Contacts of the helix formed by residues 80 - 93 (chain C) in PDB entry 3VZC
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 GLY 80 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77C VAL* 5.0 1.9 - - - +
79C SER* 1.3 84.8 + - - +
81C ASP* 1.3 66.6 + - - -
82C GLY 3.1 4.6 + - - -
83C LEU* 3.2 12.5 + - - +
84C MET* 3.7 6.9 + - - +
111C GLY* 5.0 1.7 - - - -
112C SER 4.3 7.9 - - - -
113C GLY 3.4 12.3 - - - -
114C ASN* 3.8 4.5 - - - -
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Residues in contact with ASP 81 (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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80C GLY* 1.3 71.4 - - - -
82C GLY* 1.3 58.4 + - - +
84C MET* 3.0 11.6 + - - +
85C HIS* 2.9 26.7 + - - +
112C SER 5.0 0.2 + - - -
113C GLY* 2.8 32.1 + - - +
114C ASN* 3.7 2.6 - - - +
115C ALA* 3.0 21.4 + - - +
116C LEU* 2.9 36.9 + - + +
117C ALA 4.5 0.3 + - - -
166C VAL* 5.0 1.9 - - + +
167C LEU* 3.9 18.5 - - + +
268C LEU 5.2 0.2 - - - +
341C ASP* 4.1 16.9 - - + +
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Residues in contact with GLY 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C GLY 3.1 1.6 - - - -
81C ASP* 1.3 80.0 - - - +
83C LEU* 1.3 59.9 + - - +
85C HIS* 3.4 8.3 - - - +
86C GLU* 3.2 28.8 + - - +
341C ASP 4.0 12.1 + - - -
342C GLY 6.1 0.2 - - - -
343C GLU* 5.6 7.2 - - - -
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Residues in contact with LEU 83 (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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20C LEU* 3.8 27.8 - - + +
22C ASN* 4.7 3.4 - - + +
54C THR* 4.0 22.7 - - + -
60C ALA* 3.3 29.2 - - + +
77C VAL* 3.4 27.6 - - + -
79C SER* 3.6 32.1 - - - +
80C GLY 3.2 4.5 + - - +
82C GLY* 1.3 73.4 - - - +
84C MET* 1.3 67.2 + - - +
86C GLU* 3.1 11.2 + - + +
87C VAL* 2.9 25.9 + - + +
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Residues in contact with MET 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C VAL* 3.6 26.0 - - + +
80C GLY 3.7 3.1 + - - +
81C ASP* 3.0 12.7 + - - +
83C LEU* 1.3 77.4 - - - +
85C HIS* 1.3 63.9 + - - +
87C VAL* 3.1 4.8 + - - +
88C VAL* 2.9 28.7 + - + +
105C LEU* 4.1 26.5 - - - -
106C CYS 3.2 38.6 - - - +
107C SER* 3.8 15.3 - - - +
116C LEU* 3.5 26.0 - - + -
166C VAL* 4.1 10.1 - - + -
361C MET* 4.4 9.6 - - + +
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Residues in contact with HIS 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ARG* 4.4 7.6 - - - -
81C ASP 2.9 12.1 + - - +
82C GLY* 3.4 12.1 - - - +
84C MET* 1.3 75.8 - - - +
86C GLU* 1.3 62.2 + - - +
88C VAL* 3.5 2.5 + - - +
89C ASN* 2.9 50.1 + - - +
163C LEU* 4.1 7.5 - - + +
164C PHE 3.1 22.7 + - - -
166C VAL* 4.5 4.3 - - - +
340C VAL* 3.5 21.5 - - + +
341C ASP* 2.8 41.5 - - + +
343C GLU* 3.4 37.0 + - + +
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Residues in contact with GLU 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ARG* 6.1 0.5 - - - +
58C ASN* 2.8 36.1 - - - +
60C ALA* 4.4 5.2 - - + -
61C ARG* 3.2 48.4 + - + +
82C GLY 3.2 15.1 + - - +
83C LEU* 3.1 13.7 + - + +
85C HIS* 1.3 75.4 + - - +
87C VAL* 1.3 61.0 + - - +
89C ASN* 3.5 2.5 + - - -
90C GLY* 2.8 27.9 + - - -
343C GLU* 2.8 27.7 - - - +
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Residues in contact with VAL 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LEU* 4.1 12.3 - - + -
60C ALA* 4.4 7.6 - - + -
61C ARG* 5.1 0.4 - - - +
64C VAL* 3.5 34.0 - - + +
75C LEU* 4.1 10.8 - - + -
77C VAL* 4.0 24.9 - - + -
83C LEU 2.9 18.0 + - - +
84C MET* 3.7 9.0 - - - +
86C GLU* 1.3 74.7 - - - +
88C VAL* 1.3 63.9 + - - +
90C GLY* 3.0 10.9 + - - -
91C LEU* 3.0 28.5 + - + +
105C LEU* 4.4 13.7 - - + -
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Residues in contact with VAL 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 MET* 2.9 20.7 + - - +
85C HIS* 4.0 2.9 - - - +
87C VAL* 1.3 73.9 - - - +
89C ASN* 1.3 66.5 + - - +
91C LEU* 3.2 8.9 + - - +
92C MET* 3.0 23.3 + - + +
101C ILE* 4.4 11.4 - - + -
105C LEU* 3.8 24.7 - - + -
152C LEU* 3.9 31.6 - - + -
164C PHE* 4.4 9.9 - - + -
166C VAL* 3.3 26.5 - - + -
359C PHE* 4.6 6.3 - - + -
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Residues in contact with ASN 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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61C ARG* 3.5 30.1 - - - +
85C HIS* 2.9 37.1 + - - +
86C GLU 4.0 1.3 - - - +
88C VAL* 1.3 76.8 - - - +
90C GLY* 1.3 62.3 + - - +
92C MET* 3.3 5.7 + - - +
93C GLU* 3.0 30.9 + - - +
162C ARG 5.0 0.4 + - - -
163C LEU* 3.6 14.1 - - - +
164C PHE* 2.8 56.1 - - - +
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Residues in contact with GLY 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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61C ARG* 3.7 28.2 - - - +
64C VAL* 4.1 6.5 - - - -
65C ARG* 4.0 5.6 - - - +
86C GLU 2.8 15.4 + - - -
87C VAL 3.0 4.2 + - - -
89C ASN* 1.3 75.4 - - - +
91C LEU* 1.3 63.2 + - - +
93C GLU* 3.0 20.7 + - - +
94C ARG* 3.5 10.6 + - - +
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Residues in contact with LEU 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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64C VAL* 3.5 19.0 - - + +
69C LEU* 3.8 27.8 - - + -
75C LEU* 4.5 5.2 - - + -
87C VAL* 3.0 32.0 + - + +
88C VAL* 3.6 4.5 - - - +
90C GLY* 1.3 74.0 - - - +
92C MET* 1.3 62.8 + - - +
94C ARG* 3.2 27.3 + - - +
97C TRP* 3.6 11.4 - - - +
100C ALA* 3.4 26.5 - - + +
101C ILE* 4.2 20.0 - - + -
103C LYS* 4.8 2.7 - - + +
105C LEU* 4.1 26.0 - - + -
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Residues in contact with MET 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 VAL* 3.0 23.4 + - + +
89C ASN 3.6 3.8 - - - +
90C GLY 3.2 0.2 - - - -
91C LEU* 1.3 75.8 - - - +
93C GLU* 1.3 59.5 + - + +
94C ARG 3.3 1.7 + - - +
97C TRP* 3.7 33.7 - - + +
101C ILE* 3.6 39.7 - - + -
152C LEU* 4.5 2.9 - - + -
164C PHE* 3.5 59.7 - - + -
232C GLY* 5.2 1.1 - - - -
233C PRO* 3.6 22.9 - - + -
358C TYR* 4.1 7.4 - - + -
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Residues in contact with GLU 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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61C ARG* 2.4 46.1 + - - +
65C ARG* 2.8 44.3 + - - +
89C ASN* 3.0 13.7 + - - +
90C GLY* 3.0 8.4 + - - +
92C MET* 1.3 77.5 - - + +
94C ARG* 1.3 64.0 + - - +
95C PRO* 4.0 3.1 - - - +
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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