Contacts of the helix formed by residues 90 - 101 (chain C) in PDB entry 3HCU
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 CYS 90 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54C GLN 4.8 0.9 - - - +
55C GLY* 3.8 17.0 - - - -
70C CYS* 3.1 16.3 - - - -
77C LEU* 4.2 0.9 - - - -
78C ARG 3.2 23.6 - - - -
79C GLU* 3.2 18.6 - - - +
89C PHE* 1.3 74.1 - - - +
91C LYS* 1.3 65.8 + - - +
93C CYS* 2.9 26.1 + - - -
94C ILE* 3.0 12.5 + - - +
304C ZN 2.7 33.9 - - - -
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Residues in contact with LYS 91 (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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79C GLU* 3.2 27.7 - - + +
81C VAL* 3.8 22.8 - - + +
89C PHE 3.6 3.0 + - - -
90C CYS* 1.3 70.2 - - - +
92C ALA* 1.3 60.6 + - - +
94C ILE* 3.4 5.6 - - - +
95C ILE* 3.1 53.6 + - + +
114C GLU* 5.4 2.4 + - - -
117C LEU* 4.7 10.1 - - + +
119C PRO* 6.3 0.4 - - + -
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Residues in contact with ALA 92 (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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54C GLN* 4.6 18.6 - - + -
79C GLU* 2.9 17.5 + - - +
91C LYS* 1.3 76.1 - - - +
93C CYS* 1.3 66.3 + - - +
95C ILE* 3.4 3.8 + - - +
96C LYS* 3.0 27.5 + - - +
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Residues in contact with CYS 93 (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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54C GLN* 4.4 7.4 - - - +
70C CYS* 3.0 12.8 - - - -
72C ILE* 3.2 27.9 - - + +
73C CYS* 2.9 18.2 - - - -
89C PHE* 4.8 0.2 - - + -
90C CYS* 2.9 30.4 + - - +
92C ALA* 1.3 75.2 - - - +
94C ILE* 1.3 56.6 + - - +
96C LYS* 3.5 7.6 - - - +
97C SER 3.1 19.6 + - - -
304C ZN 2.7 36.1 - - - -
64D MET* 4.2 2.9 - - - +
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Residues in contact with ILE 94 (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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72C ILE* 4.0 0.9 - - - -
81C VAL* 3.9 9.2 - - + -
83C THR* 5.0 0.4 - - + -
89C PHE* 3.8 25.6 - - + -
90C CYS 3.0 11.7 + - - +
91C LYS 3.4 6.5 - - - +
93C CYS* 1.3 77.0 - - - +
95C ILE* 1.3 64.0 + - - +
97C SER* 3.0 6.1 + - - -
98C ILE* 2.8 35.4 + - + +
106C PRO* 3.3 41.3 - - + -
112C LEU* 4.0 25.8 - - + -
117C LEU* 3.4 33.9 - - + -
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Residues in contact with ILE 95 (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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91C LYS* 3.1 48.2 + - + +
92C ALA* 4.1 4.3 - - - +
94C ILE* 1.3 78.3 - - - +
96C LYS* 1.3 69.1 + - - +
98C ILE* 3.0 19.4 + - + +
99C ARG* 3.5 32.6 + - - +
114C GLU* 3.0 37.9 - - - +
117C LEU* 4.2 10.1 - - + -
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Residues in contact with LYS 96 (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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92C ALA 3.0 18.0 + - - +
93C CYS* 3.5 7.0 - - - +
95C ILE* 1.3 78.7 - - - +
97C SER* 1.3 64.3 + - - +
99C ARG* 3.2 2.4 + - - +
100C ASP* 3.0 58.9 + - - +
61D GLU* 5.6 5.2 - - - +
64D MET* 3.9 30.6 - - + +
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Residues in contact with SER 97 (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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72C ILE* 3.6 15.6 - - - +
93C CYS 3.1 12.2 + - - -
94C ILE* 3.0 16.8 + - - -
96C LYS* 1.3 80.7 - - - +
98C ILE* 1.3 53.8 + - - +
101C ALA* 3.0 13.3 + - - +
102C GLY 2.9 25.3 + - - +
104C LYS 4.9 3.0 + - - +
106C PRO* 4.1 10.9 - - - +
64D MET* 3.9 14.6 - - - -
97D PRO* 3.5 22.2 - - - +
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Residues in contact with ILE 98 (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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94C ILE* 2.8 27.9 + - + +
95C ILE* 3.0 16.0 + - + +
97C SER* 1.3 74.4 - - - +
99C ARG* 1.3 62.2 + - + +
102C GLY* 3.0 28.9 - - - +
103C HIS* 3.0 30.1 + - + +
104C LYS 5.6 1.6 - - - +
112C LEU* 3.8 33.2 - - + +
113C LEU 4.1 0.4 - - - -
114C GLU* 3.3 50.0 - - + +
117C LEU* 5.1 3.6 - - + -
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Residues in contact with ARG 99 (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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95C ILE* 3.9 23.1 - - - +
96C LYS* 3.2 4.7 + - - +
98C ILE* 1.3 88.3 - - + +
100C ASP* 1.3 71.7 + - - +
101C ALA 3.3 1.6 + - - -
102C GLY* 4.2 3.5 + - - -
103C HIS* 5.0 6.5 - - + -
114C GLU* 4.2 22.2 + - + +
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Residues in contact with ASP 100 (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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96C LYS* 3.0 51.7 + - - +
99C ARG* 1.3 83.1 - - - +
101C ALA* 1.3 59.1 + - - +
61D GLU* 3.7 26.2 - - - +
64D MET* 4.2 13.9 - - + +
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Residues in contact with ALA 101 (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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97C SER* 3.0 29.9 + - - +
99C ARG 4.5 0.7 - - - -
100C ASP* 1.3 81.2 - - - +
102C GLY* 1.3 56.2 + - - +
104C LYS 6.1 0.9 - - - +
64D MET* 4.6 12.8 - - - +
97D PRO* 4.2 19.1 - - + -
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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