Contacts of the helix formed by residues 57 - 64 (chain E) in PDB entry 5UQ9
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 SER 57 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32E PHE* 3.5 13.9 - - - -
55E ALA* 3.3 5.3 - - - +
56E GLN* 1.3 79.8 - - - +
58E LEU* 1.3 65.2 + - - +
59E LYS* 3.7 11.1 + - - +
60E GLU* 3.3 22.6 + - - +
61E MET* 3.1 21.8 + - - +
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Residues in contact with LEU 58 (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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9E ILE* 3.7 24.2 - - + -
32E PHE* 3.5 29.0 - - + -
57E SER* 1.3 72.0 - - - +
59E LYS* 1.3 60.3 + - - +
61E MET* 3.3 14.7 + - + +
62E VAL* 3.0 34.5 + - - +
84E PHE* 4.1 8.7 - - + -
87E LYS* 3.6 55.2 - - + +
88E LEU* 4.0 8.1 - - + -
91E LEU* 3.7 13.0 - - + -
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Residues in contact with LYS 59 (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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57E SER* 3.3 10.4 + - - +
58E LEU* 1.3 78.2 - - - +
60E GLU* 1.3 62.2 + - - +
62E VAL* 4.0 2.3 - - - +
63E SER* 3.1 24.2 + - - -
91E LEU* 4.0 25.6 - - + +
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Residues in contact with GLU 60 (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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54E GLY 3.6 14.0 - - - +
55E ALA* 3.6 6.3 - - + -
56E GLN* 2.8 41.9 + - - +
57E SER* 3.3 18.1 + - - +
58E LEU 3.2 0.2 - - - -
59E LYS* 1.3 79.3 - - - +
61E MET* 1.3 64.5 + - - +
63E SER* 2.5 23.7 + - - +
64E LYS* 3.2 30.3 + - + +
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Residues in contact with MET 61 (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 ALA* 3.7 20.9 - - + -
8E LEU 5.2 0.2 - - - -
9E ILE* 3.7 30.5 - - + -
30E CYS* 3.6 21.2 - - - +
32E PHE* 3.9 15.3 - - + -
55E ALA* 3.6 14.9 - - + +
57E SER 3.1 17.6 + - - +
58E LEU* 3.3 23.5 + - + +
60E GLU* 1.3 77.0 - - - +
62E VAL* 1.3 70.8 + - + +
64E LYS* 3.3 10.2 + - - +
65E LEU* 3.2 19.5 + - + +
71E ILE* 3.8 26.9 - - + -
88E LEU* 3.9 5.8 - - + -
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Residues in contact with VAL 62 (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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58E LEU 3.0 17.9 + - - +
59E LYS* 4.1 4.3 - - - +
61E MET* 1.3 90.3 - - + +
63E SER* 1.3 62.2 + - - +
64E LYS 3.2 1.2 + - - -
65E LEU* 3.4 12.6 + - - +
69E ARG* 3.3 38.3 + - - +
71E ILE* 4.4 2.2 - - + -
88E LEU* 4.1 7.9 - - + -
91E LEU* 3.2 47.8 - - + +
92E LEU* 4.3 8.5 - - + -
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Residues in contact with SER 63 (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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2E ALA* 4.3 14.7 + - - +
59E LYS* 3.1 15.4 + - - -
60E GLU* 2.5 28.8 + - - +
62E VAL* 1.3 76.3 - - - +
64E LYS* 1.3 63.7 + - - +
65E LEU 3.5 1.4 + - - +
69E ARG* 5.9 0.7 - - - +
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Residues in contact with LYS 64 (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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2E ALA* 3.8 9.9 - - - +
3E GLN* 3.2 27.7 + - - +
4E ALA* 3.0 33.0 + - + +
30E CYS* 4.9 7.0 - - - -
53E VAL* 3.0 32.8 - - + +
54E GLY 4.5 6.2 + - - +
60E GLU* 3.2 33.8 + - + +
61E MET 3.3 5.2 + - - +
62E VAL 3.2 1.0 - - - -
63E SER* 1.3 81.5 - - - +
65E LEU* 1.3 61.1 + - - +
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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