Contacts of the helix formed by residues 5 - 25 (chain A) in PDB entry 3ZQI
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 ASP 5 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LEU* 1.3 76.1 - - - +
6A LYS* 1.3 70.0 + - - +
7A SER* 4.2 13.8 - - - +
8A LYS* 3.2 14.7 + - + +
9A VAL* 3.1 21.8 + - - +
44A HIS* 4.3 7.9 - - - -
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Residues in contact with LYS 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ASP* 1.3 78.1 + - - +
7A SER* 1.3 56.0 + - - +
9A VAL* 3.2 13.1 + - - +
10A ILE* 2.9 47.3 + - + +
44A HIS* 3.7 38.8 + - + +
45A VAL* 3.9 19.0 - - - +
50A ALA 5.4 1.2 + - - -
54A ALA* 3.8 25.5 - - - +
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Residues in contact with SER 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASP* 3.2 11.9 - - - +
6A LYS* 1.3 78.8 - - - +
8A LYS* 1.3 56.6 + - - +
10A ILE* 4.5 4.3 - - - -
11A ASN* 2.9 46.0 + - - +
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Residues in contact with LYS 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 4.2 9.9 - - + -
5A ASP* 3.2 24.0 + - + +
7A SER* 1.3 79.2 + - - +
9A VAL* 1.3 62.4 + - - +
11A ASN* 4.1 4.7 - - - +
12A SER* 3.0 27.9 + - - -
34A LEU* 4.2 17.5 - - + -
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Residues in contact with VAL 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.7 31.2 - - + -
5A ASP 3.1 14.8 + - - +
6A LYS* 3.6 13.9 - - - +
8A LYS* 1.3 76.1 - - - +
10A ILE* 1.4 58.2 + - - +
12A SER* 3.8 1.6 - - - -
13A ALA* 2.9 28.4 + - - +
30A LEU* 4.1 10.1 - - + +
34A LEU* 4.3 8.7 - - + -
41A LEU* 3.9 17.0 - - + -
44A HIS* 4.2 11.2 - - + -
45A VAL* 3.6 28.7 - - + -
51A LEU* 4.8 4.0 - - + -
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Residues in contact with ILE 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LYS* 2.9 39.7 + - + +
7A SER* 3.8 5.6 - - - +
9A VAL* 1.4 74.7 - - - +
11A ASN* 1.4 64.1 + - - +
13A ALA* 3.2 1.8 + - - +
14A LEU* 2.9 37.6 + - + +
51A LEU* 5.2 4.3 - - + -
54A ALA* 3.7 35.2 - - + +
55A LEU* 3.7 18.7 - - + +
58A GLU* 3.5 40.8 - - + +
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Residues in contact with ASN 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A SER* 2.9 32.6 + - - +
8A LYS* 4.1 4.6 - - - +
10A ILE* 1.4 79.8 - - - +
12A SER* 1.4 56.7 + - - +
14A LEU* 3.3 6.9 + - - +
15A GLU* 3.0 27.4 + - - +
58A GLU* 5.0 0.5 - - - +
62A ARG* 2.9 27.3 + - - +
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Residues in contact with SER 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LYS* 3.0 20.1 + - - -
9A VAL 3.8 1.8 - - - -
11A ASN* 1.4 76.2 - - - +
13A ALA* 1.4 58.8 + - - +
15A GLU* 3.3 7.1 + - - -
16A LEU* 2.9 25.1 + - - +
30A LEU* 3.8 5.7 - - - +
33A LYS* 3.4 34.7 + - - +
34A LEU* 3.6 23.6 - - - +
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Residues in contact with ALA 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL 2.9 19.1 + - - +
10A ILE 3.7 3.6 - - - +
12A SER* 1.4 77.7 - - - +
14A LEU* 1.3 57.6 + - - +
16A LEU* 3.3 5.5 + - - +
17A LEU* 2.8 28.1 + - - +
25A LEU* 3.7 8.1 - - + +
30A LEU* 3.6 27.5 - - + +
51A LEU* 3.9 17.3 - - + -
55A LEU* 3.9 12.8 - - + -
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Residues in contact with LEU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ILE* 2.9 31.1 + - + +
11A ASN* 3.8 5.2 - - - +
12A SER 3.3 0.2 - - - -
13A ALA* 1.3 72.6 - - - +
15A GLU* 1.3 65.6 + - - +
17A LEU* 3.4 10.5 + - + +
18A ASN* 3.1 27.5 + - - -
55A LEU* 4.1 19.5 - - + +
58A GLU* 4.1 7.6 - - + -
59A MET* 4.0 22.4 - - + -
62A ARG* 3.7 37.9 - - - +
93A HIS* 3.6 35.2 - - + +
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Residues in contact with GLU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ASN 3.0 17.9 + - - +
12A SER* 3.6 6.6 - - - +
14A LEU* 1.3 77.4 - - - +
16A LEU* 1.3 61.7 + - - +
18A ASN* 3.2 9.7 + - - +
19A GLU* 3.0 39.2 + - + +
33A LYS* 2.8 26.6 + - - -
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Residues in contact with LEU 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A SER 2.9 17.9 + - - +
13A ALA* 3.5 4.9 - - - +
15A GLU* 1.3 72.3 - - - +
17A LEU* 1.4 65.8 + - - +
19A GLU* 3.0 19.9 + - - +
20A VAL* 2.9 54.2 + - + +
25A LEU* 3.7 22.4 - - + -
26A THR 4.7 0.2 - - - +
29A LYS* 4.2 17.3 - - + +
30A LEU* 4.0 34.1 - - + +
33A LYS* 3.9 13.9 - - + +
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Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ALA 2.8 15.2 + - - +
14A LEU* 3.5 22.7 - - + +
15A GLU 3.3 0.2 - - - -
16A LEU* 1.4 75.5 - - - +
18A ASN* 1.4 58.4 + - - +
21A GLY* 2.8 34.7 + - - +
22A ILE* 3.8 31.0 - - + +
25A LEU* 4.2 13.9 - - + +
55A LEU* 4.7 4.9 - - + -
59A MET* 4.3 4.3 - - + -
93A HIS* 3.8 20.9 - - + -
94A ARG* 3.4 29.4 - - - +
95A ASP 5.3 0.2 - - - -
99A VAL* 3.8 25.6 - - + -
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Residues in contact with ASN 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU 3.1 13.4 + - - +
15A GLU* 3.2 10.3 + - + +
17A LEU* 1.4 75.2 - - - +
19A GLU* 1.3 60.6 + - + +
92A SER 5.1 1.6 + - - -
93A HIS* 3.5 27.2 + - - +
94A ARG* 2.9 51.1 + - - +
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Residues in contact with GLU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLU* 3.0 26.8 + - + +
16A LEU* 3.0 22.1 + - - +
18A ASN* 1.3 78.5 - - + +
20A VAL* 1.3 68.3 + - + +
33A LYS* 2.9 32.0 + - - +
94A ARG* 3.1 10.7 + - - -
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Residues in contact with VAL 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 2.9 44.3 + - + +
19A GLU* 1.3 81.6 - - + +
21A GLY* 1.3 71.8 + - - +
23A GLU* 5.0 1.4 + - - +
24A GLY* 3.6 34.2 + - - +
25A LEU 3.8 1.3 - - - +
94A ARG* 3.6 13.0 + - - +
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Residues in contact with GLY 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 2.8 23.6 + - - +
20A VAL* 1.3 81.0 - - - +
22A ILE* 1.3 66.2 + - - -
23A GLU* 3.3 4.0 - - - -
24A GLY 3.2 10.0 + - - -
25A LEU* 3.3 10.9 + - - +
94A ARG* 3.3 16.6 - - - -
95A ASP* 3.3 13.2 - - - -
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Residues in contact with ILE 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 3.8 10.8 - - + +
21A GLY* 1.3 74.1 - - - -
23A GLU* 1.3 82.8 + - + +
25A LEU* 3.3 9.7 + - + +
48A LYS* 2.9 26.9 + - - +
52A LEU* 4.2 23.1 - - + -
95A ASP* 2.9 32.7 + - + +
98A LYS* 3.6 45.5 - - + +
99A VAL* 3.8 16.4 - - + +
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Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL 5.2 1.2 - - - +
21A GLY* 3.3 1.8 - - - -
22A ILE* 1.3 95.9 + - + +
24A GLY* 1.3 58.5 + - - +
25A LEU 3.5 0.3 + - - -
26A THR* 4.0 9.2 - - - +
48A LYS* 4.0 11.8 + - - +
95A ASP* 4.4 0.9 - - - +
98A LYS* 4.6 9.4 + - - +
1207A MG 3.9 18.4 - - - -
23B GLU* 3.3 44.0 - - + +
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Residues in contact with GLY 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 5.0 0.2 - - - +
20A VAL* 3.6 31.6 + - - +
21A GLY 3.2 4.8 + - - -
23A GLU* 1.3 77.4 - - - +
25A LEU* 1.3 58.5 + - - +
26A THR* 3.1 9.2 + - - +
29A LYS* 3.5 23.6 - - - +
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ALA* 3.7 24.7 - - + +
16A LEU* 3.7 24.2 - - + -
17A LEU* 4.2 16.4 - - + +
20A VAL* 4.4 4.0 - - + -
21A GLY 3.3 10.9 + - - +
22A ILE* 3.3 9.8 + - - +
23A GLU 3.3 1.0 - - - -
24A GLY* 1.3 72.9 - - - +
26A THR* 1.3 60.5 + - - +
30A LEU* 5.4 0.9 - - + -
48A LYS* 2.8 32.8 + - - +
51A LEU* 3.9 22.2 - - + -
52A LEU* 4.0 21.3 - - + -
55A LEU* 3.7 26.2 - - + -
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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
------------------------------------------------------------
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