5 - - - +
44C ASP* 3.9 28.7 - - + +
48C LEU 3.4 24.0 - - - +
49C THR 3.7 1.6 - - - -
50C PRO* 3.5 30.1 - - + -
53C LEU* 3.4 24.6 - - + +
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Residues in contact with GLU 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 LYS* 3.1 27.6 + - - +
17C LYS* 3.7 15.7 - - - +
19C LEU* 1.3 73.2 - - + +
21C ALA* 1.3 61.4 + - - +
23C ARG* 3.4 7.7 + - - +
24C ALA* 2.9 32.0 + - - +
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Residues in contact with ALA 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 LYS 2.8 18.5 + - - +
18C LEU 3.8 2.2 - - - +
20C GLU* 1.3 77.0 - - - +
22C ALA* 1.3 60.5 + - - +
24C ALA* 3.3 1.9 + - - +
25C GLY* 3.1 3.6 + - - -
26C GLN* 3.0 33.8 + - + +
29C GLU* 4.0 18.6 - - + +
30C VAL* 3.8 20.1 - - + +
33C LEU* 3.9 15.3 - - + -
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Residues in contact with ALA 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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18C LEU* 2.8 17.9 + - + +
19C LEU 3.8 3.8 - - - +
21C ALA* 1.3 75.6 - - - +
23C ARG* 1.3 62.9 + - - +
25C GLY* 3.4 2.9 + - - -
30C VAL* 3.9 10.2 - - + +
50C PRO* 3.5 37.2 - - + +
53C LEU* 4.5 0.7 - - + -
54C ALA* 3.9 10.0 - - + +
59C HIS* 3.2 20.6 - - - -
62C ILE* 4.1 16.4 - - + +
66C LEU* 4.6 0.4 - - + -
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Residues in contact with ARG 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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143B LYS 5.8 0.6 + - - -
144B ARG* 3.3 29.2 + - - +
320B THR* 3.9 16.6 + - - +
321B ILE* 5.7 1.8 - - - +
19C LEU 3.1 17.9 + - - +
20C GLU* 3.7 6.5 - - - +
22C ALA* 1.3 78.4 - - - +
24C ALA* 1.3 58.0 + - - +
25C GLY 3.2 0.2 - - - -
44C ASP* 4.4 11.5 + - - -
48C LEU* 4.7 6.9 - - - +
53C LEU* 3.5 45.9 - - + +
56C VAL* 5.9 2.0 - - - +
57C SER* 3.7 12.8 + - - +
59C HIS* 3.2 17.3 + - - -
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Residues in contact with ALA 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 GLU 2.9 17.5 + - - +
21C ALA 3.3 2.7 + - - +
22C ALA 3.3 0.4 - - - -
23C ARG* 1.3 76.6 - - + +
25C GLY* 1.3 63.0 + - - +
26C GLN* 3.3 18.4 + - + +
59C HIS* 3.8 5.7 + - - -
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Residues in contact with GLY 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 ALA 3.1 3.0 + - - -
22C ALA 3.4 0.6 + - - -
23C ARG 3.2 4.4 - - - -
24C ALA* 1.3 79.8 - - - +
26C GLN* 1.3 59.4 - - - +
27C ASP* 3.1 17.8 + - - +
59C HIS* 3.3 30.8 + - - -
62C ILE* 3.4 12.6 - - - -
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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