Contacts of the strand formed by residues 67 - 74 (chain C) in PDB entry 3KDH
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 VAL 67 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60C PRO* 4.9 3.8 - - + -
61C GLU* 3.8 46.0 - - + +
64C LYS* 4.2 22.4 + - + +
65C HIS 3.2 10.3 - - - +
66C PHE* 1.3 79.9 - - - +
68C LYS* 1.3 63.7 + - - +
69C ARG 3.7 25.4 - - - +
70C CYS* 4.7 3.1 - - + -
85C VAL* 3.7 23.8 - - + -
86C THR 3.6 2.7 - - - -
87C VAL* 5.5 2.0 - - + -
88C ILE* 5.1 1.6 - - - -
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Residues in contact with LYS 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C GLU* 5.8 1.2 - - - +
66C PHE 3.9 1.2 + - - -
67C VAL* 1.3 74.9 - - - +
69C ARG* 1.3 89.7 + - - +
86C THR* 2.8 26.0 + - + +
88C ILE* 4.2 29.3 - - + +
93C ALA* 5.1 6.8 - - + +
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Residues in contact with ARG 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C GLU* 6.1 0.9 - - - -
67C VAL* 3.7 10.3 - - - +
68C LYS* 1.3 109.7 - - - +
70C CYS* 1.3 64.5 + - - +
84C GLU 4.6 0.2 - - - -
86C THR* 2.8 54.8 + - - +
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Residues in contact with CYS 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C ASP* 3.6 19.9 - - - +
59C ASN* 5.3 0.7 - - - +
60C PRO* 3.5 37.9 - - + -
61C GLU* 5.7 1.1 - - + +
67C VAL* 4.7 2.7 - - + -
69C ARG* 1.3 80.9 - - - +
71C ARG* 1.3 67.1 + - - +
83C ARG* 3.8 25.6 - - - -
84C GLU 3.3 13.7 - - - +
85C VAL* 3.9 5.8 - - + -
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Residues in contact with ARG 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A GLY* 2.7 47.5 + - - -
58C ASP* 5.2 3.4 - - - -
70C CYS* 1.3 77.3 - - - +
72C LEU* 1.3 70.8 + - - +
73C ILE* 3.6 10.6 - - + +
83C ARG* 3.3 4.1 - - - -
84C GLU* 2.8 65.7 + - + +
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Residues in contact with LEU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A SER* 5.5 0.5 - - - -
140A LYS* 3.7 23.1 - - - +
57C PHE* 4.0 17.7 - - + -
58C ASP* 3.7 32.8 - - + +
71C ARG* 1.3 81.8 + - - +
73C ILE* 1.3 60.6 - - - +
74C SER 4.3 1.1 - - - +
75C GLY 3.7 18.2 - - - +
76C ASP* 3.6 9.4 - - - -
77C GLY* 3.5 31.0 - - - +
81C SER* 4.6 2.9 - - - +
82C VAL 3.4 7.2 - - - +
83C ARG* 3.8 20.0 - - + -
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Residues in contact with ILE 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PRO* 4.5 6.1 - - + -
139A GLY 3.8 6.1 - - - +
140A LYS* 3.2 13.2 - - - +
141A VAL* 2.9 51.6 + - + +
71C ARG* 3.6 25.3 + - + +
72C LEU* 1.3 74.3 - - - +
74C SER* 1.3 60.7 + - - +
82C VAL* 2.8 40.7 + - + +
84C GLU* 3.5 48.7 - - + +
97C THR* 4.2 7.0 - - + -
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Residues in contact with SER 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A HIS* 2.8 27.9 + - - +
45A ALA* 3.3 9.3 - - - +
46A PRO* 3.9 21.8 - - - -
140A LYS* 4.6 4.2 - - - +
141A VAL* 4.5 6.0 + - - -
72C LEU* 3.5 2.7 - - - +
73C ILE* 1.3 82.1 - - - +
75C GLY* 1.3 66.2 + - - +
80C GLY 5.0 3.3 + - - -
81C SER* 3.3 3.7 - - - -
82C VAL* 2.9 38.0 + - - +
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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