Contacts of the helix formed by residues 2 - 20 (chain F) in PDB entry 4HRE
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 SER 2 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36E LYS 5.0 1.4 + - - -
37E GLU* 3.0 46.6 + - - -
39E PRO* 5.0 3.0 - - - +
1F PRO* 1.3 82.3 - - - +
3F GLN* 1.3 60.6 + - - +
4F MET* 3.0 7.0 + - - +
5F GLU* 3.2 19.1 + - - +
6F HIS* 3.0 30.5 + - - -
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Residues in contact with GLN 3 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E THR* 4.1 22.5 + - + +
37E GLU* 6.1 0.4 - - - +
1F PRO 4.9 4.8 - - - +
2F SER* 1.3 74.5 + - - +
4F MET* 1.3 57.1 - - - +
6F HIS* 3.1 19.7 + - + +
7F ALA* 2.9 24.1 + - - +
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Residues in contact with MET 4 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E THR* 4.4 7.9 - - + +
11E MET* 4.2 12.8 - - + -
14E THR* 3.5 32.1 - - + +
37E GLU* 3.3 40.3 + - + +
38E PHE* 4.8 10.1 - - + -
71E PHE* 3.6 8.5 - - + -
75E ILE* 3.5 30.3 - - + -
2F SER* 3.0 4.4 + - - +
3F GLN* 1.3 78.4 - - - +
5F GLU* 1.3 62.1 + - + +
7F ALA* 3.1 12.0 + - - +
8F MET* 2.9 50.7 + - - +
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Residues in contact with GLU 5 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER* 4.2 10.8 - - - +
4A VAL* 4.7 9.4 - - + +
5A HIS* 3.4 18.9 - - - +
8A LEU* 3.7 15.2 - - - +
38E PHE* 3.2 29.9 - - + -
39E PRO* 3.1 37.8 - - - +
1F PRO* 3.8 14.1 - - + +
2F SER* 3.2 17.0 + - - +
4F MET* 1.3 73.0 - - - +
6F HIS* 1.3 65.3 + - - +
7F ALA 3.1 0.2 - - - -
8F MET* 4.1 10.2 - - + +
9F GLU* 3.0 32.8 + - - +
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Residues in contact with HIS 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER* 5.2 0.4 + - - -
1F PRO* 3.9 29.9 - - + +
2F SER 3.0 23.6 + - - +
3F GLN* 3.1 24.6 + - + +
5F GLU* 1.3 74.8 - - - +
7F ALA* 1.3 56.3 + - - +
9F GLU* 3.2 18.0 + - - +
10F THR* 2.3 35.7 + - - +
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Residues in contact with ALA 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ALA* 3.6 42.2 - - + +
10E THR* 4.5 3.8 - - - -
11E MET* 4.4 9.0 - - + +
3F GLN 2.9 15.4 + - - +
4F MET* 3.1 15.2 + - - +
6F HIS* 1.3 76.1 - - - +
8F MET* 1.3 62.9 + - - +
10F THR* 3.3 12.0 + - - -
11F MET* 3.3 19.4 + - - +
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Residues in contact with MET 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A VAL* 4.1 21.5 - - + -
8A LEU* 3.9 20.0 - - + -
11E MET* 5.2 3.4 - - + -
38E PHE* 3.7 35.9 - - + -
75E ILE* 4.4 13.5 - - + -
78E LEU* 5.5 4.9 - - + -
79E THR* 3.2 36.3 - - + +
82E CYS* 5.3 3.6 - - - -
4F MET* 2.9 30.2 + - - +
5F GLU* 3.5 9.2 + - + +
7F ALA* 1.3 71.9 - - + +
9F GLU* 1.3 64.1 + - - +
11F MET* 3.2 16.1 + - - +
12F MET* 3.0 20.4 + - - +
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Residues in contact with GLU 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER* 3.1 43.4 + - - -
3A THR* 3.5 8.3 + - - +
4A VAL* 3.6 28.0 - - + +
5F GLU 3.0 20.6 + - - +
6F HIS* 3.2 26.7 + - - +
8F MET* 1.3 78.1 - - - +
10F THR* 1.3 66.7 + - - +
12F MET* 3.2 9.1 + - + +
13F PHE* 2.9 27.5 + - + +
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Residues in contact with THR 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E GLN* 3.7 34.4 + - + +
4E MET* 4.2 10.5 - - - +
7E ALA* 4.6 5.8 - - - +
6F HIS 2.3 29.7 + - - -
7F ALA* 3.4 9.7 - - - -
8F MET 3.2 0.4 - - - -
9F GLU* 1.3 78.0 - - - +
11F MET* 1.3 53.0 + - - +
13F PHE* 3.0 28.3 - - + -
14F THR* 2.3 40.5 + - + -
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Residues in contact with MET 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E MET* 3.8 18.6 - - + -
7E ALA* 5.2 3.1 - - + -
8E MET* 6.1 2.0 - - + -
11E MET* 3.6 30.7 - - + +
72E PHE* 5.8 0.2 - - + -
75E ILE* 5.7 0.4 - - - -
79E THR* 5.1 3.4 - - + -
7F ALA 3.3 14.1 - - - +
8F MET* 3.2 12.1 + - - +
10F THR* 1.3 72.0 - - - +
12F MET* 1.3 63.3 + - - +
14F THR* 2.3 23.6 + - - -
15F PHE* 3.0 11.8 + - - +
68F PHE* 4.2 6.1 - - + -
71F PHE* 3.8 23.5 - - + -
72F PHE* 3.4 39.3 - - + -
75F ILE* 4.5 23.8 - - + -
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Residues in contact with MET 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A THR* 3.8 13.9 - - - +
4A VAL* 3.6 27.8 - - + -
7A ILE* 4.4 4.7 - - + -
79E THR* 5.6 3.8 - - + +
82E CYS* 4.9 1.8 - - - -
83E ASN* 4.0 32.1 - - + +
86E PHE* 3.5 49.1 - - + -
8F MET 3.0 12.7 + - - +
9F GLU* 3.2 12.5 + - + +
11F MET* 1.3 78.1 - - - +
13F PHE* 1.3 64.0 + - + +
15F PHE 3.7 2.3 + - - -
16F HIS* 3.0 29.4 - - + -
68F PHE* 3.7 14.1 - - + -
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Residues in contact with PHE 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E GLN* 4.8 17.0 - - + -
86E PHE* 6.1 4.3 - - + -
9F GLU* 2.9 14.0 + - + +
10F THR* 3.0 49.1 - - + -
12F MET* 1.3 76.6 - - + +
14F THR* 1.3 71.8 + - + +
16F HIS* 3.3 6.9 + - - +
17F LYS* 2.9 58.8 + - + +
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Residues in contact with THR 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E GLN* 5.8 0.7 - - + -
4E MET* 3.6 28.1 - - + -
10F THR* 2.3 35.0 + - + +
11F MET* 2.3 25.3 + - - -
13F PHE* 1.3 96.9 - - + +
15F PHE* 1.3 62.7 + - - +
17F LYS* 3.2 15.4 + - + +
18F PHE* 3.4 22.2 + - + +
33F LEU* 5.2 7.5 - - - +
37F GLU* 4.1 14.1 - - + +
71F PHE* 4.3 4.5 - - - -
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Residues in contact with PHE 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F MET 3.0 6.5 + - - -
13F PHE 3.4 0.4 - - - -
14F THR* 1.3 75.8 - - - +
16F HIS* 1.3 76.6 + + - +
18F PHE* 3.8 0.9 + - - +
19F ALA* 3.1 32.3 + - + +
23F GLY 3.3 27.1 - - - -
24F TYR* 4.3 0.7 - - - -
25F LEU* 3.7 23.8 - - + +
33F LEU* 5.5 3.8 - - - -
66F VAL 3.3 27.4 - - - -
67F GLY* 4.0 2.0 - - - -
68F PHE* 3.3 51.8 - + + -
71F PHE* 3.6 41.2 - + + -
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Residues in contact with HIS 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E ASN* 2.9 27.7 + - - -
86E PHE* 4.4 19.7 - + + -
87E VAL* 4.0 20.4 - - + +
91E LYS* 5.6 8.7 - - + +
12F MET* 3.0 25.6 - - + -
13F PHE* 3.3 6.6 + - - +
14F THR 3.2 0.4 - - - -
15F PHE* 1.3 97.8 - + + +
17F LYS* 1.3 66.1 + - - +
19F ALA* 4.3 3.8 - - - -
20F GLY* 3.0 32.2 + - - +
21F ASP* 6.0 0.4 + - - -
23F GLY* 5.1 6.1 + - - -
68F PHE* 4.7 0.4 - + - -
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Residues in contact with LYS 17 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13F PHE* 2.9 45.9 + - + +
14F THR* 3.2 9.4 + - + +
16F HIS* 1.3 77.9 - - - +
18F PHE* 1.3 81.1 + - + +
20F GLY* 4.2 4.2 + - - -
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Residues in contact with PHE 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F THR* 3.4 17.9 + - + +
15F PHE 4.6 0.4 - - - +
16F HIS 3.3 0.2 - - - -
17F LYS* 1.3 97.0 - - + +
19F ALA* 1.3 59.3 + - - +
20F GLY* 3.0 7.2 + - - -
22F LYS* 3.7 4.5 + - - -
25F LEU* 4.3 4.7 - - + -
29F ASP* 2.7 38.5 - - + +
32F VAL* 3.9 38.8 - - + -
33F LEU* 3.7 39.0 - - + -
36F LYS* 4.2 22.0 - - + -
37F GLU* 4.5 11.2 - - - -
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Residues in contact with ALA 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F PHE* 3.1 26.0 + - + +
16F HIS* 4.2 2.7 - - - +
18F PHE* 1.3 75.1 - - - +
20F GLY* 1.3 60.0 + - - +
22F LYS* 3.2 17.7 - - - +
23F GLY* 3.1 36.7 + - - +
24F TYR 3.5 22.5 - - - +
25F LEU* 3.7 13.4 - - + +
29F ASP* 4.6 0.9 - - - -
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Residues in contact with GLY 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F HIS* 3.0 22.1 + - - +
17F LYS 4.8 3.4 - - - -
18F PHE 3.0 5.0 + - - -
19F ALA* 1.3 75.4 - - - +
21F ASP* 1.3 61.2 + - - +
22F LYS* 3.0 20.4 - - - -
23F GLY* 3.0 15.6 + - - -
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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