Contacts of the helix formed by residues 5 - 22 (chain C) in PDB entry 2ZQK
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 5 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C ALA* 1.3 59.3 + - - +
7C THR* 3.0 32.4 - - - +
8C GLU* 3.0 40.1 + - - +
9C THR* 3.5 6.9 + - - -
58C GLY* 3.7 14.6 + - - -
62C LYS* 6.2 4.5 - - - -
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Residues in contact with ALA 6 (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 SER* 1.3 73.2 - - - +
7C THR* 1.3 57.8 + - - +
9C THR* 3.3 27.1 - - - +
10C ALA* 3.8 5.9 + - - +
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Residues in contact with THR 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C SER* 3.0 27.9 - - - +
6C ALA* 1.3 77.9 - - - +
8C GLU* 1.3 60.8 + - - +
9C THR 3.0 5.7 + - - -
10C ALA* 3.5 6.3 + - - +
11C THR* 3.3 22.9 + - - +
57C ALA* 3.5 7.4 + - - +
58C GLY* 3.4 7.6 - - - -
61C ALA* 3.4 31.0 - - + +
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Residues in contact with GLU 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C SER* 3.0 30.3 + - - +
7C THR* 1.3 83.3 - - - +
9C THR* 1.3 57.4 + - - +
11C THR* 3.1 2.9 - - - +
12C ARG* 3.1 37.0 + - - +
51C GLU* 4.6 4.2 - - - +
54C ALA* 3.0 30.9 - - + +
55C LYS* 3.1 46.3 + - - +
58C GLY* 4.6 3.8 - - - -
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Residues in contact with THR 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C SER 3.5 8.9 + - - -
6C ALA* 3.3 19.2 + - - +
7C THR 3.0 0.2 - - - -
8C GLU* 1.3 75.6 - - - +
10C ALA* 1.3 65.1 + - - +
12C ARG* 3.0 18.2 + - - +
13C ASP* 2.8 50.7 + - - +
10D ALA* 5.9 7.6 - - + +
14D GLN* 5.6 6.1 - - + +
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Residues in contact with ALA 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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6C ALA 3.8 6.2 + - - +
7C THR* 3.5 8.1 + - - +
9C THR* 1.3 82.5 - - - +
11C THR* 1.3 58.0 + - - +
13C ASP* 4.8 3.6 - - - -
14C GLN* 3.1 33.4 + - - +
10D ALA* 5.0 19.1 - - + +
13D ASP* 4.2 9.6 - - - +
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Residues in contact with THR 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 THR 3.3 12.1 + - - +
8C GLU* 3.1 14.6 - - - +
10C ALA* 1.3 81.2 - - - +
12C ARG* 1.3 60.0 + - - +
14C GLN* 4.2 2.8 - - - +
15C LEU* 3.1 37.4 + - - +
53C GLN 3.9 5.7 + - - -
54C ALA* 3.1 26.2 - - - +
57C ALA* 3.3 25.5 - - + +
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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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8C GLU* 3.1 21.2 + - - +
9C THR* 3.0 21.6 + - - +
11C THR* 1.3 76.7 - - - +
13C ASP* 1.3 94.7 + - - +
14C GLN 3.1 1.8 - - - -
15C LEU* 3.5 0.6 + - - -
16C THR* 3.1 31.1 + - - +
50C ILE* 3.8 14.1 - - + +
51C GLU* 2.7 44.5 + - - +
54C ALA* 3.2 17.6 - - + +
17D LYS* 5.0 9.6 - - + +
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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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9C THR* 2.8 33.7 + - - +
10C ALA* 4.3 1.3 - - - +
12C ARG* 1.3 105.7 + - - +
14C GLN* 1.3 56.2 + - - +
16C THR* 3.8 5.1 - - - +
17C LYS* 2.9 27.2 + - - +
10D ALA 5.2 1.1 - - - +
13D ASP* 3.5 27.4 - - + +
14D GLN* 3.3 37.2 + - - +
17D LYS* 3.8 15.2 + - - +
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Residues in contact with GLN 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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10C ALA 3.1 19.7 + - - +
11C THR* 4.2 4.5 - - - +
13C ASP* 1.3 74.2 - - - +
15C LEU* 1.3 68.4 + - - +
16C THR 2.8 6.1 + - - -
17C LYS* 3.0 9.7 + - - +
18C GLU* 3.0 45.7 + - - +
9D THR* 5.0 6.1 - - - +
13D ASP* 2.8 29.9 - - - +
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Residues in contact with LEU 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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11C THR* 3.1 29.3 + - - +
12C ARG 4.0 0.2 - - - +
14C GLN* 1.3 82.4 - - + +
16C THR* 1.3 59.6 + - - +
18C GLU* 4.0 12.3 + - - +
19C ALA* 3.4 18.9 + - - +
49C ASN 5.3 0.2 - - - +
50C ILE* 3.6 34.9 - - + +
53C GLN* 3.8 47.8 - - + +
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Residues in contact with THR 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* 3.1 20.1 + - - +
13C ASP 3.8 3.6 - - - -
14C GLN 2.8 1.2 + - - -
15C LEU* 1.3 74.9 - - - +
17C LYS* 1.3 56.9 + - - +
18C GLU 2.9 4.3 - - - -
19C ALA* 2.6 27.6 + - - +
20C PHE* 3.2 35.3 + - + -
42C LEU* 3.9 7.9 - - + -
50C ILE* 3.2 18.4 - - - +
17D LYS* 3.6 27.8 - - + +
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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 2.9 20.2 + - - +
14C GLN* 3.0 8.1 + - - +
16C THR* 1.3 77.1 - - - +
18C GLU* 1.3 95.0 + - - +
20C PHE* 4.1 1.3 + - - -
21C GLN* 3.2 19.2 - - - +
12D ARG* 5.5 6.5 - - + -
13D ASP* 3.5 32.7 + - - +
16D THR* 3.4 31.6 - - + +
17D LYS* 5.2 3.8 - - - +
20D PHE* 3.8 19.5 - - + -
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Residues in contact with GLU 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 GLN* 3.0 40.5 + - - +
15C LEU* 4.1 11.5 - - - +
16C THR 2.9 0.6 - - - -
17C LYS* 1.3 101.5 + - - +
19C ALA* 1.3 65.0 + - - +
20C PHE 3.2 0.4 - - - -
21C GLN* 3.1 27.5 - - + +
22C ASN* 3.8 3.8 + - - +
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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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15C LEU 3.4 15.5 + - - +
16C THR 2.6 16.8 + - - +
18C GLU* 1.3 74.2 - - - +
20C PHE* 1.3 58.5 + - - +
22C ASN 3.2 6.4 + - - +
25C ASN* 2.5 36.6 + - - +
42C LEU* 3.5 22.7 - - + -
46C VAL* 4.5 5.2 - - + -
50C ILE* 3.6 12.8 - - + -
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Residues in contact with PHE 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 THR* 3.2 28.3 + - + -
17C LYS* 4.3 0.9 - - - +
18C GLU 3.2 0.2 - - - -
19C ALA* 1.3 71.7 - - - +
21C GLN* 1.3 63.9 + - - +
22C ASN 2.8 14.6 + - - -
26C GLN* 3.7 29.8 - - + +
40C GLY 3.5 25.4 - - - -
41C VAL* 4.6 0.4 - - - -
42C LEU* 3.3 44.4 - - + -
17D LYS* 4.8 8.1 - - + -
20D PHE* 3.2 70.0 - + + -
21D GLN* 4.9 0.7 - - + -
40D GLY* 3.7 12.6 - - - -
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Residues in contact with GLN 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* 3.2 26.3 + - - +
18C GLU* 3.1 21.6 + - - +
20C PHE* 1.3 78.9 - - - +
22C ASN* 1.3 56.0 + - + +
23C PRO* 3.0 13.7 - - - +
16D THR* 6.1 0.4 - - - +
20D PHE* 3.9 13.3 - - - -
39D SER 4.5 1.9 - - - +
40D GLY* 3.2 32.6 + - - +
41D VAL* 5.1 3.1 - - + +
42D LEU* 6.0 0.6 - - - +
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Residues in contact with ASN 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 GLU 3.8 2.7 + - - +
19C ALA 3.2 5.4 + - - +
20C PHE 2.8 5.1 + - - +
21C GLN* 1.3 79.0 - - + +
23C PRO* 1.3 53.9 - - - +
24C ASP* 2.7 52.3 + - - +
25C ASN* 2.8 42.3 + - - +
26C GLN 4.0 1.7 + - - -
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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