Contacts of the helix formed by residues 82 - 89 (chain A) in PDB entry 5E63
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 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A ILE* 3.8 0.6 - - - +
81A GLU* 1.3 75.9 - - - +
83A SER* 1.3 62.6 + - - +
84A GLU* 3.6 9.0 - - - +
85A GLN* 3.2 33.8 - - - +
86A LEU* 2.9 27.0 + - - +
5D T 2.5 42.1 + - - -
6D C 4.4 3.7 + - - -
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Residues in contact with SER 83 (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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41A ALA* 5.5 2.0 - - - -
81A GLU 3.4 4.4 + - - -
82A SER* 1.3 70.6 - - - +
84A GLU* 1.3 67.2 + - - +
86A LEU* 3.7 3.9 - - - +
87A THR* 3.0 29.1 + - - -
114A LEU* 3.9 19.6 - - - +
117A MET* 3.9 33.3 + - - +
4D A 5.1 1.9 + - - -
5D T 3.1 19.9 + - - -
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Residues in contact with GLU 84 (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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82A SER* 3.6 10.7 + - - +
83A SER* 1.3 83.3 + - - +
85A GLN* 1.3 61.6 + - + +
87A THR* 3.2 8.7 + - - +
88A LYS* 2.9 51.7 + - - +
4D A 5.6 0.2 - - - +
5D T 3.8 8.5 + - - +
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Residues in contact with GLN 85 (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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65A LEU* 3.6 30.3 - - + +
66A GLY* 3.4 31.9 - - - +
80A ILE* 4.1 12.3 - - + +
82A SER* 3.2 28.6 + - - +
84A GLU* 1.3 80.4 - - + +
86A LEU* 1.3 54.6 + - - +
88A LYS* 3.5 9.1 - - + +
89A ILE* 2.7 39.6 + - + +
90A ILE* 5.0 0.4 - - - +
6D C 5.0 10.2 + - - -
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Residues in contact with LEU 86 (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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41A ALA* 3.3 43.3 - - + +
43A PHE* 3.7 23.3 - - + -
80A ILE* 3.6 31.3 - - + +
82A SER 2.9 28.3 + - - +
83A SER* 3.7 7.2 - - - +
85A GLN* 1.3 71.6 - - - +
87A THR* 1.3 61.5 + - - +
90A ILE* 3.2 21.0 + - + +
91A LEU* 3.0 30.6 + - - +
110A PHE* 4.0 11.9 - - + -
114A LEU* 4.2 10.5 - - + -
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Residues in contact with THR 87 (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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83A SER 3.0 17.9 + - - -
84A GLU* 3.4 9.2 - - - +
86A LEU* 1.3 76.0 - - - +
88A LYS* 1.3 63.6 + - + +
91A LEU* 4.1 15.3 - - + +
92A PRO* 3.2 17.3 - - - +
114A LEU* 3.8 23.8 + - - +
118A GLY* 5.6 5.1 - - - -
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Residues in contact with LYS 88 (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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84A GLU* 2.9 42.2 + - - +
85A GLN* 3.1 10.0 + - + +
87A THR* 1.3 80.6 - - + +
89A ILE* 1.3 76.7 + - + +
92A PRO* 3.3 17.3 - - - +
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Residues in contact with ILE 89 (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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62A PHE* 3.9 41.7 - - + +
63A GLY* 5.7 1.6 - - - -
65A LEU* 3.4 30.3 - - + -
85A GLN* 2.7 14.8 + - + +
88A LYS* 1.3 97.3 - - + +
90A ILE* 1.3 66.5 + - + +
92A PRO* 3.7 2.6 - - - +
93A PHE* 3.3 22.2 + - - +
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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