Contacts of the helix formed by residues 6 - 24 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B GLU* 1.3 59.7 + - - +
8B GLU* 3.4 22.0 - - + +
9B LEU* 3.3 49.3 + - + +
10B GLU* 2.7 33.3 + - - +
57B PHE* 5.3 16.1 - - + -
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Residues in contact with GLU 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LEU* 1.3 72.3 - - - +
8B GLU* 1.3 65.2 + - - +
9B LEU 2.8 6.7 + - - -
10B GLU* 3.1 13.2 + - - +
11B GLN* 3.2 36.0 + - + +
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Residues in contact with GLU 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LEU* 3.4 25.9 - - + +
7B GLU* 1.3 78.5 - - - +
9B LEU* 1.3 60.9 + - + +
11B GLN* 4.3 9.9 - - - +
12B PHE* 4.8 2.8 + - - +
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Residues in contact with LEU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LEU* 3.3 28.0 - - + +
7B GLU 2.8 2.2 + - - -
8B GLU* 1.3 80.1 - - - +
10B GLU* 1.3 55.9 + - + +
11B GLN 2.9 1.8 - - - -
12B PHE* 2.7 38.9 + - + +
13B ALA* 3.4 3.1 + - - +
53B LEU* 5.1 3.1 - - + -
57B PHE* 4.8 9.9 - - + +
60B MET* 4.1 24.8 - - + +
61B SER* 3.8 35.0 - - - +
64B LYS* 4.6 19.7 - - + -
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Residues in contact with GLU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LEU 2.7 25.5 - - - +
7B GLU* 3.1 17.2 + - - +
9B LEU* 1.3 74.3 - - + +
11B GLN* 1.3 64.5 + - - +
13B ALA* 2.6 31.9 + - - -
14B LYS* 2.8 19.5 + - + +
53B LEU* 3.5 29.1 - - + +
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Residues in contact with GLN 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLU* 3.2 25.1 + - + +
8B GLU* 4.3 8.5 - - - +
9B LEU 2.8 0.8 + - - -
10B GLU* 1.3 87.0 + - - +
12B PHE* 1.3 52.4 + - - +
14B LYS* 4.9 9.5 - - - +
15B THR* 2.3 30.4 + - - +
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Residues in contact with PHE 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLU 4.8 2.4 + - - +
9B LEU* 2.7 16.7 + - + +
11B GLN* 1.3 74.7 - - - +
13B ALA* 1.3 63.8 + - - +
15B THR* 3.7 7.6 - - + -
16B PHE* 2.8 46.4 + + + +
19B ARG* 4.7 9.4 - - - -
50B PHE* 3.9 18.2 - + + -
60B MET* 6.5 0.2 - - + -
64B LYS* 3.8 25.1 - - + -
67B LEU* 4.2 4.9 - - + -
68B GLU* 3.2 59.2 - - + -
71B LEU* 4.3 20.0 - - + -
72B ASN* 5.5 0.2 - - - -
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Residues in contact with ALA 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU 3.4 1.5 + - - +
10B GLU* 2.6 11.7 + - - +
12B PHE* 1.3 83.9 - - - +
14B LYS* 1.3 65.0 + - - +
15B THR 2.9 0.5 + - - -
16B PHE* 3.1 8.5 + - - +
17B LYS* 3.2 12.5 + - - +
50B PHE* 4.1 20.3 - - + +
51B GLU* 4.1 15.7 - - - +
53B LEU* 3.4 38.6 - - + -
60B MET* 5.2 0.6 - - + +
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Residues in contact with LYS 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLU* 2.8 15.6 + - + +
11B GLN* 5.4 9.4 - - - +
13B ALA* 1.3 74.5 - - + +
15B THR* 1.3 60.3 + - - +
17B LYS* 4.0 11.5 - - + +
18B GLN* 3.2 32.0 + - + +
51B GLU 4.8 2.9 + - - -
53B LEU* 6.5 0.4 - - + -
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Residues in contact with THR 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLN* 2.3 31.1 + - - -
12B PHE* 3.7 10.9 - - + -
13B ALA 3.0 0.8 - - - -
14B LYS* 1.3 76.9 - - - +
16B PHE* 1.3 58.1 + - - +
18B GLN* 2.8 37.6 + - - +
19B ARG* 3.0 45.2 + - + +
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Residues in contact with PHE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B PHE* 2.8 42.3 + + + +
13B ALA* 3.5 4.5 - - - +
15B THR* 1.3 74.4 - - - +
17B LYS* 1.3 51.7 + - - +
19B ARG* 3.4 1.3 + - - +
20B ARG* 2.7 45.0 + - + +
30B VAL* 4.2 8.3 - - + -
47B ILE* 4.4 7.9 - - + -
50B PHE* 4.7 1.6 - + + -
51B GLU* 3.1 35.4 - - + -
67B LEU* 3.3 43.3 - - + -
70B TRP* 3.5 31.0 - + - -
71B LEU* 3.5 29.6 - - + -
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Residues in contact with LYS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A GLU* 5.1 7.2 - - - +
13B ALA 3.2 7.1 + - - +
14B LYS* 4.0 16.4 - - + +
15B THR 3.1 0.6 + - - -
16B PHE* 1.3 77.4 - - - +
18B GLN* 1.3 71.4 + - + +
20B ARG* 2.9 8.7 + - - +
21B ILE* 2.8 42.8 + - + +
27B GLN* 5.5 1.1 - - - +
51B GLU* 3.3 46.9 + - + +
52B ALA* 6.2 1.0 - - - +
11N C 5.8 3.4 - - - -
12N T 4.1 17.9 + - - -
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Residues in contact with GLN 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A GLU* 6.0 8.3 - - + +
14B LYS* 3.2 27.5 - - + +
15B THR* 2.8 14.7 + - - +
17B LYS* 1.3 83.1 - - + +
19B ARG* 1.3 68.1 + - + +
20B ARG 2.7 0.2 + - - -
21B ILE* 2.8 16.4 + - - +
22B LYS* 2.9 41.5 + - - +
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Residues in contact with ARG 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B PHE* 4.7 9.9 - - - -
15B THR* 3.0 30.4 + - + +
16B PHE 3.7 5.4 - - - +
18B GLN* 1.3 79.0 - - + +
20B ARG* 1.3 57.3 + - - +
22B LYS* 3.7 10.8 - - + +
23B LEU* 2.9 32.8 + - - +
71B LEU* 3.3 35.2 - - + +
72B ASN* 3.4 18.2 - - - +
75B GLU* 2.9 35.1 + - + +
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Residues in contact with ARG 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B PHE* 2.7 29.7 + - + +
17B LYS* 3.0 12.9 - - - +
18B GLN 2.7 2.6 + - - -
19B ARG* 1.3 70.6 - - - +
21B ILE* 1.3 86.9 + - - +
23B LEU* 3.0 17.0 + - - +
24B GLY 3.2 8.1 + - - -
25B PHE* 3.1 38.1 + - + +
26B THR 4.2 1.6 - - - -
27B GLN* 2.7 41.2 - - - +
30B VAL* 4.2 12.8 - - + -
47B ILE* 4.5 0.6 - - - +
51B GLU* 2.7 39.9 + - - +
70B TRP* 4.9 6.7 - - + -
71B LEU* 4.8 2.4 - - - +
11N C 2.7 32.2 + - - -
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Residues in contact with ILE 21 (chain B).
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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107A SER* 4.5 31.4 - - - +
109A GLU* 3.2 39.3 - - + +
17B LYS* 2.8 36.0 + - + +
18B GLN* 2.8 7.7 + - - +
20B ARG* 1.3 97.9 - - - +
22B LYS* 1.3 65.7 + - + +
24B GLY* 3.0 13.3 + - - -
25B PHE 4.3 7.6 + - - +
11N C 5.2 0.7 - - - +
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Residues in contact with LYS 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A GLU* 5.9 5.1 - - - +
18B GLN* 2.9 53.5 + - + +
19B ARG* 3.7 8.3 - - + +
21B ILE* 1.3 73.9 - - + +
23B LEU* 1.3 55.2 + - - +
24B GLY* 2.6 17.9 + - - -
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ARG 2.9 17.0 + - - +
20B ARG* 3.0 6.7 + - - +
22B LYS* 1.3 73.8 - - - +
24B GLY* 1.3 57.1 + - - +
25B PHE* 3.4 29.6 - - + -
70B TRP* 4.6 8.1 - - + -
71B LEU* 4.5 15.5 - - + -
74B ALA* 3.8 39.7 - - + +
75B GLU* 4.2 9.9 - - + +
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Residues in contact with GLY 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A LYS* 5.4 3.5 + - - -
21B ILE 3.0 9.9 + - - -
22B LYS 2.6 12.9 + - - -
23B LEU* 1.3 75.4 - - - +
25B PHE* 1.3 66.4 + - - +
26B THR* 5.5 0.5 - - - +
29B ASP* 4.4 5.2 - - - +
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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