Contacts of the helix formed by residues 12 - 25 (chain A) in PDB entry 3UF2
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 GLY 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A HIS* 5.6 2.0 - - - -
10A MET 3.5 4.0 + - - -
11A ILE* 1.3 77.9 - - - +
13A SER* 1.3 65.7 + - - -
14A GLY 3.1 4.3 - - - -
15A HIS* 3.0 32.5 + - - +
16A LEU* 3.7 3.6 + - - +
125A LYS* 4.3 4.9 - - - -
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Residues in contact with SER 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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12A GLY* 1.3 71.4 - - - -
14A GLY* 1.3 62.3 + - - +
15A HIS 3.1 0.2 + - - -
16A LEU* 3.2 12.2 + - - +
17A GLN* 2.9 47.6 + - - +
125A LYS* 4.2 13.7 + - - +
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Residues in contact with GLY 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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12A GLY* 3.1 2.4 - - - -
13A SER* 1.3 79.5 - - - +
15A HIS* 1.3 57.7 + - - +
17A GLN* 3.9 10.2 + - - +
18A SER* 3.1 28.2 + - - -
21A ARG* 5.3 1.2 + - - -
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Residues in contact with HIS 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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10A MET 3.8 20.0 - - - -
11A ILE* 4.0 8.5 - - + -
12A GLY* 3.0 29.7 + - - +
14A GLY* 1.3 77.5 + - - +
16A LEU* 1.3 68.5 + - + +
18A SER* 2.7 23.1 + - - -
19A LEU* 3.0 14.8 + - + +
79A GLN* 4.6 13.9 + - + +
80A LEU* 3.9 18.7 - - + +
83A LEU* 3.7 36.3 - - + +
86A ARG* 4.8 7.9 + - - -
121A PHE* 5.9 0.4 - - + -
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Residues in contact with LEU 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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11A ILE* 4.2 8.5 - - + -
12A GLY 4.1 8.7 - - - +
13A SER* 3.2 9.6 + - - +
15A HIS* 1.3 76.9 - - - +
17A GLN* 1.3 59.0 + - + +
19A LEU* 3.3 9.3 + - + +
20A GLN* 3.0 23.0 + - - +
118A LYS* 3.3 26.5 + - - +
121A PHE* 3.9 37.5 - - + +
122A ASN* 3.7 29.8 - - + +
125A LYS* 3.8 24.9 - - + -
126A ASN* 5.9 0.4 - - - +
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Residues in contact with GLN 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 SER* 2.9 36.8 + - - +
14A GLY* 4.0 8.1 + - - +
16A LEU* 1.3 76.7 - - + +
18A SER* 1.3 61.1 + - - +
20A GLN* 4.0 6.6 - - - +
21A ARG* 3.2 40.7 + - - +
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Residues in contact with SER 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 GLY 3.1 15.8 + - - -
15A HIS* 2.7 22.7 + - - -
17A GLN* 1.3 75.8 - - - +
19A LEU* 1.3 59.3 + - - +
21A ARG* 3.4 23.3 + - - +
22A LEU* 2.9 29.9 + - - +
76A ALA* 4.4 22.7 + - - +
79A GLN* 5.2 6.4 + - - -
80A LEU* 4.5 10.3 - - - +
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Residues in contact with LEU 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 HIS 3.0 15.3 + - - +
16A LEU* 3.4 14.8 - - - +
18A SER* 1.3 76.0 + - - +
20A GLN* 1.3 59.9 + - - +
22A LEU* 3.1 14.1 + - + +
23A ILE* 2.8 35.8 + - + +
65A MET* 4.8 10.8 - - + -
80A LEU* 3.8 31.6 - - + -
114A LEU* 4.9 6.5 - - + +
117A VAL* 4.2 18.2 - - + -
118A LYS* 4.1 25.6 - - + +
121A PHE* 4.0 32.1 - - + -
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Residues in contact with GLN 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 LEU 3.0 15.6 + - - +
17A GLN* 4.1 7.4 - - - +
19A LEU* 1.3 75.0 - - - +
21A ARG* 1.3 57.9 + - - +
23A ILE* 3.0 22.1 + - - +
24A ASP* 2.8 65.4 + - - +
115A GLU* 4.4 7.4 + - - +
118A LYS* 3.4 30.7 - - - +
68B ARG* 4.3 6.7 - - - +
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Residues in contact with ARG 21 (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 GLY 5.3 1.4 + - - -
17A GLN* 3.2 35.8 + - - +
18A SER* 3.4 27.3 + - - +
19A LEU 3.2 0.2 - - - -
20A GLN* 1.3 79.1 - - - +
22A LEU* 1.3 62.6 + - - +
24A ASP* 3.4 9.5 + - - +
25A SER* 3.2 25.5 + - - -
72A PRO* 6.4 1.6 - - - -
73A ASN* 4.9 2.7 - - - +
76A ALA* 5.9 1.2 - - - +
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Residues in contact with LEU 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 SER 2.9 17.3 + - - +
19A LEU* 3.1 15.2 + - + +
21A ARG* 1.3 75.4 - - - +
23A ILE* 1.3 59.5 + - + +
25A SER* 2.9 14.8 + - - -
26A GLN* 3.3 18.7 + - - +
65A MET* 4.6 2.2 - - + -
67A PHE* 3.7 23.6 - - + -
73A ASN* 3.7 28.5 + - - +
76A ALA* 4.3 10.1 - - + -
77A ILE* 3.5 34.1 - - + -
80A LEU* 5.2 1.3 - - + -
114A LEU* 3.7 34.3 - - + -
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Residues in contact with ILE 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 LEU* 2.8 20.7 + - + +
20A GLN* 3.0 20.6 + - - +
22A LEU* 1.3 76.1 - - + +
24A ASP* 1.3 65.8 + - - +
25A SER 3.1 1.8 - - - -
26A GLN 3.2 11.3 + - - +
111A LEU* 3.3 30.4 - - + +
114A LEU* 3.6 48.2 - - + +
115A GLU* 4.2 27.8 - - - +
118A LYS* 4.2 17.0 - - + -
68B ARG* 4.2 10.6 + - - +
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Residues in contact with ASP 24 (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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20A GLN* 2.8 51.7 + - - +
21A ARG* 3.4 8.8 + - + +
23A ILE* 1.3 70.8 - - - +
25A SER* 1.3 61.2 + - - +
26A GLN 3.3 5.5 + - - +
67B PHE* 4.9 1.4 - - - +
68B ARG* 2.6 48.4 + - - +
71B THR* 4.0 32.3 + - + +
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Residues in contact with SER 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ARG* 3.2 13.4 + - - -
22A LEU* 2.9 19.6 + - - -
24A ASP* 1.3 75.9 - - - +
26A GLN* 1.3 70.7 + - - +
73A ASN* 3.5 17.6 + - - -
25B SER* 4.5 5.6 - - - -
26B GLN* 2.8 22.8 + - - -
67B PHE* 3.7 2.7 - - - -
71B THR* 5.6 2.2 - - - -
72B PRO* 6.5 1.6 - - - -
73B ASN* 2.9 23.8 + - - +
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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