Contacts of the helix formed by residues 110 - 129 (chain R) in PDB entry 1VYH
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 THR 110 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109R ASN* 1.3 75.8 - - - +
111R ALA* 1.3 68.0 + - - +
112R GLU* 3.1 15.7 + - - +
113R GLU* 3.0 43.7 + - - +
114R VAL* 3.0 11.3 + - - +
152R LYS* 4.9 1.3 - - - +
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Residues in contact with ALA 111 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109R ASN 3.8 1.0 + - - -
110R THR* 1.3 71.0 - - - +
112R GLU* 1.3 69.7 + - - +
114R VAL* 3.1 5.6 + - - +
115R ALA* 2.9 22.7 + - - +
152R LYS* 3.7 40.0 - - + +
155R LYS* 3.7 26.5 - - + +
156R VAL* 3.9 15.2 - - + +
159R LEU* 4.8 2.7 - - + -
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Residues in contact with GLU 112 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110R THR* 3.7 19.9 - - - +
111R ALA* 1.3 78.1 + - - +
113R GLU* 1.3 63.2 + - + +
115R ALA* 3.1 7.1 + - - +
116R GLY* 3.0 18.2 + - - -
155R LYS* 3.4 27.1 + - - +
159R LEU* 3.9 23.9 - - + +
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Residues in contact with GLU 113 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7R ASN* 3.3 26.6 + - + +
8R PRO* 3.9 21.3 - - + +
9R ALA* 3.5 13.0 - - + +
108R GLU 4.4 1.9 - - - +
109R ASN* 3.7 16.2 - - + +
110R THR* 3.0 37.2 + - - +
112R GLU* 1.3 79.5 - - + +
114R VAL* 1.3 58.4 + - - +
116R GLY* 3.0 5.6 + - - -
117R GLY 2.9 24.1 + - - -
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Residues in contact with VAL 114 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9R ALA* 4.4 5.8 - - - -
78R THR* 4.3 3.6 - - + +
103R GLY* 4.3 20.2 - - - +
106R ASN* 3.7 29.6 - - + +
109R ASN* 3.8 14.8 - - + +
110R THR 3.0 17.5 + - - +
111R ALA* 3.1 11.0 + - - +
113R GLU* 1.3 75.7 - - - +
115R ALA* 1.3 63.7 + - - +
117R GLY* 3.0 11.7 + - - +
118R ILE* 3.0 22.9 + - + +
139R LEU* 4.6 1.3 - - + -
152R LYS* 4.6 5.6 - - - -
156R VAL* 3.7 25.8 - - + -
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Residues in contact with ALA 115 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111R ALA 2.9 12.2 + - - +
112R GLU 3.4 9.0 - - - +
114R VAL* 1.3 74.8 - - - +
116R GLY* 1.3 62.8 + - - +
117R GLY 3.3 0.2 + - - -
118R ILE* 3.3 4.8 + - - +
119R GLU* 2.9 39.2 + - - +
156R VAL* 4.1 16.4 - - + +
159R LEU* 4.1 26.2 - - + -
160R LEU* 4.0 10.9 - - + +
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Residues in contact with GLY 116 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7R ASN* 4.0 13.2 - - - -
10R ALA* 4.2 1.0 - - - +
112R GLU 3.0 9.3 + - - -
113R GLU* 3.0 9.2 + - - -
115R ALA* 1.3 75.9 - - - +
117R GLY* 1.3 56.5 + - - +
119R GLU* 3.2 16.6 + - - +
120R ALA* 2.9 29.5 + - - +
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Residues in contact with GLY 117 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7R ASN* 4.0 1.2 + - - -
9R ALA 3.9 22.0 - - - -
10R ALA* 4.0 7.2 - - - -
78R THR* 4.1 11.9 - - - -
82R LEU* 4.5 1.2 - - - +
113R GLU 2.9 11.9 + - - -
114R VAL 3.0 6.5 + - - -
116R GLY* 1.3 74.1 - - - +
118R ILE* 1.3 62.7 + - - -
120R ALA* 3.0 6.8 + - - +
121R ILE* 3.0 22.9 + - - +
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Residues in contact with ILE 118 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78R THR* 3.9 8.6 - - + +
100R VAL* 4.9 7.6 - - + -
102R VAL* 3.5 30.1 - - + +
103R GLY* 4.8 0.2 - - - -
114R VAL* 3.0 27.4 + - + +
115R ALA* 3.8 4.5 - - - +
117R GLY* 1.3 70.8 - - - +
119R GLU* 1.3 64.7 + - - +
121R ILE* 2.9 13.2 + - + +
122R VAL* 2.8 26.2 + - + +
136R VAL* 4.1 28.3 - - + -
139R LEU* 5.2 2.7 - - + -
156R VAL* 3.9 14.6 - - + -
160R LEU* 3.9 37.9 - - + -
164R LEU* 5.0 0.9 - - + -
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Residues in contact with GLU 119 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115R ALA* 2.9 29.5 + - - +
116R GLY* 3.2 16.0 + - - +
118R ILE* 1.3 75.2 - - - +
120R ALA* 1.3 58.6 + - - +
122R VAL* 3.2 10.9 + - - +
123R GLN* 2.8 36.2 + - - +
159R LEU* 5.6 0.7 - - - +
160R LEU* 4.4 6.7 - - + +
163R SER* 3.2 34.0 + - - +
164R LEU* 4.9 5.2 - - + -
167R LEU* 4.5 16.5 - - + +
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Residues in contact with ALA 120 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10R ALA* 3.7 22.9 - - + +
82R LEU* 4.1 13.6 - - + +
116R GLY 2.9 13.1 + - - +
117R GLY 3.0 9.6 + - - +
119R GLU* 1.3 71.5 - - - +
121R ILE* 1.3 60.4 + - - +
123R GLN* 3.3 15.3 + - - +
124R LEU* 2.9 29.3 + - - +
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Residues in contact with ILE 121 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78R THR* 3.7 33.9 - - + +
81R VAL* 3.7 28.0 - - + -
82R LEU* 3.5 24.2 - - + +
85R LEU* 4.2 8.2 - - + +
100R VAL* 4.1 21.8 - - + -
102R VAL* 4.8 6.3 - - + -
117R GLY 3.0 17.3 + - - +
118R ILE* 2.9 10.8 + - - +
120R ALA* 1.3 74.3 - - - +
122R VAL* 1.3 66.1 + - + +
124R LEU* 3.2 4.8 + - - +
125R ILE* 2.9 45.6 + - + +
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Residues in contact with VAL 122 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118R ILE* 2.8 16.1 + - + +
119R GLU* 3.3 10.5 - - - +
121R ILE* 1.3 78.1 - - + +
123R GLN* 1.3 65.4 + - - +
125R ILE* 3.1 11.0 + - + +
126R ASN* 3.0 28.8 + - - +
134R ILE* 4.6 8.1 - - + +
136R VAL* 3.8 22.0 - - + -
164R LEU* 4.1 11.9 - - + -
167R LEU* 4.2 15.9 - - + -
170R VAL* 3.7 43.7 - - + -
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Residues in contact with GLN 123 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119R GLU* 2.8 22.5 + - - +
120R ALA* 3.3 17.3 - - - +
122R VAL* 1.3 74.6 - - - +
124R LEU* 1.3 63.8 + - - +
126R ASN* 3.5 11.6 + - - +
127R THR* 3.1 26.8 + - - +
167R LEU* 3.8 27.9 - - + +
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Residues in contact with LEU 124 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82R LEU* 3.9 19.3 - - + +
85R LEU* 3.8 32.3 - - + +
86R LYS* 3.9 39.3 - - + +
90R LEU* 4.6 5.8 - - + -
120R ALA 2.9 12.8 + - - +
121R ILE 3.4 8.7 - - - +
123R GLN* 1.3 75.6 - - - +
125R ILE* 1.3 62.8 + - - +
127R THR* 3.0 9.5 + - + -
128R ARG* 3.0 43.1 + - - +
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Residues in contact with ILE 125 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45R VAL* 5.0 0.7 - - + -
85R LEU* 3.8 20.4 - - + -
90R LEU* 4.3 13.0 - - + -
98R ILE* 3.8 33.0 - - + -
100R VAL* 3.6 20.4 - - + -
121R ILE* 2.9 45.6 + - + +
122R VAL* 3.1 8.5 + - - +
124R LEU* 1.3 74.7 - - - +
126R ASN* 1.3 55.9 + - - +
127R THR 3.0 1.0 + - - -
128R ARG 3.2 0.3 + - - -
129R GLN* 2.6 41.8 + - + +
132R ALA* 5.1 0.9 - - + -
134R ILE* 4.0 23.6 - - + -
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Residues in contact with ASN 126 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122R VAL* 3.0 23.1 + - - +
123R GLN* 4.1 11.6 + - - +
125R ILE* 1.3 74.2 - - - +
127R THR* 1.3 61.0 + - - +
129R GLN 4.1 11.2 - - - +
130R PRO* 3.6 22.1 - - + +
132R ALA 5.2 2.7 - - - +
134R ILE* 4.0 17.3 - - + -
167R LEU* 5.1 2.6 - - - +
168R ALA* 3.5 38.2 + - + +
169R ASN* 5.5 1.8 - - - +
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Residues in contact with THR 127 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123R GLN* 3.1 14.3 + - - +
124R LEU* 3.0 14.6 + - + +
126R ASN* 1.3 78.5 + - - +
128R ARG* 1.3 83.0 + - - +
129R GLN 3.5 0.3 + - - -
130R PRO* 3.5 12.6 - - - +
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Residues in contact with ARG 128 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85R LEU 4.6 2.7 + - - -
86R LYS* 3.4 42.8 + - - +
90R LEU* 4.1 30.2 - - + +
91R GLU* 4.0 24.1 + - - +
94R LYS* 6.1 0.3 - - - +
124R LEU* 3.0 34.1 + - + +
125R ILE 4.3 1.1 - - - +
127R THR* 1.3 91.5 - - - +
129R GLN* 1.3 68.6 + - - +
130R PRO* 3.5 5.6 - - - +
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Residues in contact with GLN 129 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90R LEU* 3.3 44.7 + - + +
92R ASN 5.3 0.2 - - - +
93R ILE* 2.8 25.2 + - - +
94R LYS* 3.4 18.2 - - - +
95R PRO* 3.4 9.3 - - - +
98R ILE* 4.5 3.8 - - + -
125R ILE* 2.6 26.0 + - + +
126R ASN* 4.1 4.6 - - - -
128R ARG* 1.3 80.9 + - - +
130R PRO* 1.3 65.3 - - - +
131R GLN* 3.2 27.0 + - - +
132R ALA* 3.0 28.0 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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