Contacts of the helix formed by residues 17 - 27 (chain A) in PDB entry 5WT7
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 PHE 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A LYS* 5.1 5.2 - - + -
11A LEU* 3.6 37.9 - - + +
14A ASP* 3.0 40.5 + - + +
16A ARG* 1.3 95.1 - - + +
18A SER* 1.3 63.2 + - - +
19A THR* 3.2 3.6 - - - +
20A PHE* 3.1 22.2 + + + +
21A LEU* 3.2 12.3 + - - +
43A VAL* 3.5 27.8 - - + -
44A PRO 4.6 3.6 - - - -
45A THR* 4.1 13.7 - - + -
129A ILE* 5.9 2.5 - - + -
131A VAL* 3.8 38.8 - - + -
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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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11A LEU 5.1 1.8 - - - -
14A ASP 4.6 1.1 + - - -
15A LYS* 3.0 38.8 + - - +
16A ARG 3.4 0.8 - - - -
17A PHE* 1.3 78.0 - - - +
19A THR* 1.3 65.0 + - - +
21A LEU* 3.1 19.0 + - - +
22A SER* 3.1 12.4 + - - -
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Residues in contact with THR 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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16A ARG 5.0 3.7 + - - -
17A PHE* 3.2 1.7 - - - -
18A SER* 1.3 79.4 - - - +
20A PHE* 1.3 66.1 + - + +
22A SER* 2.9 19.3 + - - -
23A LEU* 3.0 34.8 + - + +
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Residues in contact with PHE 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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11A LEU* 5.0 11.2 - - + -
17A PHE* 3.1 20.6 + + + +
19A THR* 1.3 82.0 - - + +
21A LEU* 1.3 57.0 + - - +
22A SER 3.0 0.2 + - - -
23A LEU* 3.7 15.9 - - + -
24A LEU* 2.6 46.5 + - + +
41A LEU* 4.7 2.2 - - + -
43A VAL* 3.6 27.6 - - + -
44A PRO* 3.6 36.1 - - + -
73A TYR* 3.1 62.4 - + - -
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Residues in contact with LEU 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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8A HIS* 5.0 1.8 - - + +
11A LEU* 3.4 43.7 - - + +
12A LYS* 4.3 23.3 - - + +
17A PHE 3.2 5.3 + - - +
18A SER* 3.1 13.8 + - - +
20A PHE* 1.3 78.7 - - - +
22A SER* 1.3 54.7 + - - +
24A LEU* 3.6 15.5 - - + -
25A GLU* 2.7 48.6 + - + +
30A LYS* 5.4 5.2 - - + -
33A LEU* 5.6 1.3 - - + -
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Residues in contact with SER 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 3.1 9.8 + - - -
19A THR* 2.9 15.4 + - - -
21A LEU* 1.3 79.3 - - - +
23A LEU* 1.3 57.6 + - - -
25A GLU* 3.9 6.2 - - - +
26A ALA* 3.1 26.3 + - - +
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Residues in contact with LEU 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 THR* 3.0 44.2 + - + +
20A PHE* 3.4 14.1 - - + +
22A SER* 1.3 72.8 - - - +
24A LEU* 1.3 71.4 + - - +
26A ALA* 3.3 7.9 + - - +
27A ALA* 3.2 16.8 + - - +
67A LEU* 5.6 5.8 - - + +
70A ILE* 6.5 0.4 - - + -
71A ILE* 3.4 21.6 - - + +
73A TYR* 3.0 37.7 - - + +
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Residues in contact with LEU 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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11A LEU* 4.2 5.4 - - + -
20A PHE* 2.6 39.4 + - + +
21A LEU* 3.6 20.9 - - + +
23A LEU* 1.3 75.3 - - - +
25A GLU* 1.3 66.0 + - + +
27A ALA* 3.4 2.4 + - - +
28A ASP 3.2 4.7 + - - -
29A LEU* 3.0 34.8 + - + +
30A LYS* 3.2 35.2 - - + +
33A LEU* 3.7 22.4 - - + -
71A ILE* 3.8 6.5 - - + -
73A TYR* 2.9 28.9 - - + +
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Residues in contact with GLU 25 (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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21A LEU* 2.7 33.3 + - + +
22A SER* 3.9 4.9 - - - +
24A LEU* 1.3 83.6 - - + +
26A ALA* 1.3 69.4 + - - +
28A ASP* 2.9 18.0 + - - +
30A LYS* 4.1 22.5 + - + +
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Residues in contact with ALA 26 (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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22A SER 3.1 14.8 + - - +
23A LEU* 3.5 12.8 - - - +
25A GLU* 1.3 83.2 + - - +
27A ALA* 1.3 56.9 + - - +
28A ASP* 3.0 16.5 - - - +
64A LYS* 5.4 1.4 + - - -
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Residues in contact with ALA 27 (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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23A LEU 3.2 9.5 + - - +
24A LEU 3.4 4.7 + - - +
25A GLU 3.2 0.2 - - - -
26A ALA* 1.3 74.4 - - - +
28A ASP* 1.3 77.6 + - - +
29A LEU* 3.2 25.4 - - + +
64A LYS* 4.5 18.4 + - - +
67A LEU* 5.5 5.6 - - + +
68A GLN* 4.2 13.4 + - + +
71A ILE* 4.0 16.4 - - + -
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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