Contacts of the helix formed by residues 5 - 20 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3F GLN 4.2 6.3 - - - +
4F LEU* 1.3 92.7 - - - +
6F GLU* 1.3 61.0 + - - +
7F GLU* 3.3 10.2 + - - +
8F GLN* 2.8 50.8 + - + +
9F ILE* 3.1 9.2 + - - +
147F ALA 4.9 7.0 + - - +
13H LYS* 4.3 1.6 - - - +
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Residues in contact with GLU 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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5F THR* 1.3 75.4 - - - +
7F GLU* 1.3 59.3 + - - +
9F ILE* 3.3 6.7 - - + +
10F ALA* 3.2 23.4 + - - +
10H ALA* 4.1 19.3 - - + +
13H LYS* 3.7 34.1 - - + +
14H GLU* 3.0 41.8 + - - +
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Residues in contact with GLU 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516E LYS* 4.3 5.7 - - - +
5F THR* 3.3 8.7 + - - +
6F GLU* 1.3 77.2 - - - +
8F GLN* 1.3 65.4 + - - +
9F ILE 3.0 1.6 - - - -
10F ALA* 3.1 11.2 + - - +
11F GLU* 2.7 62.3 + - - +
147F ALA 5.3 5.2 - - - +
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Residues in contact with GLN 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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520E LYS* 3.9 18.1 + - - +
3F GLN 3.4 11.4 + - - +
4F LEU* 3.7 15.9 - - + -
5F THR* 2.8 47.2 + - - +
7F GLU* 1.3 72.5 - - - +
9F ILE* 1.3 57.4 + - - +
11F GLU* 3.2 11.4 + - - +
12F PHE* 2.8 43.8 + - + -
76F MET* 5.5 6.1 - - - +
145F MET 5.0 1.0 + - - -
146F THR* 4.4 13.1 + - - +
147F ALA 4.1 27.5 - - - +
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Residues in contact with ILE 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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4F LEU* 3.2 19.7 - - + -
5F THR 3.1 19.1 - - - +
6F GLU* 3.3 11.2 - - + +
7F GLU 3.0 0.4 - - - -
8F GLN* 1.3 73.5 - - - +
10F ALA* 1.3 68.4 + - - +
12F PHE* 2.7 21.4 + - - +
13F LYS* 2.7 11.5 + - + +
65F PHE* 4.2 10.7 - - + -
69F LEU* 4.8 3.8 - - + -
9H ILE* 3.7 31.2 - - + +
10H ALA* 6.4 0.2 - - - -
13H LYS* 3.5 24.0 - - + -
65H PHE* 3.4 33.7 - - + -
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Residues in contact with ALA 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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6F GLU 3.2 10.0 + - - +
7F GLU* 3.1 18.5 + - - +
9F ILE* 1.3 79.1 - - - +
11F GLU* 1.3 63.1 + - - +
13F LYS* 3.0 8.8 + - - +
14F GLU* 2.9 30.2 + - - +
6H GLU* 3.3 26.6 - - + +
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Residues in contact with GLU 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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516E LYS* 3.3 33.3 - - + +
517E VAL* 3.8 22.2 - - + +
520E LYS* 2.8 43.2 + - + +
7F GLU* 2.7 59.3 + - - +
8F GLN* 3.4 8.4 - - - +
9F ILE 3.1 0.2 + - - -
10F ALA* 1.3 75.7 - - - +
12F PHE* 1.3 57.7 + - - +
14F GLU* 3.5 5.4 + - - +
15F ALA* 3.0 25.5 + - - +
144F MET 4.8 0.9 - - - +
147F ALA* 4.6 11.3 - - - +
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Residues in contact with PHE 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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520E LYS* 3.8 30.1 - - + -
4F LEU* 4.8 9.2 - - + -
8F GLN* 2.8 39.7 + - + -
9F ILE* 2.7 15.3 + - - +
11F GLU* 1.3 68.8 - - - +
13F LYS* 1.3 59.5 + - - +
15F ALA* 3.2 5.0 - - + +
16F PHE* 2.9 24.3 + - - +
65F PHE* 3.8 2.9 - - + -
68F PHE* 3.3 25.4 - + + -
69F LEU* 3.8 31.6 - - + -
72F MET* 3.9 31.4 - - + -
73F ALA* 5.6 4.3 - - - -
76F MET* 3.6 28.7 - - + -
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Residues in contact with LYS 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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9F ILE* 2.7 11.8 + - + +
10F ALA* 3.0 10.3 + - - +
12F PHE* 1.3 75.8 - - - +
14F GLU* 1.3 64.5 + - - +
16F PHE* 2.9 23.4 + - + +
17F SER* 2.9 32.1 + - - -
20F ASP* 5.9 0.4 + - - -
65F PHE* 3.4 24.2 - - + -
3H GLN* 3.6 16.4 + - - -
4H LEU* 3.6 27.1 - - - -
5H THR* 4.4 0.8 - - - +
6H GLU* 3.7 35.8 + - + +
9H ILE* 3.5 22.7 - - + -
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Residues in contact with GLU 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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512E GLU 5.3 0.7 - - - +
513E ILE* 6.0 2.2 - - + +
514E PRO* 3.9 14.7 - - - +
517E VAL* 3.5 29.6 - - + +
10F ALA* 2.9 17.3 + - - +
11F GLU* 3.7 5.9 - - - +
13F LYS* 1.3 76.7 - - - +
15F ALA* 1.3 63.8 + - - +
17F SER* 2.8 24.6 + - - +
18F LEU* 3.3 8.5 + - - +
6H GLU* 3.3 27.7 - - - +
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Residues in contact with ALA 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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517E VAL* 3.6 13.9 - - - +
520E LYS* 4.3 4.9 - - + -
521E ALA* 4.1 25.5 - - - +
11F GLU 3.0 15.4 + - - +
12F PHE* 3.2 15.3 - - + +
14F GLU* 1.3 76.7 - - - +
16F PHE* 1.3 57.3 + - - +
18F LEU* 2.8 29.1 + - - +
19F PHE* 3.5 8.4 - - - -
68F PHE* 4.0 13.5 - - + -
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Residues in contact with PHE 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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12F PHE 2.9 13.2 + - - +
13F LYS* 2.9 20.8 + - - +
15F ALA* 1.3 70.9 - - - +
17F SER* 1.3 58.8 + - - +
18F LEU 2.6 15.4 + - - -
19F PHE* 2.7 21.5 + - - +
20F ASP* 3.1 17.6 + - + +
25F GLY* 3.3 31.4 - - - -
27F ILE* 3.6 22.8 - - + +
63F ILE 3.5 9.4 - - - -
64F ASP 3.4 9.9 - - - -
65F PHE* 3.1 50.0 - + + -
68F PHE* 3.3 38.3 - + + -
3H GLN* 5.4 1.1 - - - -
4H LEU* 6.0 0.4 - - + -
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Residues in contact with SER 17 (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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13F LYS* 2.9 26.6 + - - -
14F GLU* 2.8 22.1 + - - +
16F PHE* 1.3 76.9 - - - +
18F LEU* 1.3 60.9 + - - +
19F PHE 3.3 0.2 - - - -
20F ASP* 3.1 34.9 - - - +
21F LYS* 3.7 4.3 + - - +
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Residues in contact with LEU 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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513E ILE* 4.7 17.5 - - + -
517E VAL* 4.8 2.0 - - + -
518E LEU* 4.2 27.1 - - + -
521E ALA* 3.6 24.0 - - + -
14F GLU 3.3 4.0 + - - +
15F ALA* 2.8 19.2 + - - +
16F PHE 2.6 5.7 + - - -
17F SER* 1.3 77.7 + - - +
19F PHE* 1.3 60.5 + - + +
21F LYS* 2.9 44.3 + - - +
35F VAL* 4.0 5.3 - - + +
112F LEU* 4.5 16.2 - - + -
114F GLU* 4.0 21.3 - - - +
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Residues in contact with PHE 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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521E ALA* 3.5 33.7 - - + -
524E PHE* 3.2 31.2 - + - -
525E ALA* 4.3 8.3 - - + -
15F ALA 3.5 17.7 - - - -
16F PHE* 2.7 11.5 + - - -
18F LEU* 1.3 74.1 - - + +
20F ASP* 1.3 58.2 + - - +
21F LYS* 3.0 12.5 + - - +
27F ILE* 3.5 34.1 - - + -
31F GLU* 3.1 27.6 - - - +
32F LEU* 3.8 24.2 - - + -
35F VAL* 3.4 42.6 - - + -
36F MET* 5.1 0.4 - - + -
68F PHE* 4.2 4.3 - + - -
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Residues in contact with ASP 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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13F LYS* 5.9 0.3 + - - -
16F PHE* 3.1 25.0 + - + +
17F SER* 3.1 22.2 - - - +
19F PHE* 1.3 74.1 - - - +
21F LYS* 1.3 62.8 + - - +
22F ASP* 3.1 3.7 - - - +
23F GLY* 3.1 23.6 + - - +
24F ASP* 3.0 9.0 - - - +
25F GLY* 3.6 10.8 + - - -
26F THR 2.6 16.3 + - - +
27F ILE* 4.3 3.3 - - + +
31F GLU* 3.8 7.0 - - - -
201F CA 2.5 25.6 - - - -
3H GLN* 4.8 3.1 - - - +
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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
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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