Contacts of the helix formed by residues 6 - 23 (chain A) in PDB entry 1HF0
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 LEU 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A GLU* 1.3 64.7 + - - +
8A GLU* 3.9 18.4 - - + +
9A LEU* 3.3 38.3 + - + +
10A GLU* 3.2 23.3 + - - +
57A PHE* 3.6 37.5 - - + -
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Residues in contact with GLU 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 1.3 68.9 - - - +
8A GLU* 1.3 55.3 + - - +
9A LEU 2.5 18.3 + - - -
10A GLU* 3.0 20.4 + - - +
11A GLN* 2.9 34.3 + - + +
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Residues in contact with GLU 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 3.5 17.3 - - + +
7A GLU* 1.3 75.0 - - - +
9A LEU* 1.3 56.6 + - - +
11A GLN* 4.7 4.4 - - - +
12A PHE* 4.4 12.7 + - - +
64A LYS* 4.5 11.3 - - - -
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Residues in contact with LEU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 3.3 20.1 + - + +
7A GLU 2.5 6.5 + - - -
8A GLU* 1.3 75.8 - - - +
10A GLU* 1.3 65.9 + - - +
11A GLN 3.2 0.9 - - - -
12A PHE* 3.4 7.7 + - - +
13A ALA* 3.3 18.2 + - - +
50A PHE* 5.7 1.0 - - + -
53A LEU* 4.6 1.5 - - + +
57A PHE* 3.8 36.1 - - + +
60A MET* 3.8 36.1 - - + +
61A SER* 4.2 13.7 - - - +
64A LYS* 3.8 33.9 - - + -
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Residues in contact with GLU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU 3.2 6.6 + - - +
7A GLU* 3.0 31.1 + - - +
9A LEU* 1.3 75.2 - - - +
11A GLN* 1.3 87.3 + - + +
13A ALA* 3.2 11.6 + - - +
14A LYS* 3.2 11.6 + - - +
53A LEU* 3.4 37.9 - - + +
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Residues in contact with GLN 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A GLU* 2.9 26.3 + - + +
8A GLU* 5.0 3.6 - - - +
10A GLU* 1.3 92.2 + - + +
12A PHE* 1.3 64.8 - - - +
14A LYS* 2.7 39.7 + - - +
15A THR* 3.0 18.3 + - - +
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Residues in contact with PHE 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A GLU 4.4 11.2 + - - +
9A LEU* 3.4 9.9 + - + +
10A GLU 3.3 0.4 - - - -
11A GLN* 1.3 78.0 - - - +
13A ALA* 1.3 59.3 + - - +
15A THR* 4.2 11.9 - - + -
16A PHE* 2.8 49.7 + + + +
19A ARG* 5.4 3.4 - - - -
50A PHE* 4.0 26.7 - + - -
64A LYS* 4.0 34.3 - - + -
67A LEU* 4.3 4.5 - - + -
68A GLU* 3.6 50.5 - - + -
71A LEU* 4.5 12.6 - - + -
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Residues in contact with ALA 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU 3.3 5.7 + - - +
10A GLU 3.2 10.9 + - - +
11A GLN 3.0 1.0 + - - -
12A PHE* 1.3 79.4 - - - +
14A LYS* 1.3 61.9 + - - +
16A PHE* 3.5 3.2 + - - +
17A LYS* 3.3 21.0 + - - +
50A PHE* 3.9 27.1 - - + +
51A GLU* 4.3 16.7 - - - +
53A LEU* 3.6 27.1 - - + -
60A MET* 4.5 4.0 - - + -
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Residues in contact with LYS 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLU 3.2 7.7 + - - +
11A GLN* 2.7 35.7 + - - +
13A ALA* 1.3 72.4 - - - +
15A THR* 1.3 63.3 + - - +
17A LYS* 3.7 6.7 + - - +
18A GLN* 3.1 37.9 + - - +
51A GLU 5.7 0.9 - - - -
111B ASN* 5.8 4.7 - - - +
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Residues in contact with THR 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLN* 3.0 17.1 + - - +
12A PHE* 3.7 15.2 - - + -
14A LYS* 1.3 75.6 - - - +
16A PHE* 1.3 67.3 + - - +
18A GLN* 3.0 27.9 + - - +
19A ARG* 3.1 40.5 + - + +
71A LEU* 5.7 0.7 - - + -
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Residues in contact with PHE 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PHE* 2.8 39.4 + + + +
13A ALA* 3.5 6.5 - - - +
15A THR* 1.3 77.2 - - - +
17A LYS* 1.3 52.1 + - - +
19A ARG* 3.3 2.6 + - - +
20A ARG* 2.7 43.5 + - + +
30A VAL* 4.4 9.6 - - + -
47A ILE* 4.2 11.2 - - + -
50A PHE* 4.8 2.0 - + + -
51A GLU* 3.2 37.2 - - + -
67A LEU* 3.9 35.2 - - + -
70A TRP* 3.7 37.5 - + - -
71A LEU* 3.7 25.1 - - + -
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Residues in contact with LYS 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ALA 3.3 11.3 + - - +
14A LYS* 3.9 7.9 - - - +
15A THR 3.3 0.2 - - - -
16A PHE* 1.3 79.0 - - - +
18A GLN* 1.3 64.1 + - + +
20A ARG* 3.6 7.3 - - - +
21A ILE* 3.0 50.9 + - + +
27A GLN* 5.7 1.3 - - - +
51A GLU* 3.4 44.9 - - + +
108B ILE 5.8 1.9 + - - -
110B THR* 3.9 21.2 + - - +
10M A 6.1 4.0 - - - -
11M A 5.0 10.8 + - - -
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Residues in contact with GLN 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LYS* 3.1 33.8 - - + +
15A THR* 3.0 19.2 + - - +
17A LYS* 1.3 75.9 - - + +
19A ARG* 1.3 63.9 + - + +
21A ILE* 3.2 3.8 + - - +
22A LYS* 2.8 38.8 + - - +
109B GLU* 3.3 30.3 + - + +
111B ASN* 4.2 18.1 + - - +
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Residues in contact with ARG 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PHE* 5.4 3.0 - - - -
15A THR* 3.1 29.8 + - + +
16A PHE 3.8 4.0 - - - +
18A GLN* 1.3 74.2 - - + +
20A ARG* 1.3 69.2 + - - +
22A LYS* 3.0 8.5 + - - +
23A LEU* 2.7 35.0 + - + +
68A GLU* 5.2 5.1 + - - -
71A LEU* 3.2 36.6 - - + +
72A ASN* 4.0 15.3 - - - +
75A GLU* 3.0 31.1 + - - +
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Residues in contact with ARG 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A PHE* 2.7 32.2 + - + +
17A LYS* 3.6 10.0 - - - +
19A ARG* 1.3 75.5 - - - +
21A ILE* 1.3 90.9 + - - +
23A LEU* 3.0 16.3 + - - +
25A PHE* 3.0 41.8 + - + +
27A GLN* 2.9 29.6 - - - +
30A VAL* 3.9 25.4 - - + -
51A GLU* 2.5 49.0 + - - -
70A TRP* 4.7 1.8 - - + -
71A LEU* 4.4 3.3 - - - +
107B SER* 4.1 0.2 + - - -
10M A 2.3 34.8 + - - -
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Residues in contact with ILE 21 (chain A).
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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17A LYS* 3.0 37.6 + - + +
18A GLN 3.5 2.9 - - - +
20A ARG* 1.3 106.8 - - - +
22A LYS* 1.3 63.5 + - - +
24A GLY* 3.0 15.1 + - - -
25A PHE 4.3 6.1 - - - +
107B SER* 4.0 35.7 - - - +
108B ILE 4.2 2.5 - - - +
109B GLU* 3.8 41.1 - - + +
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Residues in contact with LYS 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLN* 2.8 26.0 + - - +
19A ARG* 3.0 7.6 + - - +
21A ILE* 1.3 74.0 - - - +
23A LEU* 1.3 60.0 + - + +
24A GLY* 3.1 4.9 + - - -
109B GLU* 3.1 40.3 + - - +
112B ILE* 5.0 4.3 - - - +
138B LEU 5.6 5.8 - - - -
139B ASN* 5.8 6.7 - - - +
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ARG* 2.7 25.9 + - + +
20A ARG* 3.0 8.7 + - - +
22A LYS* 1.3 73.3 - - + +
24A GLY* 1.3 60.5 + - - +
25A PHE* 3.4 21.5 + - + +
70A TRP* 4.7 2.7 - - + -
71A LEU* 3.8 19.3 - - + -
74A ALA* 4.3 22.2 - - + +
75A GLU* 3.5 37.0 - - + +
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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