Contacts of the helix formed by residues 12 - 25 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9F HIS 5.4 2.0 - - - -
10F MET 3.3 4.2 + - - -
11F ILE* 1.3 77.1 - - - +
13F SER* 1.3 66.0 + - - -
14F GLY 3.2 3.1 - - - -
15F HIS* 3.2 33.7 + - - +
16F LEU* 3.4 7.8 + - - +
125F LYS* 4.4 2.9 - - - -
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Residues in contact with SER 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F ILE 4.1 0.2 + - - -
12F GLY* 1.3 68.6 - - - -
14F GLY* 1.3 55.6 + - - +
16F LEU* 3.0 15.2 + - - +
17F GLN* 2.7 55.3 + - - +
125F LYS* 4.2 15.7 + - - +
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Residues in contact with GLY 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F GLY* 3.2 1.4 - - - -
13F SER* 1.3 79.1 - - - +
15F HIS* 1.3 56.9 + - - +
17F GLN* 3.4 12.4 + - - +
18F SER* 3.0 29.8 + - - -
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Residues in contact with HIS 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F MET 4.0 15.9 - - - -
11F ILE* 4.5 5.6 - - + -
12F GLY* 3.2 27.6 + - - +
13F SER 3.1 0.2 - - - -
14F GLY* 1.3 78.9 - - - +
16F LEU* 1.3 62.5 + - + +
18F SER* 2.7 22.9 + - - -
19F LEU* 3.2 14.0 + - - +
79F GLN* 4.3 22.7 + - + +
80F LEU* 3.7 20.7 - - + +
83F LEU* 3.9 31.3 - - + +
86F ARG* 5.7 3.0 + - - -
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Residues in contact with LEU 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F ILE* 3.9 14.1 - - + -
12F GLY 3.4 10.1 + - - +
13F SER* 3.0 11.1 + - - +
15F HIS* 1.3 76.6 - - + +
17F GLN* 1.3 63.8 + - + +
19F LEU* 3.3 11.7 - - + +
20F GLN* 3.2 18.7 + - - +
118F LYS* 4.8 4.5 - - - +
121F PHE* 3.8 35.4 - - + -
122F ASN* 3.5 36.0 + - - +
125F LYS* 3.5 29.4 - - + +
126F ASN* 5.9 0.2 - - - +
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Residues in contact with GLN 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F SER* 2.7 38.0 + - - +
14F GLY* 3.8 9.3 - - - +
16F LEU* 1.3 71.4 - - + +
18F SER* 1.3 60.1 + - - +
19F LEU 3.0 1.3 - - - -
20F GLN* 2.8 11.9 + - - +
21F ARG* 2.8 30.1 + - - +
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Residues in contact with SER 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F GLY 3.0 14.7 + - - -
15F HIS* 2.7 25.5 + - - -
17F GLN* 1.3 75.9 - - - +
19F LEU* 1.3 55.4 + - - +
21F ARG* 4.0 10.7 - - - +
22F LEU* 3.0 31.0 + - - +
73F ASN* 4.9 0.5 - - - +
76F ALA* 4.1 25.5 + - - +
79F GLN* 5.4 4.6 + - - -
80F LEU* 4.6 7.3 - - - +
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Residues in contact with LEU 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F HIS 3.2 18.6 + - - +
16F LEU* 3.3 17.0 - - + +
17F GLN 3.0 0.2 - - - -
18F SER* 1.3 77.6 + - - +
20F GLN* 1.3 58.7 + - - +
22F LEU* 3.3 10.9 + - + +
23F ILE* 2.9 35.2 + - + +
65F MET* 5.1 9.6 - - + -
80F LEU* 3.8 24.9 - - + -
114F LEU* 5.1 3.1 - - + +
117F VAL* 4.3 21.5 - - + -
118F LYS* 4.1 25.1 - - + +
121F PHE* 3.6 36.6 - - + -
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Residues in contact with GLN 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E ARG* 3.7 15.7 - - - +
16F LEU 3.2 9.0 + - - +
17F GLN* 2.8 12.5 + - - +
19F LEU* 1.3 76.5 - - - +
21F ARG* 1.3 55.0 + - - +
23F ILE* 2.9 16.1 + - - +
24F ASP* 2.7 69.7 + - - +
115F GLU* 4.9 2.4 + - - -
118F LYS* 2.6 36.9 + - - +
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Residues in contact with ARG 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E PRO* 5.9 10.8 - - + +
17F GLN 2.8 17.9 + - - +
18F SER* 4.0 9.0 - - - +
20F GLN* 1.3 73.1 - - - +
22F LEU* 1.3 57.8 + - - +
24F ASP* 3.9 10.4 + - - +
25F SER* 3.0 31.3 + - - +
72F PRO* 3.1 40.9 + - - +
73F ASN* 5.0 6.8 + - - +
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Residues in contact with LEU 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F SER 3.0 18.1 + - - +
19F LEU* 3.4 12.6 - - + +
20F GLN 3.1 0.2 - - - -
21F ARG* 1.3 78.1 - - - +
23F ILE* 1.3 58.5 + - + +
25F SER* 3.1 11.4 + - - -
26F GLN* 3.3 14.9 + - - +
65F MET* 4.5 3.4 - - + -
67F PHE* 3.6 29.4 - - + -
73F ASN* 3.5 34.3 - - - +
76F ALA* 4.1 9.2 - - + -
77F ILE* 3.6 28.0 - - + -
80F LEU* 5.8 0.7 - - + -
114F LEU* 3.6 28.5 - - + -
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Residues in contact with ILE 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F LEU* 2.9 16.7 + - + +
20F GLN* 2.9 18.5 + - - +
22F LEU* 1.3 76.9 - - + +
24F ASP* 1.3 67.3 + - - +
25F SER 3.1 2.3 + - - -
26F GLN* 3.3 17.2 + - - +
111F LEU* 3.8 19.6 - - + +
114F LEU* 3.6 45.5 - - + +
115F GLU* 4.2 15.5 - - + +
118F LYS* 3.7 39.7 - - + +
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Residues in contact with ASP 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E PHE* 4.5 5.0 - - - -
68E ARG* 3.4 40.4 + - - +
71E THR* 3.7 35.4 + - + +
72E PRO* 5.8 2.0 - - + -
73E ASN* 4.9 0.2 + - - -
20F GLN* 2.7 55.4 + - - +
21F ARG* 3.9 9.1 + - + +
23F ILE* 1.3 75.4 - - - +
25F SER* 1.3 58.1 + - - +
26F GLN 3.3 6.4 + - - +
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Residues in contact with SER 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E SER* 3.7 13.5 + - - -
26E GLN* 2.7 30.5 + - - -
67E PHE* 4.3 0.2 - - - -
71E THR* 5.9 0.4 - - - -
72E PRO* 6.5 1.3 - - - -
73E ASN* 2.8 26.8 + - - +
21F ARG* 3.0 20.3 + - - -
22F LEU 3.1 11.8 + - - -
24F ASP* 1.3 77.1 - - - +
26F GLN* 1.3 54.1 + - - +
73F ASN* 3.2 18.9 + - - -
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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