Contacts of the helix formed by residues 98 - 119 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A GLU* 6.2 0.4 - - - +
97A LEU* 1.3 75.1 - - - +
99A SER* 1.3 68.5 + - - +
100A VAL* 3.3 4.3 - - + +
101A THR* 3.0 17.7 + - - +
102A ALA* 2.9 18.8 + - - +
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Residues in contact with SER 99 (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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97A LEU 3.8 2.6 + - - -
98A GLU* 1.3 71.8 - - - +
100A VAL* 1.3 60.7 + - - +
102A ALA* 3.2 7.6 + - - +
103A LYS* 2.9 33.7 + - - +
252A GLY 5.4 5.7 + - - -
283A TYR* 4.6 2.5 + - - -
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Residues in contact with VAL 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLU* 3.2 3.8 + - + +
99A SER* 1.3 79.1 - - - +
101A THR* 1.3 63.4 + - - +
103A LYS* 3.6 10.1 + - + +
104A SER* 3.1 22.7 + - - -
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Residues in contact with THR 101 (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 LEU* 5.0 4.0 - - + -
97A LEU* 4.4 8.7 - - + -
98A GLU* 3.0 23.1 + - - +
100A VAL* 1.3 78.3 - - - +
102A ALA* 1.3 65.3 + - - +
104A SER* 3.2 6.1 + - - -
105A PHE* 3.0 55.9 + - + -
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Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 4.5 9.6 - - + +
98A GLU 2.9 12.2 + - - +
99A SER* 3.7 9.9 - - - +
101A THR* 1.3 74.7 - - - +
103A LYS* 1.3 63.9 + - - +
104A SER 3.3 0.2 + - - -
105A PHE 3.4 0.2 + - - -
106A LEU* 3.0 25.1 + - - +
191A PHE* 5.3 3.3 - - + -
194A MET* 3.9 38.8 - - + +
195A VAL* 5.0 10.3 - - + -
283A TYR* 4.7 4.5 - - - +
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Residues in contact with LYS 103 (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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99A SER* 2.9 19.2 + - - +
100A VAL* 3.8 10.5 - - + +
102A ALA* 1.3 76.7 - - - +
104A SER* 1.3 56.2 + - - +
106A LEU* 3.7 2.8 - - - +
107A LEU* 2.9 29.0 + - + +
254A ASP* 5.3 4.6 + - - -
283A TYR* 2.6 74.9 + - + +
284A PHE* 3.9 15.5 - - + -
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Residues in contact with SER 104 (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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100A VAL* 3.1 20.1 + - - -
101A THR* 3.2 8.5 + - - -
103A LYS* 1.3 74.5 - - - +
105A PHE* 1.3 68.2 + - - +
107A LEU* 3.4 10.9 + - - +
108A GLN* 3.1 42.5 + - - +
137A GLY 4.3 4.2 + - - -
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Residues in contact with PHE 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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86A LEU* 3.9 10.8 - - + -
89A LEU* 3.5 29.8 - - + -
97A LEU* 3.7 18.8 - - + -
101A THR* 3.0 33.6 + - + +
104A SER* 1.3 78.9 - - - +
106A LEU* 1.3 57.9 + - - +
108A GLN* 3.3 13.7 + - - +
109A LEU* 2.8 30.9 + - - +
133A ILE* 3.6 32.8 - - + -
137A GLY* 3.8 22.2 - - - -
139A LEU* 3.9 22.3 - - + +
194A MET* 3.7 16.4 - - - -
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Residues in contact with LEU 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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102A ALA 3.0 18.5 + - - +
103A LYS* 3.7 4.5 - - - +
105A PHE* 1.3 74.0 - - - +
107A LEU* 1.3 60.1 - - - +
109A LEU* 4.3 7.6 - - + -
110A LEU* 2.9 34.4 + - + +
187A VAL* 3.5 33.0 - - + +
191A PHE* 3.6 53.6 - - + -
194A MET* 4.0 11.1 - - + +
260A LEU* 3.8 18.8 - - + -
264A MET* 4.3 2.9 - - + -
283A TYR* 4.1 3.4 - - + -
284A PHE* 3.9 8.3 - - + -
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Residues in contact with LEU 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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103A LYS* 2.9 18.1 + - + +
104A SER* 3.8 10.3 - - - +
105A PHE 3.3 0.2 - - - -
106A LEU* 1.3 77.0 - - - +
108A GLN* 1.3 63.3 + - + +
110A LEU* 3.5 4.0 + - - +
111A ASN* 2.9 53.3 + - - +
279A LEU* 4.1 13.7 - - + +
284A PHE* 3.6 36.7 - - + -
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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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61A ASN* 3.2 35.3 + - - +
104A SER* 3.1 37.8 + - - +
105A PHE* 3.7 9.7 - - - +
107A LEU* 1.3 80.5 - - + +
109A LEU* 1.3 59.7 + - - +
111A ASN* 3.2 2.9 + - - +
112A GLY 3.0 24.6 + - - -
137A GLY 3.0 21.4 + - - -
138A GLU* 3.2 11.7 - - - +
139A LEU* 2.8 34.2 + - + +
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Residues in contact with LEU 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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105A PHE 2.8 18.3 + - - +
106A LEU* 3.7 10.5 - - + +
108A GLN* 1.3 76.1 - - - +
110A LEU* 1.3 56.8 + - - +
112A GLY* 3.4 1.6 + - - -
113A ILE* 2.9 63.1 + - + +
126A LEU* 4.6 3.8 - - + -
131A LEU* 3.9 36.3 - - + -
139A LEU* 3.8 12.4 - - + +
141A ILE* 3.9 13.9 - - + -
187A VAL* 4.0 27.8 - - + -
190A ILE* 4.3 18.2 - - + -
194A MET* 5.5 1.3 - - + -
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Residues in contact with LEU 110 (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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106A LEU* 2.9 20.5 + - + +
107A LEU 3.7 0.7 - - - +
109A LEU* 1.3 73.3 - - - +
111A ASN* 1.3 62.5 + - - +
113A ILE* 4.2 3.1 - - + +
114A ALA* 2.8 32.7 + - - +
184A ILE* 5.4 3.8 - - + -
187A VAL* 4.1 15.0 - - + -
260A LEU* 4.8 0.2 - - + -
264A MET* 3.8 28.0 - - + -
275A ALA* 4.2 19.0 - - + +
278A ALA* 3.8 25.4 - - + -
279A LEU* 3.5 18.4 - - + -
284A PHE* 3.6 36.8 - - + -
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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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59A HIS* 3.7 14.0 + - + +
61A ASN* 3.8 13.1 - - - +
107A LEU* 2.9 47.7 + - - +
108A GLN* 3.2 6.7 + - - +
110A LEU* 1.3 75.3 - - - +
112A GLY* 1.3 64.3 + - - +
114A ALA* 3.4 2.0 + - - +
115A TYR* 3.1 23.9 + - - +
279A LEU* 3.6 22.5 - - - +
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Residues in contact with GLY 112 (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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59A HIS* 3.8 18.7 + - - -
61A ASN* 4.0 7.0 - - - -
62A ILE* 3.8 3.5 - - - +
108A GLN 3.0 14.1 + - - -
109A LEU 3.7 2.7 - - - -
111A ASN* 1.3 78.2 - - - +
113A ILE* 1.3 56.3 + - - +
115A TYR* 3.5 4.0 + - - +
116A CYS* 3.2 29.1 + - - -
141A ILE* 3.8 15.7 - - - -
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Residues in contact with ILE 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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109A LEU* 2.9 30.5 + - + +
110A LEU* 4.2 4.3 - - + +
112A GLY* 1.3 73.5 - - - +
114A ALA* 1.3 67.4 + - - +
115A TYR 3.2 0.4 - - - -
116A CYS* 3.4 7.8 - - + +
117A HIS* 3.0 53.5 + - + +
123A HIS* 6.1 2.5 - - + -
126A LEU* 3.2 31.9 - - + -
141A ILE* 3.5 15.3 - - + -
183A ASP* 4.2 9.9 - - + +
184A ILE* 4.8 3.4 - - + -
187A VAL* 3.2 23.8 - - + -
275A ALA* 4.7 6.3 - - + -
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Residues in contact with ALA 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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110A LEU 2.8 19.3 + - - +
111A ASN 3.8 3.8 - - - +
113A ILE* 1.3 78.5 - - - +
115A TYR* 1.3 56.1 + - - +
117A HIS* 3.4 3.4 + - - +
118A ASP* 3.0 35.1 + - - +
275A ALA* 3.7 22.1 - - + +
276A LYS* 3.7 26.0 - - + -
279A LEU* 3.9 11.0 - - + -
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Residues in contact with TYR 115 (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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56A GLU 3.7 9.2 + - - -
57A LEU* 3.8 18.8 - - + -
58A LYS* 3.2 45.7 + - - +
59A HIS* 3.7 25.8 - + + +
62A ILE* 3.7 15.7 - - + -
111A ASN 3.1 16.6 + - - +
112A GLY 3.6 4.3 - - - +
113A ILE 3.2 0.2 - - - -
114A ALA* 1.3 74.9 - - - +
116A CYS* 1.3 68.4 + - - +
118A ASP* 3.3 7.4 + - - +
119A ARG* 3.0 69.8 + - + +
276A LYS* 6.0 0.2 - - - +
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Residues in contact with CYS 116 (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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57A LEU* 3.9 17.3 - - - -
62A ILE* 3.7 18.6 - - - -
112A GLY 3.2 19.8 + - - +
113A ILE* 3.4 14.1 - - + +
115A TYR* 1.3 82.5 - - - +
117A HIS* 1.3 59.4 + - + +
119A ARG* 3.0 14.2 + - - +
121A VAL* 2.9 41.9 + - + +
123A HIS* 5.6 6.3 - - + +
141A ILE* 5.1 4.7 - - - -
144A PHE* 4.0 17.9 - - - -
183A ASP* 5.9 0.2 - - - +
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Residues in contact with HIS 117 (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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113A ILE* 3.0 34.7 + - + +
114A ALA* 3.8 4.9 - - - +
116A CYS* 1.3 78.0 - - + +
118A ASP* 1.3 68.3 + - - +
120A ARG* 3.1 15.0 + - - +
121A VAL 3.2 20.9 - - - +
122A LEU* 4.1 4.4 - - + +
180A THR* 3.3 56.7 + - + +
183A ASP* 2.6 29.2 + - + +
184A ILE* 4.1 11.1 - - + +
275A ALA* 4.6 6.2 + - + +
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Residues in contact with ASP 118 (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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114A ALA 3.0 19.8 + - - +
115A TYR* 3.3 8.7 + - - +
117A HIS* 1.3 77.7 - - - +
119A ARG* 1.3 77.4 + - - +
120A ARG* 3.3 7.8 + - - +
276A LYS* 3.0 32.3 + - - +
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Residues in contact with ARG 119 (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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56A GLU* 5.0 14.3 + - - +
57A LEU* 3.8 16.6 - - + -
115A TYR* 3.0 62.6 + - + +
116A CYS 3.0 6.9 + - - +
118A ASP* 1.3 96.6 + - - +
120A ARG* 1.3 69.7 + - - +
121A VAL* 3.3 8.2 + - - +
149A ALA* 5.9 0.2 - - - +
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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
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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