Contacts of the helix formed by residues 12 - 25 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9E HIS 5.4 2.7 - - - -
10E MET 3.3 8.7 + - - -
11E ILE* 1.3 76.3 - - - +
13E SER* 1.3 65.4 + - - +
14E GLY 3.2 3.9 + - - -
15E HIS* 3.3 21.9 + - - +
16E LEU* 3.8 11.8 + - - +
125E LYS* 4.1 5.8 - - - -
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Residues in contact with SER 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E GLY* 1.3 71.5 - - - -
14E GLY* 1.3 66.1 + - - +
16E LEU* 3.1 10.6 + - - +
17E GLN* 2.9 44.9 + - - +
125E LYS* 4.2 14.2 + - - +
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Residues in contact with GLY 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E GLY* 3.2 1.8 - - - -
13E SER* 1.3 78.5 - - - +
15E HIS* 1.3 61.8 - - - +
17E GLN* 3.4 12.6 + - - +
18E SER* 3.2 24.8 + - - -
21E ARG* 5.1 0.7 + - - -
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Residues in contact with HIS 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E MET 3.6 19.2 + - - -
11E ILE* 4.1 6.8 - - + -
12E GLY* 3.3 26.1 + - - +
13E SER 3.2 0.6 - - - -
14E GLY* 1.3 76.1 - - - +
16E LEU* 1.3 60.8 + - + +
18E SER* 2.9 20.4 + - - -
19E LEU* 3.3 11.1 + - - +
79E GLN* 4.8 17.2 + - + +
80E LEU* 4.2 18.0 - - + +
83E LEU* 3.8 39.1 - - + +
86E ARG* 4.6 12.3 + - - -
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Residues in contact with LEU 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E ILE* 4.0 11.9 - - + -
12E GLY 3.9 10.3 - - - +
13E SER* 3.1 8.9 + - - +
15E HIS* 1.3 75.9 - - + +
17E GLN* 1.3 61.8 + - + +
19E LEU* 3.0 12.0 + - + +
20E GLN* 2.9 28.7 + - - +
80E LEU* 6.4 0.7 - - + -
118E LYS* 5.2 1.9 - - + +
121E PHE* 4.0 35.4 - - + +
122E ASN* 3.7 24.5 - - + +
125E LYS* 3.7 26.9 - - + +
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Residues in contact with GLN 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E SER* 2.9 40.6 + - - +
14E GLY* 3.7 9.4 - - - +
16E LEU* 1.3 77.5 - - + +
18E SER* 1.3 57.8 + - - +
20E GLN* 3.1 8.7 + - - +
21E ARG* 2.8 48.4 + - - +
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Residues in contact with SER 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E GLY 3.2 10.7 + - - -
15E HIS* 2.9 24.3 + - - -
17E GLN* 1.3 79.2 - - - +
19E LEU* 1.3 56.5 + - - +
21E ARG* 3.4 27.4 + - - +
22E LEU* 3.1 25.1 + - - +
73E ASN* 5.3 0.2 - - - +
76E ALA* 4.5 23.9 + - - +
79E GLN* 4.9 10.5 + - - -
80E LEU* 5.3 4.2 - - - +
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Residues in contact with LEU 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E HIS 3.3 9.1 + - - +
16E LEU* 3.0 15.6 + - + +
18E SER* 1.3 79.8 + - - +
20E GLN* 1.3 59.1 + - - +
21E ARG 3.2 0.2 - - - -
22E LEU* 3.1 23.1 + - + +
23E ILE* 2.9 36.2 + - + +
65E MET* 5.1 5.8 - - + -
80E LEU* 3.9 24.7 - - + -
114E LEU* 5.3 4.0 - - + +
117E VAL* 4.5 8.7 - - + -
118E LYS* 3.7 38.8 - - + +
121E PHE* 4.1 27.4 - - + -
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Residues in contact with GLN 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E LEU 2.9 11.8 + - - +
17E GLN* 3.6 9.4 - - - +
19E LEU* 1.3 76.0 - - - +
21E ARG* 1.3 58.2 + - - +
23E ILE* 3.2 19.5 + - - +
24E ASP* 2.8 67.5 + - - +
115E GLU* 5.1 2.4 + - - -
118E LYS* 2.6 42.9 + - - +
68F ARG* 5.2 4.0 - - - +
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Residues in contact with ARG 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E GLY 5.1 0.8 + - - -
17E GLN* 2.8 43.4 + - - +
18E SER* 3.4 29.8 + - - +
20E GLN* 1.3 76.6 - - - +
22E LEU* 1.3 60.5 - - - +
24E ASP* 4.0 9.0 - - + +
25E SER* 3.4 22.3 + - - -
73E ASN* 4.8 1.2 - - - +
72F PRO* 5.9 10.1 - - + -
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Residues in contact with LEU 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E SER 3.1 14.5 + - - +
19E LEU* 3.2 18.4 - - + +
21E ARG* 1.3 75.4 - - - +
23E ILE* 1.3 64.6 + - + +
25E SER* 2.7 18.7 + - - -
26E GLN* 3.4 8.3 + - - +
65E MET* 4.5 0.9 - - + -
67E PHE* 3.9 17.7 - - + -
73E ASN* 3.6 32.3 - - - +
76E ALA* 4.5 7.4 - - + -
77E ILE* 3.3 37.2 - - + -
80E LEU* 5.7 0.4 - - + -
114E LEU* 3.6 35.0 - - + -
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Residues in contact with ILE 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E LEU* 2.9 23.9 + - + +
20E GLN* 3.6 21.1 - - - +
22E LEU* 1.3 80.7 - - + +
24E ASP* 1.3 62.5 + - - +
26E GLN* 3.0 25.3 + - - +
111E LEU* 4.0 12.9 - - + +
114E LEU* 3.9 25.4 - - + +
115E GLU* 3.6 23.3 - - + +
118E LYS* 3.7 41.3 - - + -
68F ARG* 4.0 16.4 + - - +
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Residues in contact with ASP 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E GLN* 2.8 55.5 + - - +
21E ARG* 4.0 9.1 - - + +
22E LEU 3.4 0.2 - - - -
23E ILE* 1.3 77.0 - - - +
25E SER* 1.3 59.5 + - - +
26E GLN 3.4 6.1 + - - +
67F PHE* 4.7 1.7 - - - -
68F ARG* 3.4 36.7 + - - +
71F THR* 3.7 37.7 + - + +
72F PRO* 6.0 1.1 - - + -
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Residues in contact with SER 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ARG 3.4 11.4 + - - -
22E LEU 2.7 22.5 + - - -
24E ASP* 1.3 77.7 - - - +
26E GLN* 1.3 70.6 + - - +
73E ASN* 3.4 11.6 + - - -
25F SER* 4.1 11.4 - - - -
26F GLN* 2.9 13.5 + - - -
67F PHE* 3.4 3.5 - - - -
71F THR* 5.4 1.3 - - - -
72F PRO* 6.5 0.2 - - - -
73F ASN* 2.8 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