Contacts of the helix formed by residues 6 - 22 (chain A) in PDB entry 2ISZ
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 6 (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 2.5 11.1 + - - -
5A VAL* 1.3 75.2 - - - +
7A THR* 1.3 63.6 + - - +
8A THR* 3.4 9.9 + - - -
9A GLU* 2.6 57.8 + - + +
10A MET* 3.0 23.2 + - - +
106A HIS* 4.0 3.4 - - - +
1B MET* 2.7 53.8 + - + +
17F G 5.5 0.4 + - - -
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Residues in contact with THR 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 ASN* 2.3 38.3 + - - +
4A LEU* 4.1 10.5 - - + +
6A ASP* 1.3 71.7 - - - +
8A THR* 1.3 64.6 + - - +
10A MET* 3.0 2.4 + - - +
11A TYR* 2.9 47.3 + - + -
44A THR* 3.9 20.0 - - + +
1B MET* 6.0 0.2 - - - +
17F G 3.6 26.3 + - - +
18F C 3.1 21.4 + - - +
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Residues in contact with THR 8 (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 ASP* 3.4 10.1 + - - -
7A THR* 1.3 77.4 - - - +
9A GLU* 1.3 64.1 + - + +
11A TYR* 3.1 5.5 + - - +
12A LEU* 3.0 33.8 + - + +
44A THR* 5.6 0.4 - - - +
48A MET* 4.0 23.5 - - + +
53A LEU* 3.6 31.6 - - + -
71A LEU* 4.9 5.2 - - + -
1B MET 5.9 0.2 + - - -
17F G 4.2 17.2 + - - -
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Residues in contact with GLU 9 (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 ASP* 2.6 35.4 + - - +
8A THR* 1.3 74.6 - - - +
10A MET* 1.3 57.8 + - - +
12A LEU* 3.8 8.3 - - - +
13A ARG* 3.0 31.4 + - - +
71A LEU* 4.2 22.5 - - + +
75A VAL* 3.7 27.8 - - + +
78A LYS* 6.6 0.2 - - - -
105A GLU 4.0 1.0 - - - +
106A HIS* 2.7 55.9 + - + +
1B MET* 5.4 1.7 - - - +
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Residues in contact with MET 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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4A LEU* 3.5 42.4 - - + +
6A ASP 3.0 9.4 + - - +
7A THR 3.0 8.7 + - - +
9A GLU* 1.3 75.8 - - - +
11A TYR* 1.3 57.7 + - - +
13A ARG* 4.3 16.2 - - - +
14A THR* 2.4 43.0 + - - +
34A LEU* 4.0 22.2 - - + -
102A CYS* 3.8 11.7 - - - -
105A GLU* 3.0 5.8 - - - +
106A HIS* 3.2 3.6 - - + -
1002A NI 2.4 44.4 - - + -
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Residues in contact with TYR 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 4.6 1.3 - - + -
7A THR* 2.9 37.1 + - + +
8A THR 3.1 7.6 + - - +
10A MET* 1.3 74.3 - - - +
12A LEU* 1.3 64.6 + - - +
14A THR* 3.3 4.9 + - - -
15A ILE* 3.0 31.9 + - + +
30A ILE* 3.9 20.2 - - + +
34A LEU* 3.6 20.2 - - + -
36A GLN* 2.5 30.5 + - - -
40A THR* 4.1 1.0 + - - +
41A VAL* 3.2 33.0 + - + +
44A THR* 3.6 29.8 + - + -
45A VAL* 3.8 22.0 - - + -
48A MET* 3.6 18.2 - - + -
18F C 5.0 0.2 + - - -
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Residues in contact with LEU 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 THR* 3.0 23.2 + - + +
9A GLU* 3.8 7.4 - - - +
11A TYR* 1.3 76.2 - - - +
13A ARG* 1.3 61.7 + - - +
15A ILE* 3.3 5.1 + - - +
16A TYR* 3.0 22.7 + - - +
48A MET* 3.5 20.4 - - + -
53A LEU* 4.3 11.7 - - + +
54A LEU* 5.2 0.9 - - + -
64A LEU* 3.6 27.4 - - + +
68A GLY* 4.0 12.8 - - - +
71A LEU* 3.2 45.3 - - + -
72A ALA* 3.8 19.5 - - + +
75A VAL* 5.9 0.4 - - + -
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Residues in contact with ARG 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 GLU 3.0 16.3 + - - +
10A MET* 4.0 16.7 - - - +
12A LEU* 1.3 77.1 - - - +
14A THR* 1.3 54.2 + - - +
16A TYR* 3.1 7.5 + - - +
17A ASP* 2.5 72.6 + - - +
72A ALA* 4.5 5.8 - - - +
75A VAL* 3.5 29.4 - - + -
76A MET* 3.5 36.9 - - + +
79A HIS* 4.0 10.4 + - - -
98A HIS* 3.6 29.3 + - - -
102A CYS* 4.1 9.9 - - - -
105A GLU* 3.2 27.0 + - - +
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Residues in contact with THR 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 MET* 2.4 31.7 + - - +
11A TYR* 3.7 5.6 - - - -
12A LEU 3.2 0.2 - - - -
13A ARG* 1.3 74.1 + - - +
15A ILE* 1.3 66.7 + - - +
17A ASP* 3.3 11.7 + - - +
18A LEU* 3.0 31.6 + - + +
30A ILE* 4.5 21.8 - - + -
33A ARG* 4.1 35.4 - - + -
34A LEU* 3.8 18.6 - - + +
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Residues in contact with ILE 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 TYR* 3.0 21.4 + - + +
12A LEU 3.3 6.5 + - - +
14A THR* 1.3 75.6 - - - +
16A TYR* 1.3 57.9 + - - +
18A LEU* 3.2 12.7 + - + +
19A GLU* 3.0 38.2 + - - +
25A PRO* 4.2 15.7 - - + +
30A ILE* 4.1 16.8 - - + -
54A LEU* 3.7 31.2 - - + -
62A LEU* 3.9 27.4 - - + +
64A LEU* 3.8 33.0 - - + -
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Residues in contact with TYR 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 LEU 3.0 14.3 + - - +
13A ARG* 3.3 11.4 - - - +
15A ILE* 1.3 76.9 - - - +
17A ASP* 1.3 65.6 + - - +
19A GLU* 3.1 10.9 + - + +
20A GLU* 2.9 40.1 + - + +
64A LEU* 4.7 4.2 - - + +
69A ARG* 4.3 20.6 - - - -
72A ALA* 4.2 22.4 - - + +
73A ILE* 3.6 26.7 - - + +
76A MET* 3.7 33.9 - - + -
80A ARG* 5.5 0.2 - - - -
133A PRO* 3.7 23.3 - - + +
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Residues in contact with ASP 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 ARG* 2.5 43.4 + - - +
14A THR* 3.5 12.7 - - - +
16A TYR* 1.3 71.4 - - - +
18A LEU* 1.3 59.2 + - - +
20A GLU* 3.0 12.0 + - - +
21A GLU* 2.8 48.7 + - - +
33A ARG* 4.0 10.1 + - - +
76A MET* 3.0 29.3 - - - +
80A ARG* 5.1 0.2 + - - -
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Residues in contact with LEU 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 THR* 3.0 26.1 + - + +
15A ILE* 3.3 14.1 - - - +
16A TYR 3.2 0.2 - - - -
17A ASP* 1.3 81.2 - - - +
19A GLU* 1.3 57.6 + - - +
21A GLU* 3.2 4.9 + - - +
22A GLY 3.0 8.5 + - - -
23A VAL* 3.0 55.9 + - + +
25A PRO* 3.9 20.6 - - + -
26A LEU 4.7 1.8 - - - +
29A ARG* 3.7 29.4 - - + -
30A ILE* 5.0 4.9 - - + -
33A ARG* 3.5 37.5 - - - +
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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 ILE* 3.0 33.0 + - - +
16A TYR* 3.1 13.2 + - + +
18A LEU* 1.3 75.9 - - - +
20A GLU* 1.3 62.6 + - - +
22A GLY* 3.3 11.6 + - - -
23A VAL 4.6 3.1 - - - -
25A PRO* 4.2 15.2 - - + +
62A LEU 5.0 2.1 - - - +
63A GLU* 5.5 0.7 - - - -
64A LEU* 4.1 8.9 + - - +
69A ARG* 3.1 42.8 + - - -
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Residues in contact with GLU 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 TYR* 2.9 32.3 + - + +
17A ASP* 3.0 13.0 + - - +
19A GLU* 1.3 77.5 - - - +
21A GLU* 1.3 61.8 + - + +
22A GLY 3.2 0.8 + - - -
76A MET* 4.0 6.9 - - - +
80A ARG* 2.7 45.1 + - - -
130A ASN* 5.0 3.7 + - - +
131A PRO* 4.8 7.1 - - - +
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Residues in contact with GLU 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 ASP* 2.8 26.9 + - - +
18A LEU* 3.2 0.8 + - - +
20A GLU* 1.3 79.8 - - + +
22A GLY* 1.3 61.6 + - - +
23A VAL* 3.5 17.6 + - + +
33A ARG* 2.5 49.3 + - - -
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Residues in contact with GLY 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 LEU 3.0 4.9 + - - -
19A GLU* 3.3 9.3 + - - -
20A GLU 3.2 5.2 + - - -
21A GLU* 1.3 80.3 - - - +
23A VAL* 1.3 60.1 + - - +
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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