Contacts of the helix formed by residues 80 - 93 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A VAL* 5.2 2.4 - - - +
79A SER* 1.3 85.9 + - - +
81A ASP* 1.3 66.1 + - - +
82A GLY 3.2 4.4 + - - -
83A LEU* 3.5 9.4 + - - +
84A MET* 3.7 9.9 + - - +
107A SER* 5.0 7.6 + - - -
111A GLY* 4.6 2.6 - - - +
112A SER 4.8 6.1 - - - -
113A GLY 3.3 12.3 - - - -
114A ASN* 3.7 6.1 - - - -
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Residues in contact with ASP 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A GLY* 1.3 73.5 - - - -
82A GLY* 1.3 62.1 + - - +
83A LEU 3.3 0.5 + - - -
84A MET* 3.4 8.7 + - - +
85A HIS* 3.0 22.3 + - - +
113A GLY* 2.7 25.6 + - - +
114A ASN* 3.8 2.1 - - - -
115A ALA* 2.9 26.4 + - - +
116A LEU* 2.9 34.7 + - + +
117A ALA 4.6 0.2 + - - -
166A VAL* 4.9 3.1 - - + +
167A LEU* 3.7 18.7 - - + +
341A ASP* 3.8 20.7 - - + +
342A GLY* 5.9 0.2 - - - -
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Residues in contact with GLY 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLY* 3.2 2.0 - - - -
81A ASP* 1.3 80.2 - - - +
83A LEU* 1.3 58.5 + - - +
85A HIS* 3.3 9.4 + - - +
86A GLU* 3.3 26.2 + - - +
341A ASP 4.0 9.2 + - - -
343A GLU* 5.8 7.6 - - - -
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU* 3.8 19.5 - - + +
22A ASN* 4.5 7.0 - - + +
54A THR* 3.9 22.4 - - + +
60A ALA* 3.5 29.2 - - + -
77A VAL* 3.5 25.6 - - + -
79A SER* 3.7 34.5 + - - +
80A GLY 3.5 5.2 + - - +
81A ASP 3.2 0.6 - - - -
82A GLY* 1.3 73.6 - - - +
84A MET* 1.3 67.7 + - - +
86A GLU* 2.9 21.8 + - + +
87A VAL* 2.9 17.3 + - + +
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Residues in contact with MET 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL* 3.7 24.2 - - + +
80A GLY 3.7 8.9 + - - +
81A ASP* 3.4 10.0 + - - +
83A LEU* 1.3 77.1 - - - +
85A HIS* 1.3 62.4 + - - +
87A VAL* 3.1 3.6 + - - +
88A VAL* 2.8 34.5 + - + +
105A LEU* 4.1 22.7 - - + -
106A CYS 3.6 31.9 - - - +
107A SER* 3.6 24.2 - - - +
116A LEU* 3.7 24.9 - - + -
166A VAL* 4.1 12.3 - - + -
359A PHE* 5.3 0.9 - - + -
361A MET* 4.5 4.9 - - - +
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Residues in contact with HIS 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ARG* 4.3 9.9 - - - -
81A ASP 3.0 13.6 + - - +
82A GLY* 3.3 13.1 + - - +
84A MET* 1.3 75.9 - - - +
86A GLU* 1.3 69.1 + - - +
88A VAL* 3.9 2.8 - - - +
89A ASN* 3.0 44.5 + - - +
163A LEU* 4.1 10.3 - - + +
164A PHE 3.0 25.3 + - - -
166A VAL* 4.4 5.5 - - - +
340A VAL* 3.6 13.4 - - + +
341A ASP* 2.8 41.3 - - + +
343A GLU* 3.3 32.5 + - + +
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Residues in contact with GLU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ASN* 3.4 22.0 - - - +
60A ALA* 4.7 1.6 - - + +
61A ARG* 2.9 69.1 + - - +
82A GLY 3.4 13.8 - - - +
83A LEU* 2.9 23.3 + - + +
85A HIS* 1.3 87.2 + - - +
87A VAL* 1.3 59.1 + - - +
89A ASN 3.4 0.3 + - - -
90A GLY* 2.8 27.2 + - - -
343A GLU* 4.3 11.1 - - - +
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 4.1 22.9 - - + -
60A ALA* 4.7 9.2 - - + +
64A VAL* 3.3 26.9 - - + +
75A LEU* 4.5 4.3 - - + -
77A VAL* 4.0 27.6 - - + -
83A LEU 2.9 16.0 + - - +
84A MET* 3.5 9.2 - - - +
86A GLU* 1.3 73.1 - - - +
88A VAL* 1.3 65.1 + - - +
90A GLY 3.2 1.4 + - - -
91A LEU* 3.0 33.9 + - + +
105A LEU* 4.5 17.0 - - + -
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Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A MET* 2.8 29.9 + - - +
85A HIS 4.0 2.0 - - - +
87A VAL* 1.3 72.0 - - - +
89A ASN* 1.3 63.2 + - - +
91A LEU* 3.3 8.6 + - - +
92A MET* 3.1 24.1 + - + +
101A ILE* 4.4 11.7 - - + -
105A LEU* 3.7 28.3 - - + -
152A LEU* 3.8 25.1 - - + -
164A PHE* 4.7 4.5 - - + -
166A VAL* 3.6 32.1 - - + -
359A PHE* 4.7 5.4 - - + -
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Residues in contact with ASN 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ARG* 3.8 28.7 - - - +
85A HIS* 3.0 36.2 + - - +
86A GLU 3.9 1.1 - - - +
88A VAL* 1.3 76.1 - - - +
90A GLY* 1.3 57.5 + - - +
92A MET* 3.3 4.5 + - - +
93A GLU* 2.9 42.8 + - - +
162A ARG 5.2 0.2 + - - -
163A LEU* 3.7 9.9 - - - +
164A PHE* 2.9 58.7 - - - +
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Residues in contact with GLY 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ARG* 3.8 21.0 - - - +
64A VAL* 3.5 14.8 - - - -
65A ARG* 3.8 5.9 - - - +
86A GLU 2.8 15.6 + - - -
87A VAL 3.2 4.4 + - - -
89A ASN* 1.3 77.3 - - - +
91A LEU* 1.3 60.4 + - - +
93A GLU* 3.5 11.2 + - - +
94A ARG* 3.4 16.8 + - - +
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Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A VAL* 3.4 15.5 - - + +
69A LEU* 3.9 29.6 - - + -
75A LEU* 4.4 5.6 - - + -
87A VAL* 3.0 21.4 + - + +
88A VAL* 3.3 6.3 + - - +
90A GLY* 1.3 75.1 - - - +
92A MET* 1.3 62.8 + - - +
94A ARG* 3.2 27.8 + - - +
97A TRP* 3.6 11.7 - - - +
100A ALA* 3.8 29.4 - - + +
101A ILE* 4.2 16.4 - - + -
103A LYS* 5.1 2.0 - - + +
105A LEU* 4.0 36.3 - - + -
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Residues in contact with MET 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 3.1 21.6 + - + +
89A ASN 3.8 2.2 - - - +
91A LEU* 1.3 71.1 - - - +
93A GLU* 1.3 60.4 - - - +
94A ARG 3.1 7.6 + - - +
97A TRP* 3.5 36.5 - - + +
101A ILE* 3.8 35.2 - - + -
152A LEU* 4.0 17.5 - - + -
164A PHE* 3.5 54.5 - - + -
231A GLN 5.8 0.7 + - - -
232A GLY* 4.7 5.7 + - - -
233A PRO* 3.6 25.6 - - + -
358A TYR* 4.5 2.9 - - + -
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Residues in contact with GLU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ARG* 3.1 36.6 + - - +
65A ARG* 2.8 44.9 + - - -
89A ASN* 2.9 29.5 + - + +
90A GLY 3.8 6.3 - - - +
91A LEU 3.2 0.4 - - - -
92A MET* 1.3 75.3 - - + +
94A ARG* 1.3 62.0 + - - +
95A PRO* 3.9 3.8 - - - +
164A PHE* 6.1 2.5 - - + -
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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