Contacts of the helix formed by residues 7 - 18 (chain E) in PDB entry 5UK7
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 7 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E SER* 1.3 81.3 + - - +
8E GLN* 1.3 64.2 + - - +
9E ASP 3.5 1.3 - - - -
10E PRO* 3.7 4.1 - - + +
11E PHE* 3.2 22.7 + - + +
38F SER* 3.3 51.4 - - - +
39F PHE* 3.6 10.3 - - - +
40F ASP* 3.3 18.9 + - + +
43F VAL* 3.8 16.8 - - + -
45F LEU* 3.7 27.1 - - + +
53F MET* 5.0 2.0 - - + +
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Residues in contact with GLN 8 (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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4E GLY 3.7 16.3 + - - +
5E GLN* 3.3 16.2 + - - +
7E LEU* 1.3 78.6 - - - +
9E ASP* 1.3 61.4 + - - +
11E PHE* 3.4 2.1 + - - +
12E LEU* 2.9 45.7 + - + +
41E GLN 5.4 1.0 + - - -
56E LYS* 3.0 25.3 + - - +
40F ASP* 3.2 11.2 + - - +
42F PHE* 4.7 7.1 - - - +
43F VAL* 3.9 12.3 - - + +
53F MET* 3.8 20.2 - - - -
55F TYR* 2.6 37.0 + - - -
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Residues in contact with ASP 9 (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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2D ALA 4.0 4.5 - - - +
3D LYS* 3.2 27.4 + - - +
5E GLN* 2.7 52.6 + - + +
8E GLN* 1.3 81.3 - - - +
10E PRO* 1.4 64.2 - - + +
13E ASN* 2.8 40.7 + - - +
39E PHE* 3.2 27.6 - - + -
56E LYS* 4.8 0.3 + - - -
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Residues in contact with PRO 10 (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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5E GLN 3.2 5.2 - - - +
6E SER* 3.0 30.5 - - - +
7E LEU* 3.7 5.2 - - + +
9E ASP* 1.4 91.7 - - + +
11E PHE* 1.3 55.5 + - - +
13E ASN* 3.9 6.9 - - + +
14E ALA* 2.9 30.7 + - - +
17E ARG* 5.6 1.2 + - - -
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Residues in contact with PHE 11 (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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7E LEU* 3.2 22.4 + - + +
8E GLN 3.4 4.7 + - - +
9E ASP 3.1 0.4 - - - -
10E PRO* 1.3 79.1 - - - +
12E LEU* 1.3 58.6 + - + +
14E ALA* 3.2 8.6 + - + +
15E LEU* 3.0 53.9 + - + +
62E VAL* 4.0 11.7 - - + -
64E PRO* 3.8 28.5 - - + -
45F LEU* 4.5 28.5 - - + -
51F SER* 5.0 4.5 - - - -
52F GLN 4.5 0.9 - - - -
53F MET* 3.6 45.5 - - + -
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Residues in contact with LEU 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E GLN* 2.9 43.7 + - + +
11E PHE* 1.3 75.9 - - + +
13E ASN* 1.3 57.3 + - - +
15E LEU* 3.1 21.7 + - + +
16E ARG* 2.9 28.1 + - - +
36E ILE* 4.4 14.2 - - + +
39E PHE* 3.6 43.4 - - + -
44E ILE* 3.8 29.6 - - + -
56E LYS* 4.3 1.3 - - - +
62E VAL* 4.7 2.9 - - + -
53F MET* 3.9 19.5 - - + -
55F TYR* 4.4 0.2 - - - +
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Residues in contact with ASN 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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2D ALA 5.0 2.6 + - - +
3D LYS* 5.2 6.3 - - - +
9E ASP* 2.8 29.2 + - - +
10E PRO* 3.9 6.9 - - + +
12E LEU* 1.3 73.7 - - - +
14E ALA* 1.3 61.5 + - - +
16E ARG* 3.0 12.3 + - - +
17E ARG* 2.9 57.9 + - + +
39E PHE* 3.1 23.8 - - - -
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Residues in contact with ALA 14 (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 PRO 2.9 19.4 + - - +
11E PHE* 3.2 9.6 + - + +
13E ASN* 1.3 76.2 - - - +
15E LEU* 1.3 63.6 + - + +
16E ARG 3.3 0.3 + - - -
17E ARG* 4.9 11.6 - - - +
18E GLU* 3.5 31.7 + - + +
20E VAL* 4.7 1.6 - - - +
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Residues in contact with LEU 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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11E PHE* 3.0 47.5 + - + +
12E LEU* 3.1 16.4 + - + +
14E ALA* 1.3 78.3 - - + +
16E ARG* 1.3 59.3 + - - +
19E ARG* 3.6 4.3 + - - -
20E VAL* 3.5 40.6 + - + +
22E VAL* 3.7 29.2 - - + -
36E ILE* 4.1 19.0 + - + +
62E VAL* 3.8 14.1 - - + -
64E PRO* 4.1 19.7 - - + -
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Residues in contact with ARG 16 (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 LEU 2.9 14.3 + - - +
13E ASN* 3.0 19.1 + - - +
15E LEU* 1.3 78.5 - - - +
17E ARG* 1.3 71.4 + - + +
19E ARG* 3.2 34.3 + - - +
36E ILE* 3.3 25.7 - - + +
37E GLU* 2.4 29.4 + - - +
38E SER* 3.9 16.1 + - - +
39E PHE* 4.6 8.1 - - - -
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Residues in contact with ARG 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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10E PRO 5.6 0.8 + - - -
13E ASN* 2.9 38.9 + - + +
14E ALA* 4.5 10.7 - - - +
16E ARG* 1.3 83.3 - - + +
18E GLU* 1.3 74.5 + - + +
19E ARG* 3.0 26.8 + - - +
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Residues in contact with GLU 18 (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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14E ALA* 3.5 20.0 + - + +
16E ARG 3.5 0.2 - - - -
17E ARG* 1.3 93.2 - - + +
19E ARG* 1.3 69.1 + - - +
20E VAL* 3.3 19.1 + - + +
66E ARG* 5.4 8.1 + - - +
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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