Contacts of the helix formed by residues 7 - 20 (chain A) in PDB entry 1HUL
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 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ILE 4.1 0.4 + - - -
6A PRO* 1.3 71.2 - - - +
8A SER* 1.3 60.8 + - - +
10A LEU* 3.5 16.2 + - + +
11A VAL* 3.0 36.4 + - + +
75A ILE* 5.1 8.7 - - + -
78A TYR* 3.8 51.0 - - + +
107B MET* 5.4 0.9 - - + -
112B ILE* 6.5 0.7 - - + -
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Residues in contact with SER 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 PRO* 4.3 11.3 - - - +
7A THR* 1.3 73.7 - - - +
9A ALA* 1.3 64.1 + - - +
11A VAL* 3.5 8.7 + - - +
12A LYS* 3.0 40.7 + - - +
108B ASN* 4.5 1.8 - - - +
112B ILE* 5.7 9.7 - - - +
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Residues in contact with ALA 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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5A ILE* 3.5 23.3 - - + -
6A PRO* 2.7 32.2 + - + +
8A SER* 1.3 72.8 + - - +
10A LEU* 1.3 65.9 + - - +
12A LYS* 2.8 22.1 + - - +
13A GLU* 3.0 10.9 + - - +
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Residues in contact with LEU 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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5A ILE* 3.5 36.8 - - + +
6A PRO 2.9 7.3 + - - +
7A THR* 3.6 25.4 - - + +
9A ALA* 1.3 76.7 - - - +
11A VAL* 1.3 61.1 + - - +
13A GLU* 3.2 9.6 + - - +
14A THR* 3.0 31.2 + - - -
70A LYS* 4.3 9.4 - - - +
71A ASN* 4.1 27.4 - - + +
74A LEU* 4.2 29.2 - - + -
75A ILE* 4.6 10.1 - - + -
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Residues in contact with VAL 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 THR* 3.0 26.3 + - + +
8A SER* 3.9 8.7 - - - +
9A ALA 3.0 0.6 + - - -
10A LEU* 1.3 74.5 - - - +
12A LYS* 1.3 62.4 + - - +
13A GLU 3.4 0.2 + - - -
14A THR* 4.2 1.9 - - - -
15A LEU* 3.4 23.9 + - + +
75A ILE* 3.8 25.4 - - + -
104B LEU* 3.7 33.2 - - + +
107B MET* 4.3 23.1 - - + -
108B ASN* 3.8 22.9 - - + +
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Residues in contact with LYS 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 SER* 3.0 30.7 + - - +
9A ALA* 2.8 12.1 + - - +
11A VAL* 1.3 79.9 - - - +
13A GLU* 1.3 61.1 + - - +
15A LEU* 3.7 9.1 + - - +
16A ALA* 3.6 16.5 + - - +
108B ASN* 3.3 30.8 + - - +
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Residues in contact with GLU 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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5A ILE* 4.9 10.3 - - + +
9A ALA 3.0 9.9 + - - +
10A LEU* 3.2 17.9 + - - +
12A LYS* 1.3 73.8 - - - +
14A THR* 1.4 56.0 + - - +
16A ALA* 2.9 12.9 + - + +
17A LEU* 2.8 46.2 + - + +
67A ARG* 3.9 15.0 + - - +
70A LYS* 4.6 1.0 + - - -
71A ASN* 3.0 27.2 + - - +
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Residues in contact with THR 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 LEU 3.0 11.6 + - - -
11A VAL 4.2 3.4 - - - -
13A GLU* 1.4 74.4 - - - +
15A LEU* 1.3 59.9 + - - +
17A LEU* 3.3 11.7 - - - +
18A LEU* 2.8 29.3 + - + +
68A LEU* 3.7 14.1 - - + -
71A ASN* 2.9 29.2 + - + +
72A LEU* 3.7 29.2 - - + -
75A ILE* 4.1 8.8 - - - +
104B LEU* 3.8 16.8 - - + -
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Residues in contact with LEU 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 VAL* 3.4 22.2 + - + +
12A LYS* 4.0 8.7 - - - +
13A GLU 3.3 1.0 - - - -
14A THR* 1.3 77.9 - - - +
16A ALA* 1.4 61.5 + - - +
18A LEU* 3.2 9.7 + - - +
19A SER* 2.9 27.5 + - - +
101B GLN* 3.6 36.6 - - + +
104B LEU* 3.7 29.6 - - + +
105B GLY* 3.8 8.3 - - - +
108B ASN* 4.4 19.1 - - + +
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Residues in contact with ALA 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 LYS 3.6 9.4 + - - +
13A GLU* 2.9 12.7 + - - +
15A LEU* 1.4 74.3 - - - +
17A LEU* 1.3 66.7 + - + +
19A SER* 3.2 9.0 + - - -
20A THR* 3.0 27.1 + - - -
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Residues in contact with LEU 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 GLU* 2.8 24.9 + - + +
14A THR* 3.3 9.6 - - - +
16A ALA* 1.3 77.6 - - + +
18A LEU* 1.3 61.9 + - - +
20A THR* 3.1 11.5 + - + -
21A HIS* 3.0 39.8 + - + +
64A THR 5.3 1.3 - - - +
67A ARG* 3.9 14.4 - - + -
68A LEU* 3.9 34.3 - - + +
71A ASN* 3.7 26.5 - - - +
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Residues in contact with LEU 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 THR 2.8 20.2 + - - +
15A LEU* 3.2 6.5 + - - +
17A LEU* 1.3 71.3 - - - +
19A SER* 1.3 62.5 + - - +
21A HIS* 3.3 9.5 + - - -
22A ARG* 3.4 19.4 + - + +
25A LEU* 4.7 4.8 - - + +
68A LEU* 3.5 33.8 - - + +
72A LEU* 5.0 3.6 - - + -
97B LEU* 4.7 18.8 - - + +
100B LEU* 4.3 20.4 - - + -
101B GLN* 4.0 33.2 - - + +
104B LEU* 3.6 29.2 - - + -
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Residues in contact with SER 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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15A LEU* 2.9 14.1 + - - +
16A ALA* 3.2 10.2 + - - -
18A LEU* 1.3 75.8 - - - +
20A THR* 1.3 65.0 + - - +
22A ARG* 4.1 15.7 + - - +
101B GLN* 3.6 18.9 + - - -
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Residues in contact with THR 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 ALA 3.0 13.9 + - - -
17A LEU* 3.2 15.3 - - + +
19A SER* 1.3 77.5 - - - +
21A HIS* 1.3 86.3 + - + +
22A ARG 3.4 4.2 + - - -
23A THR* 4.5 6.6 + - - -
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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
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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