Contacts of the helix formed by residues 85 - 96 (chain C) in PDB entry 2C47
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 85 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77C GLU* 2.7 11.8 + - - +
83C ALA 3.4 6.0 + - - +
84C PRO* 1.3 72.8 - - - +
86C LEU* 1.3 60.5 + - - +
87C HIS* 3.3 3.6 - - - -
88C LEU* 3.0 23.3 + - + +
89C GLU* 3.2 12.6 + - - +
190C GLY* 6.0 3.4 - - - +
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Residues in contact with LEU 86 (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 LYS* 4.6 19.5 - - + +
76C LEU 5.3 0.2 - - - -
77C GLU* 3.3 34.4 + - + +
85C GLN* 1.3 79.7 - - - +
87C HIS* 1.3 56.7 + - - +
89C GLU* 3.3 11.2 + - - +
90C TYR* 2.9 28.4 + - - +
108C PHE* 3.9 14.5 - - + -
115C ASN 5.4 1.1 - - - +
117C MET* 3.7 28.9 - - + +
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Residues in contact with HIS 87 (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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77C GLU* 4.6 1.6 - - - -
84C PRO* 2.5 52.0 + - + +
86C LEU* 1.3 77.4 - - - +
88C LEU* 1.3 81.0 + - + +
90C TYR* 3.4 6.3 + - - +
91C ARG* 3.1 33.4 + - + +
108C PHE* 3.6 33.7 - + + -
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Residues in contact with LEU 88 (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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84C PRO 4.7 0.9 - - - +
85C GLN* 3.0 16.2 + - + +
87C HIS* 1.3 99.3 - - + +
89C GLU* 1.3 63.9 + - - +
91C ARG* 3.1 11.5 + - - +
92C PHE* 3.1 39.6 + - + -
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Residues in contact with GLU 89 (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 LYS* 5.4 6.2 - - - +
85C GLN 3.2 8.3 + - - +
86C LEU* 3.3 13.7 + - - +
88C LEU* 1.3 76.1 - - - +
90C TYR* 1.3 65.9 + - - +
92C PHE* 3.2 12.0 + - - +
93C TYR* 3.1 53.9 + - + -
117C MET* 4.1 12.2 - - + +
188C ASP* 3.7 12.4 - - - +
189C PHE* 3.4 33.5 + - + +
190C GLY* 4.0 12.3 + - - +
1300C 5ID 6.0 1.4 - - - +
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Residues in contact with TYR 90 (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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86C LEU 2.9 13.5 + - - +
87C HIS 3.4 11.2 - - - +
89C GLU* 1.3 75.9 - - - +
91C ARG* 1.3 69.0 + - + +
93C TYR* 3.2 5.2 + - - +
94C LYS* 3.1 30.5 + - + +
105C VAL* 4.0 28.0 - - + +
106C TYR 5.7 0.9 - - - -
107C TYR* 4.3 4.9 + - - -
108C PHE* 3.6 51.0 + + + -
117C MET* 3.9 25.6 - - + +
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Residues in contact with ARG 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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87C HIS* 3.1 24.2 + - + +
88C LEU* 3.1 11.2 + - - +
90C TYR* 1.3 84.9 - - + +
92C PHE* 1.3 60.0 + - + +
94C LYS* 3.3 7.0 + - - +
95C GLN* 3.0 33.5 + - + +
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Residues in contact with PHE 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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88C LEU* 3.1 30.9 + - + -
89C GLU* 3.5 9.6 - - - +
91C ARG* 1.3 78.8 - - + +
93C TYR* 1.3 61.5 + - - +
95C GLN* 3.2 16.7 + - - +
96C LEU* 3.1 29.7 + - - +
161C LEU* 3.3 40.6 - - + -
189C PHE* 3.5 39.9 - - + -
190C GLY 5.8 0.9 - - - -
192C ALA* 3.8 23.1 - - + -
193C LYS* 4.4 3.4 - - - -
194C GLU* 4.6 8.7 - - + -
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Residues in contact with TYR 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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89C GLU* 3.1 49.8 + - + -
90C TYR 3.2 6.9 + - - +
92C PHE* 1.3 76.1 - - - +
94C LYS* 1.3 57.8 + - - +
96C LEU* 3.4 7.7 + - - +
97C SER* 3.1 25.8 + - - -
102C VAL* 3.8 17.8 - - + +
103C PRO* 3.6 32.4 - - + +
105C VAL* 3.8 24.6 - - + +
117C MET* 3.7 15.3 - - - -
119C LEU* 3.9 18.1 - - + +
187C ILE* 3.7 6.8 - - - +
188C ASP 2.9 24.3 + - - -
189C PHE* 3.8 23.6 - + - -
1300C 5ID 4.3 7.4 - - - +
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Residues in contact with LYS 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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90C TYR* 3.1 27.3 + - + +
91C ARG* 3.7 9.4 - - - +
92C PHE 3.2 0.2 - - - -
93C TYR* 1.3 73.7 - - - +
95C GLN* 1.3 65.8 + - - +
96C LEU 3.1 1.3 - - - -
97C SER* 3.0 25.3 + - - -
105C VAL* 4.8 6.2 - - + +
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Residues in contact with GLN 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 ARG* 3.0 16.6 + - - +
92C PHE* 3.4 33.3 - - - +
94C LYS* 1.3 76.1 - - - +
96C LEU* 1.3 60.5 + - + +
97C SER 3.7 0.2 + - - -
98C ALA* 5.1 1.6 + - - +
159C LYS* 3.2 46.2 - - + +
160C SER* 5.0 1.7 - - - -
161C LEU* 4.0 13.3 - - + +
194C GLU* 3.5 24.7 + - - +
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Residues in contact with LEU 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C PHE 3.1 18.6 + - - +
93C TYR* 3.5 6.5 - - - +
94C LYS 3.1 0.8 - - - -
95C GLN* 1.3 74.8 - - - +
97C SER* 1.3 63.9 + - - +
98C ALA* 3.0 5.0 + - - -
99C THR* 3.2 23.9 - - + +
102C VAL* 3.4 18.6 - - + +
155C TYR 4.4 1.6 - - - +
156C VAL* 3.9 25.6 - - + +
159C LYS* 3.7 33.7 - - + +
161C LEU* 4.1 14.8 - - + -
186C ILE* 5.9 0.2 - - + -
189C PHE* 3.5 44.4 - - + -
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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