Contacts of the helix formed by residues 5 - 20 (chain H) in PDB entry 3HR4
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 THR 5 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F LYS* 4.4 3.1 - - - +
3H GLN* 4.2 10.1 - - - +
4H LEU* 1.3 74.8 - - - +
6H GLU* 1.3 65.1 + - - +
7H GLU* 3.3 10.6 + - - +
8H GLN* 3.2 40.8 + - - +
9H ILE* 3.1 27.7 + - - +
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Residues in contact with GLU 6 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F ALA* 3.3 28.8 - - + +
13F LYS* 3.7 33.0 + - + +
14F GLU* 3.3 38.2 - - - +
5H THR* 1.3 74.6 - - - +
7H GLU* 1.3 65.1 + - - +
9H ILE* 3.0 9.0 + - + +
10H ALA* 2.9 23.1 + - - +
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Residues in contact with GLU 7 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5H THR* 3.3 9.8 + - - +
6H GLU* 1.3 79.6 - - - +
8H GLN* 1.3 63.8 + - + +
10H ALA* 3.1 12.7 + - - +
11H GLU* 3.0 44.6 + - - +
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Residues in contact with GLN 8 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520G LYS* 4.3 19.4 + - - +
3H GLN 3.7 10.1 + - - +
4H LEU* 4.3 9.6 - - + +
5H THR* 3.2 47.2 + - - +
7H GLU* 1.3 73.9 - - + +
9H ILE* 1.3 67.1 + - - +
10H ALA 3.0 1.6 - - - -
11H GLU* 3.1 8.4 + - - +
12H PHE* 3.0 37.2 + - + -
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Residues in contact with ILE 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ILE* 3.7 28.3 - - + -
13F LYS* 3.5 28.0 - - + -
65F PHE* 3.4 33.2 - - + -
4H LEU* 3.6 27.4 - - + -
5H THR 3.1 13.8 + - - +
6H GLU* 3.0 8.2 + - + +
8H GLN* 1.3 76.9 - - - +
10H ALA* 1.3 57.9 + - - +
12H PHE* 3.3 10.1 + - - +
13H LYS* 3.0 24.8 + - - +
65H PHE* 3.8 13.8 - - + -
69H LEU* 4.8 3.8 - - + -
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Residues in contact with ALA 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F GLU* 4.1 21.3 - - + +
9F ILE* 6.4 0.4 - - - -
6H GLU 2.9 11.5 + - - +
7H GLU* 3.2 21.5 - - - +
8H GLN 3.0 0.2 - - - -
9H ILE* 1.3 74.7 - - - +
11H GLU* 1.3 67.2 + - - +
13H LYS* 2.9 17.4 + - - +
14H GLU* 3.0 24.1 + - - +
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Residues in contact with GLU 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516G LYS* 3.8 31.7 - - + +
517G VAL* 3.7 28.5 - - + +
520G LYS* 2.6 42.6 + - + +
7H GLU* 3.0 40.5 + - - +
8H GLN* 3.1 10.5 + - - +
10H ALA* 1.3 76.4 - - - +
12H PHE* 1.3 58.1 + - - +
14H GLU* 3.6 2.2 + - - +
15H ALA* 2.9 28.6 + - - +
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Residues in contact with PHE 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520G LYS* 3.7 33.4 - - + -
4H LEU* 5.9 4.7 - - + -
8H GLN* 3.0 36.9 + - + -
9H ILE* 3.6 7.9 - - + +
10H ALA 3.0 0.2 - - - -
11H GLU* 1.3 75.5 - - - +
13H LYS* 1.3 55.3 + - - +
15H ALA* 3.1 5.2 - - + +
16H PHE* 2.7 29.6 + - - +
65H PHE* 3.8 3.8 - - + -
68H PHE* 3.4 14.9 - + + -
69H LEU* 3.9 30.3 - - + -
72H MET* 3.7 31.0 - - + -
73H ALA* 4.7 12.1 - - + -
76H MET* 3.5 34.8 - - + -
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Residues in contact with LYS 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F LEU 3.6 22.9 + - - -
5F THR* 5.0 0.2 - - - +
6F GLU* 3.7 37.9 - - + +
9F ILE* 3.5 22.2 - - + -
9H ILE* 3.0 13.3 + - + +
10H ALA* 2.9 10.2 + - - +
12H PHE* 1.3 74.2 - - - +
14H GLU* 1.3 67.2 + - - +
16H PHE* 2.9 30.1 + - + +
17H SER* 3.0 20.9 + - - -
65H PHE* 3.4 26.7 - - + -
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Residues in contact with GLU 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F GLU* 3.0 32.1 - - - +
513G ILE* 5.0 9.0 - - + +
514G PRO* 4.1 12.5 - - - +
517G VAL* 3.4 32.9 - - + +
10H ALA* 3.0 18.1 + - - +
11H GLU* 3.9 0.9 - - - +
13H LYS* 1.3 74.4 - - - +
15H ALA* 1.3 64.2 + - - +
17H SER* 2.8 24.3 + - - -
18H LEU* 3.4 12.0 + - - +
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Residues in contact with ALA 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517G VAL* 3.4 23.9 - - - +
520G LYS* 4.4 7.0 - - + -
521G ALA* 4.3 11.2 - - + +
11H GLU 2.9 17.0 + - - +
12H PHE* 3.1 15.5 - - + +
13H LYS 3.1 0.2 - - - -
14H GLU* 1.3 75.8 - - - +
16H PHE* 1.3 65.6 + - - +
18H LEU* 3.1 21.5 + - - +
19H PHE* 3.4 10.8 - - - -
68H PHE* 4.2 11.0 - - + -
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Residues in contact with PHE 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H PHE 2.7 16.1 + - - +
13H LYS* 2.9 22.2 + - - +
15H ALA* 1.3 72.2 - - - +
17H SER* 1.3 57.6 + - - +
19H PHE* 2.6 33.8 + - - +
20H ASP* 3.2 21.5 + - + -
25H GLY* 3.4 25.1 - - - -
27H ILE* 3.2 31.2 - - + -
63H ILE 3.5 9.9 - - - -
64H ASP 3.8 2.2 - - - -
65H PHE* 3.4 44.0 - + + -
68H PHE* 3.5 38.6 - + + -
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Residues in contact with SER 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H LYS* 3.0 17.7 + - - -
14H GLU* 2.8 26.5 + - - -
16H PHE* 1.3 79.7 - - - +
18H LEU* 1.3 64.3 + - - +
19H PHE 3.1 0.7 - - - -
20H ASP* 3.0 34.4 - - - +
21H LYS* 4.0 2.1 + - - +
23H GLY* 6.5 0.4 - - - -
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Residues in contact with LEU 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513G ILE* 4.5 26.5 - - + -
517G VAL* 3.7 17.7 - - + +
518G LEU* 4.2 18.6 - - + -
521G ALA* 3.7 26.2 - - + -
14H GLU 3.4 13.9 - - - +
15H ALA* 3.1 10.6 + - - +
16H PHE 2.7 4.0 + - - -
17H SER* 1.3 78.0 + - - +
19H PHE* 1.3 63.8 + - + +
21H LYS* 3.8 22.2 + - - +
35H VAL* 4.3 5.9 - - - +
112H LEU* 5.6 12.6 - - + +
114H GLU* 6.5 1.3 - - + -
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Residues in contact with PHE 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521G ALA* 3.2 48.9 - - + -
524G PHE* 3.3 29.6 - + - -
525G ALA* 4.3 11.2 - - + -
15H ALA 3.4 13.7 - - - -
16H PHE* 2.6 17.0 + - - +
18H LEU* 1.3 76.3 - - + +
20H ASP* 1.3 58.5 + - - +
21H LYS* 3.0 12.1 + - - +
27H ILE* 3.6 25.1 - - + -
31H GLU* 3.6 22.2 - - - +
32H LEU* 4.1 21.1 - - + -
35H VAL* 4.0 34.3 - - + +
39H LEU* 6.1 0.2 - - + -
68H PHE* 4.3 7.4 - + - -
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Residues in contact with ASP 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H PHE* 3.2 24.2 + - + -
17H SER* 3.0 22.9 - - - +
19H PHE* 1.3 74.9 - - - +
21H LYS* 1.3 62.3 + - - +
22H ASP* 2.4 13.7 - - - +
23H GLY* 3.2 16.6 + - - -
24H ASP* 2.8 2.4 - - - +
25H GLY* 2.8 24.7 + - - -
26H THR 3.2 15.0 - - - +
27H ILE* 4.4 1.7 - - + +
31H GLU* 3.6 3.4 - - - -
201H CA 2.1 31.6 - - - -
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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