Contacts of the helix formed by residues 12 - 26 (chain C) in PDB entry 4CQM
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 ARG 12 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9C GLY 3.3 17.3 + - - +
11C SER* 1.3 94.7 + - - +
13C GLY* 1.3 68.3 + - - +
14C ILE 3.6 1.4 + - - -
15C GLY 3.6 0.3 + - - -
16C ARG* 3.4 9.5 + - - -
34C ARG* 5.1 11.1 - - - +
35C ASN* 5.8 6.5 - - - +
38C GLY* 6.3 0.4 - - - -
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Residues in contact with GLY 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 ARG* 1.3 75.1 - - - +
14C ILE* 1.3 64.1 + - - -
16C ARG* 3.3 4.5 + - - +
17C ALA* 3.1 19.8 + - - +
183C THR* 5.0 11.0 - - - -
206C THR* 3.9 18.8 + - - +
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Residues in contact with ILE 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 ARG 3.6 0.6 + - - -
13C GLY* 1.3 68.5 - - - -
15C GLY* 1.3 56.0 + - - +
17C ALA* 3.0 2.9 + - - +
18C VAL* 2.7 47.6 + - + +
83C ALA* 4.9 2.0 - - + -
133C VAL* 3.8 26.5 - - + -
134C GLY 5.6 0.4 - - - +
178C PRO* 3.6 33.2 - - + -
181C VAL* 4.8 8.5 - - + -
206C THR* 4.2 17.2 - - + +
209C VAL* 3.7 33.9 - - + -
213C VAL* 4.9 0.7 - - + -
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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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7C VAL* 3.4 17.2 - - - +
9C GLY 3.4 16.1 + - - -
10C GLY* 3.4 10.8 - - - -
12C ARG 3.6 2.4 + - - -
13C GLY 3.3 0.4 - - - -
14C ILE* 1.3 79.8 - - - +
16C ARG* 1.3 56.4 + - - +
18C VAL* 3.4 3.7 + - - +
19C ALA* 3.1 23.4 + - - +
83C ALA* 3.8 19.3 + - - +
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Residues in contact with ARG 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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10C GLY 3.3 19.6 + - - +
11C SER 3.6 11.7 - - - +
12C ARG* 3.4 20.3 + - - -
13C GLY 3.3 10.4 + - - +
14C ILE 3.2 0.4 - - - -
15C GLY* 1.3 74.9 - - - +
17C ALA* 1.3 58.7 + - - +
19C ALA* 3.4 3.8 + - - +
20C GLN* 3.1 36.3 + - - +
42C ALA* 5.1 4.7 - - + +
46C LEU* 5.5 0.2 - - - +
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Residues in contact with ALA 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 3.1 4.8 + - - +
14C ILE 3.0 6.6 + - - +
16C ARG* 1.3 73.6 - - - +
18C VAL* 1.3 65.9 + - - +
20C GLN* 3.4 16.1 + - - +
21C LEU* 3.1 19.4 + - - +
206C THR* 3.3 50.7 - - - +
207C ILE* 3.9 7.0 - - + +
210C ALA* 3.6 10.6 - - + +
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Residues in contact with VAL 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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7C VAL* 4.0 15.3 - - + -
14C ILE* 2.7 34.5 + - + +
15C GLY* 3.5 9.2 - - - +
17C ALA* 1.3 73.0 - - - +
19C ALA* 1.3 58.0 + - - +
21C LEU* 3.3 1.4 + - - +
22C MET* 2.9 60.0 + - + +
81C VAL* 4.2 17.7 - - + -
210C ALA* 3.8 24.5 - - - -
213C VAL* 4.1 18.8 - - + -
214C VAL* 5.4 1.3 - - + -
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Residues in contact with ALA 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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7C VAL* 4.7 11.4 - - + -
10C GLY 4.6 1.1 - - - +
15C GLY 3.1 13.0 + - - +
16C ARG* 3.7 10.5 - - - +
17C ALA 3.3 0.2 - - - -
18C VAL* 1.3 79.5 - - - +
20C GLN* 1.3 62.3 + - - +
23C ALA* 3.1 23.0 + - - +
29C LEU* 3.1 19.1 - - + +
31C VAL* 4.4 15.3 - - + -
42C ALA* 6.1 1.1 - - + -
46C LEU* 4.1 21.9 - - + +
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Residues in contact with GLN 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 ARG* 3.1 21.4 + - + +
17C ALA* 3.7 20.7 + - - +
18C VAL 3.3 0.2 - - - -
19C ALA* 1.3 76.8 - - - +
21C LEU* 1.3 62.2 + - - +
23C ALA* 3.7 3.6 + - - +
24C ARG* 3.6 16.1 + - - +
45C ASP* 5.9 4.5 + - - +
46C LEU* 4.2 18.4 - - + -
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Residues in contact with LEU 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 ALA 3.1 16.6 + - - +
18C VAL 3.9 2.9 - - - +
20C GLN* 1.3 74.3 - - - +
22C MET* 1.3 59.4 + - - +
23C ALA 3.1 2.0 - - - -
24C ARG* 3.0 27.4 + - + +
25C LYS* 3.3 27.3 + - + +
207C ILE* 4.7 10.1 - - + +
210C ALA* 3.8 7.0 - - + -
211C HIS* 3.5 64.4 - - + +
214C VAL* 3.8 15.7 - - + -
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Residues in contact with MET 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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5C CYS* 3.6 34.1 - - + -
18C VAL* 2.9 40.1 + - + +
21C LEU* 1.3 75.5 - - - +
23C ALA* 1.3 60.1 + - - +
25C LYS* 3.4 8.2 + - - -
26C GLY 3.2 3.8 + - - -
27C TYR* 3.0 64.5 + - + +
29C LEU* 3.7 16.6 - - + -
79C PHE* 4.8 2.0 - - + -
214C VAL* 3.8 22.0 - - + -
217C LEU* 4.1 23.8 - - + -
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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 ALA 3.1 19.1 + - - +
20C GLN* 3.7 6.7 - - - +
21C LEU 3.1 0.4 - - - -
22C MET* 1.3 78.0 - - - +
24C ARG* 1.3 60.9 + - - +
26C GLY* 3.3 12.5 + - - -
27C TYR 4.4 0.4 - - - -
29C LEU* 3.4 11.1 - - + +
46C LEU* 3.9 25.8 - - + +
50C HIS* 4.0 19.3 + - - +
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Residues in contact with ARG 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 GLN 3.6 8.8 + - - +
21C LEU* 3.0 18.9 + - + +
23C ALA* 1.3 79.1 - - - +
25C LYS* 1.3 61.7 + - + +
26C GLY* 4.8 0.3 - - - -
4D GLN* 3.8 7.6 - - - +
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Residues in contact with LYS 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 LEU* 3.3 32.4 + - + +
22C MET* 3.9 11.9 - - - +
23C ALA 3.2 0.4 - - - -
24C ARG* 1.3 79.2 - - + +
26C GLY* 1.3 59.7 + - - +
27C TYR* 3.6 15.1 - - + -
211C HIS* 5.4 5.5 + - - -
214C VAL* 3.6 33.5 - - + +
218C GLU* 4.0 13.6 + - - +
4D GLN* 3.3 37.5 + - - +
5D LEU* 4.4 21.2 - - - +
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Residues in contact with GLY 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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3C LYS 5.5 2.6 + - - -
22C MET 3.2 2.6 + - - -
23C ALA 3.3 10.8 + - - -
24C ARG 3.4 0.6 - - - -
25C LYS* 1.3 80.0 - - - +
27C TYR* 1.3 67.0 + - - +
28C ARG* 3.4 2.6 + - - -
50C HIS* 5.7 1.3 - - - -
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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