Contacts of the helix formed by residues 4 - 21 (chain D) in PDB entry 4HSZ
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 PRO 4 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C VAL* 3.9 25.3 - - + +
41C GLU* 4.5 9.4 - - - +
3D CYS* 1.3 90.0 - - + +
5D LEU* 1.3 52.0 + - - +
7D LYS* 3.1 6.5 + - + +
8D ALA* 2.7 36.0 + - - +
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Residues in contact with LEU 5 (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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11C VAL* 3.9 10.0 - - + +
12C MET* 4.1 27.8 - - + -
15C THR* 4.0 22.4 - - + +
37C LEU* 4.2 9.0 - - + -
41C GLU* 3.6 27.6 + - + +
42C LEU* 4.0 27.6 - - + -
75C TYR* 4.1 19.3 - - - +
79C LEU* 4.4 11.4 - - + -
3D CYS 3.3 1.0 - - - -
4D PRO* 1.3 78.5 - - - +
6D GLU* 1.3 66.8 + - - +
8D ALA* 3.0 3.8 + - + +
9D LEU* 3.0 27.4 + - + +
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Residues in contact with GLU 6 (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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41C GLU 3.3 14.4 - - - +
42C LEU* 3.0 18.2 - - + +
43C PRO* 2.8 19.6 - - - +
44C SER* 2.5 51.9 + - - -
45C PHE* 4.1 12.1 + - + -
3D CYS 3.3 22.0 + - - +
5D LEU* 1.3 78.0 - - - +
7D LYS* 1.3 57.5 + - - +
9D LEU* 3.5 5.3 + - - +
10D ASP* 3.1 25.3 + - - +
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Residues in contact with LYS 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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3D CYS 3.0 17.5 + - - +
4D PRO* 3.7 6.3 - - + +
6D GLU* 1.3 76.5 - - - +
8D ALA* 1.3 59.5 + - - +
10D ASP* 4.2 11.9 - - - +
11D VAL* 2.9 39.7 + - + +
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Residues in contact with ALA 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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8C ALA* 3.6 40.3 - - + +
11C VAL* 4.2 10.8 - - + -
12C MET* 4.4 8.7 - - + -
4D PRO 2.7 20.2 + - - +
5D LEU* 3.0 7.2 + - - +
7D LYS* 1.3 72.3 - - - +
9D LEU* 1.3 58.2 + - - +
11D VAL* 3.5 3.5 + - - +
12D MET* 2.9 33.6 + - - +
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Residues in contact with LEU 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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12C MET* 4.4 1.6 - - - -
42C LEU* 3.8 29.4 - - + -
45C PHE* 5.0 5.2 - - + -
79C LEU* 4.0 46.2 - - + +
82C ILE* 4.5 21.1 - - + -
83C ALA* 4.9 6.5 - - + -
86C CYS* 6.4 1.8 - - - -
5D LEU* 3.0 17.8 + - + +
6D GLU* 3.6 7.2 - - - +
8D ALA* 1.3 74.0 - - - +
10D ASP* 1.3 64.7 + - - +
12D MET* 3.1 31.3 + - + +
13D VAL* 3.0 28.0 + - + +
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Residues in contact with ASP 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D GLU 3.1 14.6 + - - +
7D LYS* 3.7 15.1 - - - +
9D LEU* 1.3 78.6 - - - +
11D VAL* 1.3 62.3 + - - +
13D VAL* 3.2 8.5 + - - +
14D SER* 2.8 35.7 + - - -
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Residues in contact with VAL 11 (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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4C PRO* 3.9 39.3 - - + +
5C LEU* 3.9 8.5 - - + +
8C ALA* 3.9 9.2 - - + -
7D LYS* 2.9 29.9 + - + +
8D ALA* 3.6 3.4 - - - +
10D ASP* 1.3 78.7 - - - +
12D MET* 1.3 57.1 + - - +
14D SER* 3.8 8.1 - - - +
15D THR* 2.5 48.9 + - - +
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Residues in contact with MET 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C LEU* 3.8 23.8 - - + -
8C ALA* 4.6 4.0 - - + -
9C LEU* 4.6 6.7 - - + -
12C MET* 2.6 45.1 - - + +
79C LEU* 5.4 3.8 - - + +
80C SER* 5.9 2.9 - - - +
83C ALA* 4.7 13.0 - - + -
8D ALA 2.9 18.3 + - - +
9D LEU* 3.1 24.4 + - + +
11D VAL* 1.3 76.0 - - - +
13D VAL* 1.3 66.1 + - + +
16D PHE 3.6 2.1 + - - -
72D PHE* 5.3 0.2 - - - -
75D TYR* 2.7 29.5 + - + -
76D CYS* 5.6 6.5 - - + -
79D LEU* 3.8 26.0 - - + -
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Residues in contact with VAL 13 (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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83C ALA* 3.8 35.7 - - + +
86C CYS* 4.6 13.0 - - + +
87C ASN* 4.0 17.5 - - + +
9D LEU 3.0 15.0 + - - +
10D ASP* 3.8 7.6 - - - +
12D MET* 1.3 76.3 - - - +
14D SER* 1.3 63.9 + - - +
16D PHE* 3.1 14.2 + - - +
17D HIS* 3.2 35.1 - - + +
72D PHE* 4.1 13.7 - - + -
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Residues in contact with SER 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ASP* 2.8 29.2 + - - -
11D VAL* 3.5 11.3 + - - +
13D VAL* 1.3 75.0 - - - +
15D THR* 1.3 67.8 + - - +
17D HIS* 3.2 9.5 + - - +
18D LYS* 3.0 25.8 + - - +
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Residues in contact with THR 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C PRO* 5.5 1.0 - - - +
5C LEU* 4.0 20.0 + - + +
11D VAL* 2.5 34.9 + - - +
14D SER* 1.3 78.4 + - - +
16D PHE* 1.3 64.5 + - - +
18D LYS* 3.3 22.5 - - - +
19D TYR* 3.3 13.4 - - + -
37D LEU* 3.6 8.0 - - + +
41D GLU* 3.7 37.4 + - + +
75D TYR* 3.9 9.2 - - - +
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Residues in contact with PHE 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 MET 3.6 2.2 + - - -
13D VAL 3.1 12.4 + - - +
14D SER 3.1 0.4 - - - -
15D THR* 1.3 78.4 - - - +
17D HIS* 1.3 74.2 + + - +
19D TYR* 3.3 2.9 + - - -
20D SER* 2.9 44.4 + - - -
27D PHE* 3.4 30.1 - - + -
29D LEU* 3.3 34.0 - - + +
37D LEU* 4.3 4.5 - - - -
70D VAL 3.7 8.5 - - - -
71D ASP 3.5 12.6 - - - -
72D PHE* 3.4 37.7 - + + -
75D TYR* 3.5 38.3 + + + -
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Residues in contact with HIS 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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87C ASN* 2.7 32.5 + - - -
13D VAL* 3.2 34.8 + - + +
14D SER* 3.2 7.4 + - - +
16D PHE* 1.3 91.8 - + - +
18D LYS* 1.3 62.8 + - - +
19D TYR 3.0 6.9 + - - -
20D SER* 3.4 9.5 + - - -
21D GLY* 3.4 17.7 + - - -
26D LYS 4.8 5.8 + - - +
27D PHE* 4.9 14.4 - + + -
72D PHE* 4.7 0.4 - - - -
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Residues in contact with LYS 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 SER* 3.0 14.9 + - - +
15D THR* 3.3 20.0 - - - +
17D HIS* 1.3 77.5 - - - +
19D TYR* 1.3 85.6 + - + +
22D LYS* 3.3 22.9 + - - +
41D GLU* 3.2 23.6 + - - -
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Residues in contact with TYR 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 THR* 3.3 20.2 - - + -
16D PHE 3.3 1.8 + - - -
18D LYS* 1.3 107.6 + - - +
20D SER* 1.3 60.2 - - - +
21D GLY 3.3 2.0 + - - -
22D LYS* 3.4 30.2 + - + +
29D LEU* 4.0 7.9 - - + -
33D GLU* 3.0 34.8 - - + +
36D GLU* 3.9 26.5 - - + -
37D LEU* 3.6 43.3 - - + -
40D ARG* 3.4 16.3 - - - +
41D GLU* 2.6 43.5 + - + +
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Residues in contact with SER 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 PHE* 2.9 39.5 + - - -
17D HIS* 3.4 12.5 + - - -
19D TYR* 1.3 78.4 - - - +
21D GLY* 1.3 58.2 + - - +
22D LYS 3.2 0.6 + - - -
23D GLU 3.6 0.3 - - - +
25D ASP 3.0 6.8 - - - +
26D LYS 2.9 17.4 + - - -
27D PHE* 4.0 0.2 - - - -
28D LYS 3.7 15.7 - - - -
29D LEU* 3.7 15.7 - - - +
33D GLU* 2.8 4.3 - - - +
101D CA 2.5 25.6 - - - -
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Residues in contact with GLY 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 HIS 3.4 10.1 + - - -
19D TYR 3.3 1.0 - - - -
20D SER* 1.3 81.2 + - - +
22D LYS* 1.3 61.4 + - - +
23D GLU 3.6 0.7 - - - -
26D LYS* 3.4 40.7 + - - +
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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