Contacts of the helix formed by residues 104 - 114 (chain A) in PDB entry 2VXO
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 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A GLY 3.2 14.1 - - - +
77A GLY 4.6 4.3 - - - +
102A GLY 3.8 1.0 + - - -
103A ILE* 1.3 69.2 - - - +
105A TYR* 1.3 68.1 + - - +
106A GLY 3.1 0.4 - - - -
107A MET* 3.1 6.3 + - - +
108A GLN* 3.0 25.4 + - - +
152A THR* 3.5 13.5 - - - -
187A ALA 2.7 17.7 + - - -
188A GLN* 2.8 41.1 - - - +
190A HIS* 2.9 34.5 - - + +
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Residues in contact with TYR 105 (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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33A ALA* 4.2 11.7 - - + -
76A GLY* 3.4 24.4 + - - +
77A GLY 3.7 11.5 + - - +
78A PRO 4.7 11.7 - - - -
86A ALA* 3.8 13.0 - - - +
87A PRO* 3.1 39.5 + - + +
89A PHE* 5.9 2.4 - + - -
103A ILE 3.2 0.4 + - - -
104A CYS* 1.3 78.7 - - - +
106A GLY* 1.3 52.9 + - - +
108A GLN* 2.9 16.1 + - + +
109A MET* 2.8 83.4 + - + +
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Residues in contact with GLY 106 (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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74A ILE* 3.6 38.8 + - - -
75A SER* 4.4 1.8 - - - +
94A PHE* 4.2 4.0 - - - -
102A GLY* 3.6 9.3 - - - -
103A ILE 3.3 5.8 + - - -
104A CYS 3.1 0.6 - - - -
105A TYR* 1.3 80.3 - - - +
107A MET* 1.3 55.7 + - - +
109A MET* 3.4 5.8 + - - +
110A MET* 2.9 29.3 + - - +
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Residues in contact with MET 107 (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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102A GLY* 3.4 25.3 - - - +
104A CYS 3.1 10.2 + - - +
106A GLY* 1.3 76.8 - - - +
108A GLN* 1.3 57.9 + - - +
110A MET* 3.4 6.0 + - - +
111A ASN* 2.9 28.1 + - - +
157A VAL* 3.8 27.4 - - + -
174A VAL* 3.8 17.9 - - + +
175A ALA 4.2 0.7 - - - +
176A GLY 4.1 4.9 - - - +
177A ILE* 3.8 25.0 - - + +
186A GLY* 3.5 14.8 - - - +
187A ALA* 3.4 12.3 - - - +
188A GLN* 3.3 39.7 - - - +
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Residues in contact with GLN 108 (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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104A CYS 3.0 17.0 + - - +
105A TYR* 2.9 22.0 + - + +
107A MET* 1.3 74.5 - - - +
109A MET* 1.3 59.7 + - - +
111A ASN* 3.3 6.1 + - - +
112A LYS* 2.8 32.0 + - - +
118A VAL* 3.6 25.6 - - - +
155A ASP* 3.8 27.0 + - + +
156A SER* 4.0 6.5 + - - +
157A VAL* 4.2 16.5 - - - +
188A GLN* 2.9 30.6 + - - +
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Residues in contact with MET 109 (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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33A ALA* 4.5 4.7 - - + -
57A LEU* 3.8 17.5 - - + -
74A ILE* 3.5 30.7 - - + -
75A SER 4.6 1.3 - - - +
89A PHE* 3.8 43.5 - - + -
93A ILE* 5.6 1.3 - - - -
94A PHE* 4.1 11.7 - - + -
105A TYR* 2.8 57.0 + - + +
106A GLY* 3.5 9.4 - - - +
108A GLN* 1.3 71.3 - - - +
110A MET* 1.3 58.4 + - - +
112A LYS* 3.2 7.0 + - - +
113A VAL* 2.8 35.3 + - - +
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Residues in contact with MET 110 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A PHE* 3.6 36.9 - - + -
100A VAL* 3.8 17.3 - - + +
102A GLY* 3.9 6.3 - - - +
106A GLY 2.9 15.6 + - - +
107A MET* 3.5 5.8 - - - +
109A MET* 1.3 77.9 - - - +
111A ASN* 1.3 61.7 + - - +
113A VAL 3.4 0.5 + - - -
114A PHE* 3.3 29.8 + - + +
164A PHE* 3.6 37.0 - - + -
177A ILE* 4.3 4.7 - - + -
184A LEU* 3.9 8.7 - - + -
185A TYR 3.4 43.5 - - - +
186A GLY* 3.9 3.1 - - - -
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Residues in contact with ASN 111 (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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107A MET 2.9 17.6 + - - +
108A GLN* 3.7 6.3 + - - +
109A MET 3.3 0.2 - - - -
110A MET* 1.3 76.9 - - - +
112A LYS* 1.3 61.9 + - - +
114A PHE 3.1 8.0 + - - -
115A GLY 3.3 0.3 + - - -
116A GLY* 3.0 30.2 + - - -
117A THR 3.4 12.3 + - - -
118A VAL* 5.5 0.8 - - - +
157A VAL* 3.4 37.0 - - + +
159A LYS 3.4 9.3 + - - -
160A VAL* 3.9 3.5 - - - +
161A ALA* 2.9 34.0 + - - +
164A PHE* 5.9 0.2 - - - -
177A ILE* 4.2 17.0 - - + +
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Residues in contact with LYS 112 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A PHE* 6.3 4.7 - - + -
108A GLN 2.8 22.1 + - - +
109A MET* 3.7 6.3 - - - +
111A ASN* 1.3 72.8 - - - +
113A VAL* 1.3 66.0 + - + +
115A GLY* 3.1 14.2 + - - -
116A GLY 3.8 14.8 + - - +
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Residues in contact with VAL 113 (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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89A PHE* 3.5 33.9 - - + -
91A PRO* 4.3 21.8 - - + +
94A PHE* 4.0 15.0 - - + -
95A THR* 5.4 4.0 - - + -
109A MET 2.8 23.4 + - - +
110A MET 3.8 4.3 - - - +
111A ASN 3.3 0.2 - - - -
112A LYS* 1.3 75.6 - - + +
114A PHE* 1.3 77.7 + - + +
115A GLY 3.6 0.7 + - - -
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Residues in contact with PHE 114 (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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94A PHE* 3.6 37.9 - + + -
95A THR* 4.8 8.3 - - + -
110A MET 3.3 20.4 + - - +
111A ASN 3.1 3.6 + - - -
113A VAL* 1.3 88.8 - - + +
115A GLY* 1.3 55.3 - - - +
116A GLY 3.5 2.9 - - - -
161A ALA* 3.4 25.7 - - + +
162A ASP* 3.5 21.6 + - - +
164A PHE* 3.6 20.4 - + + -
179A ASN* 5.7 1.1 - - - -
182A LYS* 4.3 23.3 - - + -
184A LEU* 3.6 25.1 - - + -
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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