Contacts of the helix formed by residues 55 - 65 (chain I) in PDB entry 3KL8
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 GLN 55 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56I LYS* 1.3 66.3 + - + +
57I LEU* 3.3 8.7 - - - +
58I GLU* 3.5 32.6 - - + +
59I ARG* 3.8 7.3 + - - +
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Residues in contact with LYS 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55I GLN* 1.3 82.6 - - + +
57I LEU* 1.3 67.0 - - + +
59I ARG* 3.8 13.0 + - - +
60I GLU* 3.3 25.5 + - - +
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Residues in contact with LEU 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44I ILE* 4.0 38.6 - - + -
55I GLN 4.1 3.8 - - - +
56I LYS* 1.3 86.5 - - + +
58I GLU* 1.3 65.8 + - - +
60I GLU* 3.8 22.2 - - - +
61I ALA* 2.8 29.0 + - + +
87I LEU* 6.3 3.6 - - + -
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Residues in contact with GLU 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165G ASP* 5.4 3.6 - - - +
55I GLN* 3.5 33.1 - - + +
57I LEU* 1.3 80.1 - - - +
59I ARG* 1.3 70.1 + - - +
61I ALA* 3.8 2.7 - - - +
62I ARG* 3.1 23.8 + - - +
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Residues in contact with ARG 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55I GLN 3.8 6.8 + - - +
56I LYS* 3.8 14.8 + - - +
57I LEU 3.4 0.4 - - - -
58I GLU* 1.3 83.1 - - - +
60I GLU* 1.3 76.6 + - - +
62I ARG* 3.1 48.1 + - - +
63I ILE* 3.2 34.9 - - + +
157I PHE 4.5 0.6 + - - -
158I GLY 3.3 24.5 + - - -
160I ALA 2.9 24.3 + - - -
161I ILE* 4.5 4.7 - - - +
162I GLU* 4.5 6.2 - - - +
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Residues in contact with GLU 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42I LYS* 5.4 5.9 + - - -
56I LYS 3.3 14.7 + - - +
57I LEU* 3.9 24.3 - - - +
58I GLU 3.4 0.2 - - - -
59I ARG* 1.3 91.9 - - - +
61I ALA* 1.3 65.1 + - - +
63I ILE* 3.2 24.6 + - - +
64I CYS* 3.4 16.7 - - - -
156I ASP* 4.9 2.6 - - - +
157I PHE* 4.1 16.9 + - + +
158I GLY* 3.9 24.9 + - - -
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Residues in contact with ALA 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57I LEU* 2.8 22.9 + - + +
58I GLU* 3.8 2.9 - - - +
60I GLU* 1.3 71.1 - - - +
62I ARG* 1.3 67.5 + - - +
63I ILE 3.0 3.2 + - - -
64I CYS* 3.2 18.5 + - - +
65I ARG* 3.4 11.5 + - - +
75I LEU* 4.1 8.7 - - + +
78I SER* 5.6 3.4 - - - +
85I HIS* 6.2 0.7 - - - +
87I LEU* 4.6 24.2 - - + -
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Residues in contact with ARG 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165G ASP* 4.6 20.0 + - - +
58I GLU* 3.1 16.9 + - - +
59I ARG* 3.1 40.5 + - - +
61I ALA* 1.3 76.9 - - - +
63I ILE* 1.3 66.2 + - + +
65I ARG* 3.2 28.0 + - - +
66I LYS* 3.4 33.3 + - - +
162I GLU* 3.0 29.9 + - - -
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Residues in contact with ILE 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I ARG* 3.2 42.8 - - + +
60I GLU* 3.3 10.1 - - - +
61I ALA 3.0 0.4 - - - -
62I ARG* 1.3 77.9 - - + +
64I CYS* 1.3 56.5 + - - +
65I ARG 2.9 4.5 - - - -
66I LYS* 2.7 35.9 + - - +
67I LEU* 3.3 21.0 + - + +
131I ILE* 3.7 32.8 - - + -
157I PHE* 4.5 4.0 - - + +
160I ALA* 3.9 27.1 - - + +
161I ILE* 4.4 4.9 - - - +
162I GLU* 4.8 9.9 - - - +
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Residues in contact with CYS 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60I GLU* 3.4 25.4 - - - -
61I ALA* 3.2 8.2 + - - +
63I ILE* 1.3 73.1 - - - +
65I ARG* 1.3 57.5 + - - +
66I LYS 3.2 0.2 - - - -
67I LEU* 3.2 33.6 - - - +
68I GLN* 3.6 6.2 + - - -
72I ILE* 5.9 2.0 - - + +
73I VAL 5.4 3.4 - - - +
74I ARG* 5.2 0.2 - - - -
75I LEU* 3.9 26.8 + - + +
89I PHE* 4.5 15.5 - - + -
157I PHE* 4.3 30.1 - - + -
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Residues in contact with ARG 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61I ALA 3.4 8.4 + - - +
62I ARG* 3.3 22.0 - - - +
63I ILE 2.9 0.6 + - - -
64I CYS* 1.3 76.9 - - - +
66I LYS* 1.3 63.3 + - + +
67I LEU 3.2 0.7 - - - -
68I GLN* 3.6 20.5 + - - +
75I LEU* 4.6 14.3 - - + +
78I SER* 5.8 7.4 - - - -
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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