Contacts of the helix formed by residues 6 - 22 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C MET* 3.4 42.5 + - + +
4D LEU 2.8 9.6 + - - -
5D VAL* 1.3 74.5 - - - +
7D THR* 1.3 62.8 + - - +
8D THR* 3.0 13.7 + - - -
9D GLU* 2.8 42.9 + - - +
10D MET* 3.1 25.8 + - - +
106D HIS* 3.8 17.1 - - + +
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Residues in contact with THR 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET 4.7 0.6 - - - +
2D ASN* 2.8 24.1 + - - +
4D LEU* 3.9 11.0 - - + +
5D VAL 4.1 1.2 - - - -
6D ASP* 1.3 69.5 + - - +
8D THR* 1.3 67.6 + - - +
10D MET* 3.2 1.6 + - - -
11D TYR* 2.9 39.2 + - + -
44D THR* 3.7 30.7 - - + +
22F T 3.7 24.7 + - - +
23F G 2.6 29.3 + - - +
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Residues in contact with THR 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ASP* 3.0 8.1 + - - -
7D THR* 1.3 78.4 - - - +
9D GLU* 1.3 59.4 + - - +
11D TYR* 3.1 7.5 + - - +
12D LEU* 2.9 37.2 + - + +
44D THR* 5.4 1.2 - - - +
48D MET* 4.2 17.2 - - + +
53D LEU* 3.5 31.6 - - + +
71D LEU* 4.9 6.5 - - + -
22F T 4.3 16.4 + - - -
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Residues in contact with GLU 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET* 4.8 5.1 - - - +
6D ASP* 2.8 32.0 + - - +
8D THR* 1.3 72.6 - - - +
10D MET* 1.3 52.9 + - - +
12D LEU* 3.4 8.3 + - - +
13D ARG* 2.7 37.2 + - - +
71D LEU* 3.8 28.1 - - + +
75D VAL* 3.7 24.3 - - + +
78D LYS* 5.9 2.6 - - - +
105D GLU 4.2 0.8 - - - +
106D HIS* 2.8 49.8 + - + +
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Residues in contact with MET 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 3.7 32.3 - - + +
6D ASP 3.1 16.7 + - - +
7D THR 3.2 3.8 + - - +
9D GLU* 1.3 76.1 - - - +
11D TYR* 1.3 57.9 + - - +
13D ARG* 3.7 25.8 - - - +
14D THR* 2.7 37.7 + - - +
34D LEU* 3.8 25.2 - - + +
102D CYS* 3.9 9.2 - - - -
105D GLU* 3.1 5.2 - - - +
106D HIS* 3.2 9.9 - - + +
1002D NI 2.3 44.6 - - + -
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Residues in contact with TYR 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LEU* 4.4 2.9 - - + -
7D THR* 2.9 37.1 + - + +
8D THR 3.1 8.9 + - - +
10D MET* 1.3 74.7 - - - +
12D LEU* 1.3 65.5 + - - +
14D THR* 3.4 4.8 + - - -
15D ILE* 3.0 31.5 + - + +
30D ILE* 3.8 29.4 - - + +
34D LEU* 3.7 22.4 - - + -
36D GLN* 2.7 26.3 + - - -
40D THR 4.2 0.2 - - - -
41D VAL* 3.2 35.1 + - + +
44D THR* 3.6 29.7 + - + -
45D VAL* 4.2 6.7 - - + -
48D MET* 3.6 21.3 - - + -
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Residues in contact with LEU 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D THR* 2.9 27.1 + - + +
9D GLU* 3.6 5.6 - - - +
11D TYR* 1.3 77.6 - - - +
13D ARG* 1.3 63.7 + - - +
15D ILE* 3.2 7.4 + - + +
16D TYR* 3.0 22.5 + - - +
48D MET* 3.7 20.0 - - + -
53D LEU* 4.3 12.8 - - + +
64D LEU* 3.6 25.6 - - + +
68D GLY* 3.7 16.6 - - - +
71D LEU* 3.4 45.1 - - + -
72D ALA* 3.7 17.4 - - + +
75D VAL* 5.9 0.7 - - + -
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Residues in contact with ARG 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D GLU 2.7 21.8 + - - +
10D MET* 3.7 26.7 - - - +
12D LEU* 1.3 72.9 - - - +
14D THR* 1.3 59.0 + - - +
16D TYR* 3.4 7.3 + - + +
17D ASP* 2.9 56.1 + - - +
72D ALA* 4.4 4.9 - - - +
75D VAL* 4.2 8.7 - - + -
76D MET* 4.1 41.8 - - + +
79D HIS* 3.8 16.7 + - - -
98D HIS* 4.1 18.8 + - - -
102D CYS* 3.9 7.1 - - - -
105D GLU* 2.7 49.5 + - - +
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Residues in contact with THR 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D MET* 2.7 27.1 + - - +
11D TYR* 3.7 5.4 - - - -
13D ARG* 1.3 76.5 + - - +
15D ILE* 1.3 65.2 + - - +
17D ASP* 3.3 12.2 + - + +
18D LEU* 3.1 35.2 + - + +
30D ILE* 4.3 24.7 - - + -
33D ARG* 4.5 22.2 - - + +
34D LEU* 3.5 20.7 - - + +
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Residues in contact with ILE 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D TYR* 3.0 25.2 + - + +
12D LEU* 3.6 6.3 - - - +
14D THR* 1.3 73.9 - - - +
16D TYR* 1.3 65.1 + - - +
18D LEU* 3.2 13.9 + - + +
19D GLU* 3.1 33.5 + - - +
25D PRO* 4.3 14.5 - - + +
30D ILE* 4.2 17.7 - - + -
48D MET* 5.0 0.4 - - + -
54D LEU* 3.7 30.7 - - + -
62D LEU* 4.4 24.2 - - + +
64D LEU* 3.7 32.1 - - + -
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Residues in contact with TYR 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU 3.0 13.1 + - - +
13D ARG* 3.4 10.8 - - - +
15D ILE* 1.3 79.2 - - - +
17D ASP* 1.3 61.1 + - - +
19D GLU* 3.0 12.3 + - + +
20D GLU* 2.9 46.7 + - + +
64D LEU* 4.7 5.4 - - + +
69D ARG* 4.1 23.3 - - - -
72D ALA* 4.1 21.1 - - + -
73D ILE* 3.9 21.6 - - + +
76D MET* 3.4 42.4 - - + -
133D PRO* 3.3 26.1 - - + +
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Residues in contact with ASP 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ARG* 2.9 46.6 + - - +
14D THR* 3.3 14.8 + - - +
16D TYR* 1.3 72.0 - - - +
18D LEU* 1.3 64.2 + - - +
20D GLU* 3.0 13.5 + - - +
21D GLU* 2.9 39.4 + - - +
33D ARG* 4.0 9.5 + - - +
76D MET* 3.0 23.7 - - - +
80D ARG* 4.7 2.3 + - - -
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Residues in contact with LEU 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D THR* 3.1 29.3 + - + +
15D ILE* 3.5 10.5 - - - +
17D ASP* 1.3 78.7 - - - +
19D GLU* 1.3 57.6 + - - +
21D GLU* 3.2 4.3 + - - -
22D GLY 2.8 23.2 + - - -
23D VAL* 2.9 50.0 + - + +
25D PRO* 4.2 16.8 - - + -
26D LEU 5.0 1.1 - - - +
29D ARG* 3.5 33.9 - - + -
30D ILE* 4.8 4.0 - - + +
33D ARG* 3.5 31.9 - - - +
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Residues in contact with GLU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ILE* 3.1 29.8 + - - +
16D TYR* 3.0 16.3 + - + +
18D LEU* 1.3 74.6 - - - +
20D GLU* 1.3 65.1 + - - +
22D GLY* 3.2 12.0 + - - +
23D VAL 4.7 1.6 - - - -
25D PRO* 4.1 17.6 - - + +
62D LEU 4.6 5.0 - - - +
63D GLU* 5.1 2.8 - - - +
64D LEU* 4.5 7.1 + - - +
69D ARG* 2.7 40.3 + - - -
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Residues in contact with GLU 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D TYR* 2.9 40.7 + - + +
17D ASP* 3.3 11.7 - - - +
19D GLU* 1.3 76.8 - - - +
21D GLU* 1.3 62.7 + - + +
22D GLY 3.2 0.7 + - - -
76D MET* 3.9 6.6 - - - +
80D ARG* 2.9 43.5 + - - -
130D ASN* 5.2 1.7 + - - -
131D PRO* 4.6 9.5 - - - +
133D PRO* 5.1 0.7 - - - +
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Residues in contact with GLU 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ASP* 2.9 26.4 + - - +
18D LEU* 3.2 4.9 + - - +
20D GLU* 1.3 78.7 - - + +
22D GLY* 1.3 61.9 + - - +
23D VAL* 3.5 16.7 + - + +
33D ARG* 2.4 48.8 + - - -
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Residues in contact with GLY 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU 2.8 5.3 + - - -
19D GLU* 3.2 8.4 + - - -
20D GLU 3.2 5.4 - - - -
21D GLU* 1.3 79.3 - - - +
23D VAL* 1.3 61.0 + - - +
24D THR 4.1 0.7 + - - -
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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