Contacts of the strand formed by residues 72 - 79 (chain C) in PDB entry 3K0T
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 ILE 72 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A LYS* 3.8 13.3 + - - -
30C MSE 4.9 1.8 - - - -
58C LEU* 5.5 1.6 - - + -
69C PHE* 3.1 48.3 + - + +
70C LYS 3.4 0.2 - - - -
71C ASP* 1.3 76.9 - - - +
73C VAL* 1.3 60.4 + - - +
74C LYS 3.6 24.9 - - - +
75C LEU* 4.4 6.7 - - + +
96C PHE* 3.9 17.3 - - + -
101C PRO* 3.3 30.3 - - + +
121C ALA* 3.9 15.7 - - + -
122C ILE 3.4 6.5 - - - +
123C LEU* 3.1 26.7 - - + -
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Residues in contact with VAL 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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3A LYS* 4.0 10.8 - - + -
22A ILE* 3.8 33.2 - - + +
24A ALA* 4.1 7.2 - - + -
29A TYR* 3.5 38.5 - - + +
71C ASP 3.8 9.4 - - - +
72C ILE* 1.3 76.8 - - - +
74C LYS* 1.3 62.2 + - - +
101C PRO* 3.9 1.1 - - - -
102C ALA* 2.9 30.0 + - - +
122C ILE* 2.9 23.7 + - + +
124C VAL* 3.9 22.2 - - + -
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Residues in contact with LYS 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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29A TYR* 4.0 24.7 - - + -
30A MSE 4.0 12.2 + - - +
76A ASN* 5.5 1.0 + - - -
120A ASP* 2.9 31.5 + - - -
121A ALA 5.8 0.2 + - - -
122A ILE* 6.2 2.2 - - - +
72C ILE* 3.6 3.9 - - - +
73C VAL* 1.3 83.7 - - + +
75C LEU* 1.3 63.0 + - - +
76C ASN* 3.3 28.7 + - - +
102C ALA* 3.3 26.2 - - + +
103C ARG* 3.8 22.2 - - - +
104C ALA* 3.8 0.9 - - - +
121C ALA* 3.2 6.1 - - - +
122C ILE* 2.9 39.5 + - + -
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Residues in contact with LEU 75 (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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55C PHE* 4.4 3.1 - - + -
58C LEU* 4.0 24.7 - - + -
72C ILE* 4.5 8.1 - - + -
74C LYS* 1.3 74.9 - - - +
76C ASN* 1.3 67.2 + - - +
77C ILE* 3.8 23.1 - - + -
92C MSE 3.6 37.7 - - + -
96C PHE* 4.5 15.9 - - + -
101C PRO* 4.8 1.1 - - + -
102C ALA 3.0 10.2 + - - +
103C ARG* 3.0 31.2 - - + +
104C ALA 3.1 3.5 + - - +
119C MSE 4.0 12.3 - - + -
120C ASP 3.5 12.1 - - - +
121C ALA* 4.0 8.3 - - + -
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Residues in contact with ASN 76 (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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78A PHE* 5.9 2.6 - - - -
120A ASP* 4.0 2.4 + - - -
74B LYS* 5.6 0.2 + - - -
74C LYS* 3.3 33.5 + - - +
75C LEU* 1.3 73.9 - - - +
77C ILE* 1.3 62.6 + - - +
78C PHE* 3.7 22.5 - - + -
104C ALA* 3.4 19.6 - - - +
118C GLU 4.0 0.2 - - - +
119C MSE 3.1 28.1 - - - +
120C ASP* 2.9 33.9 + - - +
121C ALA* 5.8 0.2 - - - -
122C ILE* 6.0 1.2 - - - +
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Residues in contact with ILE 77 (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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75C LEU* 3.8 20.9 - - + -
76C ASN* 1.3 75.3 - - - +
78C PHE* 1.3 66.2 + - - +
79C LEU* 3.9 31.4 - - + -
85C PHE* 4.1 12.3 - - + -
88C VAL* 3.9 26.5 - - + -
92C MSE 4.3 3.6 - - - -
103C ARG* 3.9 28.7 - - + +
104C ALA 2.9 15.9 + - - +
105C ALA* 3.3 7.8 - - + -
106C ILE* 3.0 27.4 + - - +
117C VAL* 4.8 1.6 - - + -
118C GLU 3.9 2.2 - - - -
119C MSE 4.0 14.1 - - + -
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Residues in contact with PHE 78 (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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78A PHE* 6.0 3.1 - + - -
76B ASN* 5.8 1.3 - - - -
78B PHE* 5.9 3.6 - + - -
104B ALA* 4.8 6.1 - - + -
106B ILE* 3.7 34.1 - - + -
76C ASN* 3.7 34.5 - - + -
77C ILE* 1.3 73.6 - - - +
79C LEU* 1.3 61.3 + - - +
106C ILE* 3.7 35.7 - - + -
108C VAL* 4.1 10.8 - - + -
111C LEU* 3.7 10.6 - - + +
117C VAL* 3.3 7.3 - - - +
118C GLU* 2.9 66.1 + - + +
120C ASP* 4.3 21.1 - - + -
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Residues in contact with LEU 79 (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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47C ILE* 4.8 4.7 - - + -
77C ILE* 3.9 9.9 - - + -
78C PHE* 1.3 74.4 - - - +
80C THR* 1.3 62.0 + - - +
81C ASP 3.8 13.4 - - - +
82C LEU* 3.9 23.8 - - + -
84C HIS* 4.3 13.9 - - + +
85C PHE* 3.9 26.7 - - + +
88C VAL* 3.9 28.7 - - + -
106C ILE 3.1 6.3 + - - -
107C GLY* 3.1 8.7 - - - -
108C VAL* 2.8 28.2 + - - +
111C LEU* 4.6 0.2 - - - -
116C GLN 3.6 5.8 - - - +
117C VAL* 3.8 28.7 - - + -
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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