Contacts of the helix formed by residues 98 - 119 (chain B) in PDB entry 1V0O
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 GLU 98 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ILE* 4.2 24.9 - - + +
97B LEU* 1.3 75.0 - - - +
99B SER* 1.3 64.9 + - - +
100B VAL* 3.4 12.8 - - + +
101B THR* 3.2 22.6 + - - +
102B ALA* 3.0 20.3 + - - +
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Residues in contact with SER 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU 3.5 3.9 + - - -
98B GLU* 1.3 72.0 - - - +
100B VAL* 1.3 63.4 + - - +
102B ALA* 3.4 6.2 + - - +
103B LYS* 3.1 26.5 + - - +
252B GLY 4.8 8.7 + - - -
283B TYR* 4.6 2.3 + - - -
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Residues in contact with VAL 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLU* 4.4 16.4 - - + +
99B SER* 1.3 78.6 - - - +
101B THR* 1.3 68.3 + - - +
103B LYS* 3.6 10.7 + - + +
104B SER* 3.1 26.0 + - - -
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Residues in contact with THR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LEU* 5.5 1.8 - - + -
97B LEU* 4.9 5.8 - - + -
98B GLU* 3.2 28.1 + - - +
100B VAL* 1.3 83.0 - - - +
102B ALA* 1.3 64.2 + - - +
104B SER* 3.2 6.3 + - - -
105B PHE* 3.0 56.5 + - + -
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU* 4.5 11.1 - - + +
98B GLU 3.0 15.9 + - - +
99B SER* 3.8 7.4 - - - +
101B THR* 1.3 76.6 - - - +
103B LYS* 1.3 57.0 + - - +
105B PHE 3.5 0.2 + - - -
106B LEU* 3.0 25.5 + - - +
191B PHE* 5.5 4.9 - - + -
194B MET* 3.2 46.6 - - + +
195B VAL* 5.3 2.5 - - + +
283B TYR* 4.4 5.2 - - - +
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Residues in contact with LYS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B SER* 3.1 17.7 + - - +
100B VAL* 3.7 10.3 - - + +
101B THR 3.2 0.2 - - - -
102B ALA* 1.3 74.5 - - - +
104B SER* 1.3 58.5 + - - +
106B LEU* 3.4 1.1 + - - +
107B LEU* 2.9 28.8 + - - +
254B ASP* 5.2 4.8 + - - -
283B TYR* 2.8 71.3 + - + +
284B PHE* 3.6 18.0 - - + +
286B GLU* 3.8 3.0 + - - +
287B ASN 3.3 24.9 - - - +
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Residues in contact with SER 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B VAL* 3.1 15.7 + - - -
101B THR* 3.2 11.0 + - - -
103B LYS* 1.3 77.2 - - - +
105B PHE* 1.3 65.5 + - - +
107B LEU* 3.2 9.7 + - - +
108B GLN* 3.0 45.1 + - - +
137B GLY 4.3 3.3 + - - -
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Residues in contact with PHE 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B LEU* 3.8 14.8 - - + -
89B LEU* 3.6 29.8 - - + -
97B LEU* 3.8 21.8 - - + -
101B THR* 3.0 43.2 + - + +
102B ALA 3.8 0.2 - - - +
104B SER* 1.3 77.1 - - - +
106B LEU* 1.3 57.5 + - - +
108B GLN* 3.4 12.2 + - - +
109B LEU* 2.9 31.6 + - - +
133B ILE* 3.9 20.6 - - + -
137B GLY* 3.7 22.7 - - - -
139B LEU* 3.5 24.5 - - + +
194B MET* 3.8 14.8 - - - -
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ALA 3.0 17.4 + - - +
103B LYS* 3.7 5.6 - - - +
104B SER 3.3 0.2 - - - -
105B PHE* 1.3 75.8 - - - +
107B LEU* 1.3 57.6 + - - +
109B LEU* 3.3 8.1 + - + +
110B LEU* 2.9 37.4 + - + +
187B VAL* 3.6 31.9 - - + +
191B PHE* 3.7 50.5 - - + +
194B MET* 4.0 9.8 - - + +
260B LEU* 4.1 6.5 - - + -
264B MET* 4.4 3.4 - - + -
283B TYR* 3.8 10.3 - - + -
284B PHE* 3.7 21.5 - - + -
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LYS 2.9 17.6 + - - +
104B SER* 3.2 8.7 + - - +
106B LEU* 1.3 75.5 - - - +
108B GLN* 1.3 60.2 + - + +
110B LEU* 3.5 3.7 + - - +
111B ASN* 3.0 43.5 + - - +
279B LEU* 3.7 26.5 - - + +
284B PHE* 3.7 36.3 - - + -
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Residues in contact with GLN 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ASN* 3.4 36.1 - - - +
104B SER* 3.0 37.0 + - - +
105B PHE* 3.8 8.5 - - - +
107B LEU* 1.3 78.7 - - + +
109B LEU* 1.3 60.2 + - - +
111B ASN* 3.3 2.5 + - - +
112B GLY 3.0 24.3 + - - -
137B GLY 3.0 19.4 + - - -
138B GLU* 3.3 9.8 - - - +
139B LEU* 2.8 34.1 + - + +
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B PHE 2.9 19.0 + - - +
106B LEU* 3.7 9.9 - - + +
108B GLN* 1.3 77.3 - - - +
110B LEU* 1.3 56.6 + - - +
112B GLY* 3.3 1.9 + - - -
113B ILE* 2.9 56.5 + - + +
126B LEU* 4.3 5.2 - - + -
131B LEU* 3.7 42.0 - - + -
139B LEU* 4.1 11.8 - - + +
141B ILE* 3.8 13.1 - - + +
187B VAL* 4.0 28.0 - - + -
190B ILE* 4.2 18.6 - - + -
194B MET* 6.1 0.7 - - + -
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LEU* 2.9 16.8 + - + +
109B LEU* 1.3 77.3 - - - +
111B ASN* 1.3 56.8 + - - +
113B ILE* 4.0 3.7 - - + +
114B ALA* 2.9 31.9 + - - +
184B ILE* 5.0 4.0 - - + -
187B VAL* 4.1 20.2 - - + -
264B MET* 3.9 25.8 - - + -
275B ALA* 4.0 21.2 - - + +
278B ALA* 3.8 25.6 - - + -
279B LEU* 3.6 17.1 - - + +
284B PHE* 3.5 37.9 - - + -
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Residues in contact with ASN 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B HIS* 3.6 14.3 + - - +
61B ASN* 3.7 13.9 - - - +
107B LEU* 3.0 35.5 + - - +
108B GLN* 3.6 5.5 - - - +
110B LEU* 1.3 73.5 - - - +
112B GLY* 1.3 66.4 + - - +
114B ALA* 3.8 2.1 - - - +
115B TYR* 3.1 23.0 + - - +
279B LEU* 3.7 27.6 - - - +
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Residues in contact with GLY 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B HIS* 3.8 19.0 + - - -
61B ASN* 3.9 9.4 - - - -
62B ILE* 3.8 3.1 - - - +
108B GLN 3.0 14.1 + - - -
109B LEU 3.7 2.9 - - - -
111B ASN* 1.3 78.0 - - - +
113B ILE* 1.3 55.7 + - - +
115B TYR* 3.4 5.0 + - - +
116B CYS* 3.1 29.8 + - - -
141B ILE* 3.8 13.0 - - - -
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Residues in contact with ILE 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LEU* 2.9 39.4 + - + +
110B LEU* 4.0 6.1 - - + +
112B GLY* 1.3 71.5 - - - +
114B ALA* 1.3 61.8 + - - +
116B CYS* 3.3 9.9 + - + +
117B HIS* 3.0 57.7 + - + +
123B HIS* 6.2 1.3 - - + -
126B LEU* 3.6 15.9 - - + -
141B ILE* 3.8 12.8 - - + -
183B ASP* 4.3 7.2 - - + +
184B ILE* 4.5 4.0 - - + -
187B VAL* 3.0 36.3 - - + -
275B ALA* 4.3 7.6 - - + -
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Residues in contact with ALA 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LEU 2.9 19.2 + - - +
111B ASN* 3.8 4.5 - - - +
113B ILE* 1.3 76.1 - - - +
115B TYR* 1.3 62.6 + - - +
117B HIS* 3.4 4.5 + - - +
118B ASP* 3.0 30.1 + - - +
275B ALA* 3.7 20.1 - - + +
276B LYS* 4.5 15.7 - - + +
279B LEU* 4.2 15.3 - - + -
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Residues in contact with TYR 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B GLU 3.6 10.0 + - - -
57B LEU* 3.6 19.3 - - + -
58B LYS* 3.1 44.8 + - - +
59B HIS* 3.7 34.3 - + + +
62B ILE* 3.7 9.9 - - + -
111B ASN 3.1 11.8 + - - +
112B GLY 3.5 7.9 - - - +
113B ILE 3.2 0.2 - - - -
114B ALA* 1.3 78.3 - - - +
116B CYS* 1.3 64.6 + - - +
118B ASP* 3.2 9.3 + - + +
119B ARG* 3.0 64.8 + - + +
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Residues in contact with CYS 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B LEU* 4.0 7.6 - - - -
62B ILE* 3.6 19.7 - - - -
112B GLY 3.1 22.6 + - - -
113B ILE* 3.3 12.3 + - - +
115B TYR* 1.3 78.2 - - - +
117B HIS* 1.3 59.1 + - + +
119B ARG 3.1 8.8 + - - -
120B ARG 3.1 0.2 + - - -
121B VAL* 2.8 47.4 + - + +
123B HIS* 5.6 7.2 - - + +
141B ILE* 5.0 4.9 - - - -
144B PHE* 4.0 25.1 - - - -
183B ASP* 5.8 0.4 - - - +
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Residues in contact with HIS 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ILE* 3.0 38.9 + - + +
114B ALA* 3.8 5.2 - - - +
115B TYR 3.3 0.2 - - - -
116B CYS* 1.3 75.7 - - + +
118B ASP* 1.3 65.7 - - - +
120B ARG* 3.1 15.2 + - - +
121B VAL 3.3 17.9 - - - +
122B LEU* 4.3 1.8 - - + -
178B TYR* 4.9 2.0 + - - -
180B THR* 3.3 55.1 + - + +
183B ASP* 2.8 29.2 + - + +
184B ILE* 4.2 8.9 - - + +
275B ALA* 4.6 8.9 + - - +
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Residues in contact with ASP 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ALA* 3.0 18.2 + - - +
115B TYR* 3.5 12.1 - - - +
117B HIS* 1.3 78.0 - - - +
119B ARG* 1.3 78.5 + - - +
120B ARG* 3.3 8.2 + - - +
276B LYS* 3.0 39.5 + - - +
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Residues in contact with ARG 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B GLU* 5.3 4.6 + - + +
57B LEU* 3.8 16.2 - - + -
115B TYR* 3.0 64.3 + - + +
116B CYS 3.1 3.7 + - - +
118B ASP* 1.3 96.3 + - - +
120B ARG* 1.3 70.7 + - - +
121B VAL* 3.4 9.2 + - - +
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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
------------------------------------------------------------
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