Contacts of the helix formed by residues 6 - 26 (chain A) in PDB entry 2MZD
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 GLY 6 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLN* 3.6 7.6 - - - +
4A SER 2.8 6.7 + - - -
5A PRO* 1.2 91.3 - - - +
7A ASP* 1.2 62.1 + - - -
8A SER* 3.1 5.6 - - - -
9A ARG* 2.8 15.5 - - - -
10A ARG* 2.7 28.8 + - - +
7B ASP* 3.5 6.5 - - - +
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Residues in contact with ASP 7 (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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2A THR* 2.7 31.8 + - - +
3A GLN* 2.7 36.9 + - + +
6A GLY* 1.2 73.8 - - - -
8A SER* 1.3 58.9 + - - +
11A LEU* 2.7 65.6 + - - +
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Residues in contact with SER 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER 5.4 1.4 + - - -
5A PRO 4.9 0.7 + - - -
6A GLY* 2.8 5.1 + - - -
7A ASP* 1.3 84.7 - - - +
9A ARG* 1.4 58.5 + - - -
11A LEU* 4.9 1.3 - - - -
12A SER* 2.9 31.0 + - - -
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Residues in contact with ARG 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PRO* 2.8 30.4 + - + +
6A GLY* 2.8 14.4 - - - +
8A SER* 1.4 74.0 + - - +
10A ARG* 1.3 57.1 + - - +
12A SER* 3.4 4.3 - - - -
13A ILE* 2.9 30.2 + - - +
7B ASP* 3.5 26.9 - - + +
13B PRO* 3.6 30.7 - - + +
17B GLU* 4.0 6.1 + - - +
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Residues in contact with ARG 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLN* 3.3 33.5 + - - +
6A GLY 2.7 19.6 + - - +
7A ASP 4.0 1.1 - - - +
9A ARG* 1.3 73.7 - - - +
11A LEU* 1.3 65.0 + - - +
13A ILE* 2.9 10.6 + - - +
14A GLN* 2.6 63.5 + - - +
4B GLN* 4.5 15.0 - - - +
5B ALA* 3.0 46.3 - - - +
6B MET* 3.4 9.5 - - - +
7B ASP* 3.9 9.2 - - - +
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Residues in contact with LEU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLN* 4.9 0.7 - - + -
7A ASP* 2.7 67.3 + - - +
8A SER* 4.7 1.1 - - - +
10A ARG* 1.3 94.9 - - + +
12A SER* 1.3 59.3 + - - +
14A GLN* 3.3 26.5 - - - +
15A ARG* 2.9 39.2 + - + +
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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
----------------------------------------------------------
8A SER 2.9 23.1 + - - -
9A ARG* 3.4 2.0 - - - -
10A ARG 3.0 0.6 - - - -
11A LEU* 1.3 80.8 - - - +
13A ILE* 1.4 54.9 + - - +
15A ARG* 3.1 32.1 + - - +
16A ALA* 2.9 23.4 + - - +
17B GLU* 2.6 38.9 + - - +
20B PHE* 4.8 0.3 - - - -
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Residues in contact with ILE 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG 2.9 14.6 + - - +
10A ARG* 3.5 5.8 - - - +
12A SER* 1.4 69.4 - - - +
14A GLN* 1.3 57.2 + - - +
15A ARG 3.0 1.6 - - - -
16A ALA* 3.0 6.4 - - + +
17A ILE* 2.6 37.1 + - - +
66A LEU* 3.6 24.7 - - + -
7B ASP* 3.6 22.2 - - + -
10B MET* 3.4 48.9 - - + -
11B LEU 4.5 1.1 - - - +
13B PRO* 3.5 36.6 - - + -
17B GLU* 3.6 0.8 + - - -
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Residues in contact with GLN 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 ARG* 2.6 47.0 + - + +
11A LEU* 3.3 32.6 - - - +
13A ILE* 1.3 72.8 - - - +
15A ARG* 1.3 53.0 + - + +
17A ILE* 3.5 9.8 - - - +
18A GLN* 2.6 53.6 + - - +
3B SER 4.9 0.3 - - - +
4B GLN* 3.1 51.5 + - + +
5B ALA 5.1 1.3 - - - +
10B MET* 4.9 1.2 - - - +
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Residues in contact with ARG 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 2.9 25.1 + - + +
12A SER* 3.1 33.5 + - - +
14A GLN* 1.3 78.5 - - + +
16A ALA* 1.3 57.8 + - - +
18A GLN* 4.1 11.0 - - - +
19A SER* 2.7 39.7 + - - -
20B PHE* 3.4 45.2 - - + -
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Residues in contact with ALA 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 14.2 + - - +
13A ILE* 3.0 20.9 - - + +
15A ARG* 1.3 77.0 - - - +
17A ILE* 1.3 49.5 + - - +
20A LEU* 2.7 34.0 + - - +
39A MET* 3.3 7.6 - - - +
66A LEU* 3.5 15.4 - - + +
16B ILE* 4.0 3.4 - - + -
17B GLU* 3.9 24.0 - - + +
20B PHE* 4.2 10.3 - - - -
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Residues in contact with ILE 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE 2.6 15.7 + - - +
14A GLN* 3.5 4.3 - - - +
16A ALA* 1.3 70.1 - - - +
18A GLN* 1.3 56.6 + - - +
19A SER 3.1 0.2 - - - -
20A LEU* 3.7 5.8 - - + -
21A VAL* 2.5 46.2 + - + +
66A LEU* 3.0 27.1 - - + +
70A HIS* 3.3 41.5 - - + -
73A HIS* 4.0 1.3 - - + -
3B SER* 3.4 22.9 - - - +
10B MET* 3.2 31.4 - - + -
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Residues in contact with GLN 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLN* 2.6 54.7 + - + +
15A ARG* 4.0 9.9 - - - +
17A ILE* 1.3 72.4 - - - +
19A SER* 1.3 58.7 + - - +
21A VAL* 3.9 7.3 - - - +
22A HIS* 2.9 29.8 + - - +
3B SER* 4.2 17.8 - - - -
4B GLN* 3.7 11.9 + - - +
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Residues in contact with SER 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG 2.7 24.0 + - - -
18A GLN* 1.3 76.2 - - - +
20A LEU* 1.3 54.2 + - - +
22A HIS* 3.2 5.0 + - - +
23A ALA* 2.6 36.8 + - - +
35A SER 5.4 0.7 - - - -
36A CYS* 5.5 7.4 - - - -
39A MET* 3.4 26.5 - - - -
20B PHE* 2.9 25.5 + - - -
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Residues in contact with LEU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ALA 2.7 17.8 + - - +
17A ILE* 2.9 7.8 + - + +
19A SER* 1.3 77.4 - - - +
21A VAL* 1.3 52.1 + - - +
23A ALA* 3.2 4.1 + - - +
24A ALA* 2.7 34.1 + - - +
39A MET* 3.2 29.8 - - + +
43A VAL* 3.6 17.6 - - + +
63A LEU* 3.2 38.8 - - + -
66A LEU* 3.4 16.4 - - + -
67A ALA* 4.0 4.7 - - + -
81A VAL* 3.4 29.6 - - + -
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Residues in contact with VAL 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 ILE* 2.5 32.5 + - + +
18A GLN* 3.9 7.0 - - - +
20A LEU* 1.3 69.0 - - - +
22A HIS* 1.3 62.4 + - + +
24A ALA* 3.0 3.1 - - - +
25A GLN* 2.8 45.9 + - - +
70A HIS* 3.3 36.8 - - + +
80A PRO* 3.5 6.9 - - + +
81A VAL* 3.3 18.2 - - + -
1B LEU* 5.8 6.1 - - + -
3B SER* 4.1 12.1 - - - +
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Residues in contact with HIS 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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18A GLN 2.9 21.0 + - - +
19A SER* 3.4 5.8 - - - +
21A VAL* 1.3 78.8 - - - +
23A ALA* 1.3 54.3 + - - +
25A GLN* 3.6 14.7 + - - +
26A CYS* 2.6 60.1 + - + +
31A CYS* 4.9 4.2 - - - -
36A CYS* 3.3 32.8 - - + -
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Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A SER 2.6 22.2 + - - +
20A LEU 3.4 5.8 - - - +
22A HIS* 1.3 77.4 - - - +
24A ALA* 1.3 58.9 + - - +
26A CYS* 3.3 6.7 - - - +
36A CYS* 3.6 7.0 - - - +
39A MET* 3.3 11.2 - - + -
40A LYS* 2.9 64.7 - - - +
43A VAL* 4.9 1.2 - - - +
44A GLN* 5.9 0.5 - - - +
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Residues in contact with ALA 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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20A LEU 2.7 16.8 + - - +
21A VAL 3.0 10.5 - - - +
23A ALA* 1.3 77.8 - - - +
25A GLN* 1.3 60.5 + - - +
26A CYS 4.2 2.1 - - - +
27A ARG* 5.1 4.5 - - - +
43A VAL* 4.8 8.7 - - + -
79A CYS 5.2 0.2 - - - +
80A PRO* 3.2 38.1 - - + +
81A VAL* 3.4 11.9 - - + +
82A PRO* 4.3 5.4 - - + -
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Residues in contact with GLN 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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21A VAL* 2.8 29.9 + - - +
22A HIS* 3.6 14.1 + - - +
24A ALA* 1.3 76.6 - - - +
26A CYS* 1.3 66.7 + - - +
27A ARG* 3.3 14.3 + - - +
79A CYS* 5.3 9.8 - - + -
80A PRO* 3.6 22.4 - - + +
1B LEU* 5.4 7.5 - - - +
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Residues in contact with CYS 26 (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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22A HIS* 2.6 48.0 + - + +
23A ALA 3.3 8.1 - - - +
24A ALA 4.2 1.0 - - - +
25A GLN* 1.3 76.6 - - - +
27A ARG* 1.3 61.6 + - - +
28A ASN* 4.0 9.0 - - - -
31A CYS* 4.0 15.9 - - - -
40A LYS* 3.0 47.5 - - - +
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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