Contacts of the helix formed by residues 3 - 21 (chain C) in PDB entry 4CFQ
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 3 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C ALA* 1.3 76.2 - - - +
4C PRO* 1.3 75.6 - - - +
5C LEU* 3.2 4.2 + - - +
6C GLU* 3.0 24.9 + - - +
7C LYS* 3.0 21.5 + - - +
40D ARG 4.5 4.7 - - - -
41D GLU* 2.6 44.6 + - - -
43D PRO* 5.0 1.6 - - - -
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Residues in contact with PRO 4 (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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2C ALA 4.5 0.9 - - - +
3C SER* 1.3 87.7 - - - +
5C LEU* 1.3 55.6 + - - +
7C LYS* 3.3 11.7 + - + +
8C ALA* 2.9 28.4 + - - +
11D VAL* 3.6 23.2 - - + +
15D THR* 5.3 1.8 - - - +
18D LYS* 6.2 1.1 - - - +
41D GLU* 4.2 8.7 - - - +
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Residues in contact with LEU 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C SER* 3.2 7.2 + - - +
4C PRO* 1.3 76.2 - - - +
6C GLU* 1.3 66.0 + - - +
8C ALA* 3.2 4.2 + - + +
9C LEU* 3.0 29.8 + - + +
11D VAL* 3.8 6.0 - - + +
12D MET* 4.1 25.1 - - + +
15D THR* 3.9 27.7 + - + +
37D LEU* 4.3 7.2 - - + -
41D GLU* 4.2 7.3 + - + +
42D LEU* 3.8 33.2 - - + -
75D TYR* 3.8 25.6 - - - +
79D LEU* 4.3 16.4 - - + -
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Residues in contact with GLU 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ALA* 3.7 15.0 - - + -
3C SER* 3.0 31.7 + - - +
5C LEU* 1.3 75.6 - - - +
7C LYS* 1.3 63.2 + - - +
9C LEU* 3.4 9.2 + - - +
10C ASP* 3.0 30.6 + - - +
41D GLU 3.4 18.4 - - - +
42D LEU* 3.4 12.2 - - + -
43D PRO* 3.3 17.3 - - - +
44D SER* 2.5 49.2 + - - +
45D PHE* 4.2 5.1 - - + -
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Residues in contact with LYS 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ALA* 3.4 36.8 + - + +
3C SER 3.0 14.6 + - - +
4C PRO* 3.5 11.7 - - + +
6C GLU* 1.3 74.6 - - - +
8C ALA* 1.3 58.5 + - - +
10C ASP* 3.2 11.3 + - - +
11C VAL* 3.0 33.9 + - + +
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Residues in contact with ALA 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C PRO 2.9 14.3 + - - +
5C LEU* 3.2 14.6 + - + +
7C LYS* 1.3 73.9 - - - +
9C LEU* 1.3 59.0 + - - +
11C VAL* 3.2 6.1 + - - +
12C MET* 2.9 32.9 + - - +
8D ALA* 3.7 39.2 - - + +
11D VAL* 4.1 11.0 - - + -
12D MET* 5.1 2.7 - - + -
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Residues in contact with LEU 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C LEU* 3.0 24.1 + - + +
6C GLU* 3.4 4.7 + - - +
8C ALA* 1.3 75.7 - - - +
10C ASP* 1.3 59.5 + - - +
12C MET* 3.2 27.0 + - + +
13C VAL* 3.0 33.4 + - - +
12D MET* 5.4 0.7 - - + -
42D LEU* 3.9 25.6 - - + -
45D PHE* 4.0 22.7 - - + -
79D LEU* 4.3 36.6 - - + +
82D ILE* 4.4 6.5 - - + -
83D ALA* 4.5 19.7 - - + +
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Residues in contact with ASP 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C GLU* 3.0 21.5 + - - +
7C LYS* 3.4 12.0 - - - +
8C ALA 3.2 0.2 - - - -
9C LEU* 1.3 78.8 - - - +
11C VAL* 1.3 57.7 + - + +
13C VAL* 3.3 8.5 + - - +
14C SER* 2.9 32.2 + - - -
45D PHE* 6.0 2.4 - - - -
83D ALA 5.8 0.3 - - - +
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Residues in contact with VAL 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LYS* 3.0 17.1 + - + +
8C ALA* 3.5 8.1 - - - +
10C ASP* 1.3 71.5 - - + +
12C MET* 1.3 66.1 + - - +
14C SER* 3.6 7.9 - - - +
15C THR* 2.7 42.0 + - - +
4D PRO* 3.8 42.0 - - + +
5D LEU* 3.9 7.9 - - - +
8D ALA* 4.3 5.6 - - + -
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Residues in contact with MET 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ALA 2.9 20.2 + - - +
9C LEU* 3.2 28.9 + - + +
11C VAL* 1.3 76.8 - - - +
13C VAL* 1.3 62.4 + - + +
16C PHE 3.3 7.6 + - - -
72C PHE* 4.5 2.7 - - + -
75C TYR* 2.8 32.2 + - + -
76C CYS* 4.5 20.2 - - + +
79C LEU* 3.7 27.1 - - + -
5D LEU* 3.8 19.5 - - + -
8D ALA* 4.5 6.1 - - + -
9D LEU* 4.7 2.0 - - + -
12D MET* 3.6 35.7 - - + +
79D LEU* 6.1 3.1 - - + +
80D SER* 6.0 0.9 - - - +
83D ALA* 5.4 2.7 - - + -
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Residues in contact with VAL 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU 3.0 19.2 + - - +
10C ASP* 3.7 10.1 - - - +
12C MET* 1.3 75.0 - - - +
14C SER* 1.3 67.7 + - - +
16C PHE* 3.3 3.6 + - - +
17C HIS* 3.1 47.6 + - + +
72C PHE* 3.6 26.5 - - + -
83D ALA* 3.8 22.4 - - + +
84D MET* 4.2 13.2 - - + -
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Residues in contact with SER 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ASP 2.9 22.5 + - - -
11C VAL* 3.3 11.4 + - - +
13C VAL* 1.3 75.0 - - - +
15C THR* 1.3 64.7 + - - +
17C HIS* 3.3 5.4 + - - +
18C LYS* 3.0 24.3 + - - +
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Residues in contact with THR 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C VAL* 2.7 34.8 + - - +
14C SER* 1.3 75.2 + - - +
16C PHE* 1.3 67.3 + - - +
18C LYS* 3.3 9.5 + - + +
19C TYR* 3.2 24.8 - - + -
37C LEU* 3.9 5.5 - - + +
41C GLU* 3.8 31.9 - - + -
75C TYR* 3.8 7.9 - - - +
4D PRO* 5.8 0.3 - - - +
5D LEU* 4.1 21.2 + - + +
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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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12C MET 3.3 3.4 + - - +
13C VAL 3.3 9.0 + - - +
15C THR* 1.3 78.5 - - - +
17C HIS* 1.3 75.9 + + - +
19C TYR* 3.2 4.3 + - - +
20C SER* 2.9 46.3 + - - -
27C PHE 3.4 23.8 - - - -
29C LEU* 3.6 25.9 - - + +
37C LEU* 4.3 4.5 - - - -
70C VAL 3.7 10.8 - - - -
71C ASP 3.6 12.8 - - - -
72C PHE* 3.4 37.7 - + + -
75C TYR* 3.5 44.5 + + + -
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Residues in contact with HIS 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 VAL* 3.1 37.7 + - + +
14C SER* 4.1 5.4 - - - +
15C THR 3.3 0.2 - - - -
16C PHE* 1.3 96.8 - + - +
18C LYS* 1.3 65.4 + - - +
19C TYR 3.4 0.3 + - - -
20C SER* 3.4 9.7 + - - -
21C GLY* 3.4 19.1 + - - -
26C LYS 4.7 0.8 + - - -
27C PHE* 4.4 24.4 - + + -
72C PHE* 4.8 1.4 - - + -
84D MET* 3.2 33.6 - - + +
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Residues in contact with LYS 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A THR* 5.9 4.9 + - - +
40A ARG* 6.1 0.4 - - - +
43A PRO* 6.2 2.2 - - - +
14C SER 3.0 17.6 + - - +
15C THR* 3.5 10.5 - - + +
16C PHE 3.2 0.4 - - - -
17C HIS* 1.3 78.1 - - - +
19C TYR* 1.3 95.4 + - + +
21C GLY* 4.4 1.6 + - - -
22C LYS* 3.8 22.3 + - - +
40C ARG* 5.4 3.9 - - - +
41C GLU* 4.2 6.8 + - - +
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Residues in contact with TYR 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 THR* 3.2 18.6 - - + -
16C PHE 3.2 3.1 + - - +
18C LYS* 1.3 102.4 + - + +
20C SER* 1.3 63.8 + - - +
21C GLY 3.2 2.9 + - - -
22C LYS* 3.3 35.7 + - + +
29C LEU* 3.7 17.9 - - + -
33C GLU* 3.1 32.2 - - + +
36C GLU* 3.7 28.5 - - + -
37C LEU* 3.8 20.0 - - + -
40C ARG* 3.3 23.7 - - - +
41C GLU* 2.6 42.8 + - + -
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Residues in contact with SER 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C PHE* 2.9 43.6 + - - -
17C HIS* 3.4 12.3 + - - -
19C TYR* 1.3 77.5 - - - +
21C GLY* 1.3 58.6 + - - +
22C LYS 3.3 0.9 - - - -
25C ASP 3.1 8.7 - - - +
26C LYS 2.9 16.2 + - - -
28C LYS 3.6 20.9 - - - -
29C LEU* 3.5 6.7 - - - +
33C GLU* 3.1 2.1 - - - +
501C CA 2.4 27.4 - - - -
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Residues in contact with GLY 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C HIS 3.4 12.6 + - - -
18C LYS 4.4 1.5 + - - -
19C TYR 3.2 1.4 - - - -
20C SER* 1.3 79.4 + - - +
22C LYS* 1.3 63.3 + - - +
23C GLU 3.7 0.2 - - - -
26C LYS* 3.3 36.5 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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