Contacts of the helix formed by residues 108 - 125 (chain A) in PDB entry 2VK2
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 ASP 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A ALA* 1.3 71.3 - - - +
109A ASN* 1.3 57.9 + - - +
110A ILE* 3.2 13.5 + - - +
111A LEU* 3.0 40.7 + - + +
112A GLU* 3.1 26.7 + - - +
274A LEU* 3.8 25.1 - - + +
275A THR 4.5 4.7 + - - +
277A SER* 4.2 3.2 + - - +
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Residues in contact with ASN 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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91A ARG* 5.7 0.2 - - - +
92A SER* 5.5 2.8 + - - -
106A THR* 3.4 22.0 + - - +
107A ALA* 3.3 14.6 + - - +
108A ASP* 1.3 71.7 + - - +
110A ILE* 1.3 64.4 - - - +
111A LEU 3.3 0.2 - - - -
112A GLU* 2.9 29.0 + - - +
113A GLY 3.3 16.1 + - - -
141A SER* 4.9 2.8 + - - -
142A VAL* 3.4 33.1 - - - +
145A ASP* 3.7 26.2 + - + +
146A ARG* 3.5 25.8 + - + +
247A LEU* 5.2 0.2 - - - +
1298A GZL 4.6 2.6 + - - -
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Residues in contact with ILE 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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108A ASP* 3.2 8.7 + - - +
109A ASN* 1.3 76.3 - - - +
111A LEU* 1.3 63.4 + - - +
113A GLY 3.2 2.6 + - - -
114A LYS* 2.9 22.6 + - + +
145A ASP* 3.5 37.0 - - + +
148A LYS* 3.9 34.5 - - + +
149A GLY* 3.3 20.9 - - - +
152A GLU* 6.0 2.0 - - + -
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Residues in contact with LEU 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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108A ASP* 3.0 37.1 + - + +
110A ILE* 1.3 77.9 - - - +
112A GLU* 1.3 56.6 + - - +
114A LYS* 3.1 23.0 + - + +
115A LEU* 2.8 52.9 + - + +
277A SER* 4.1 24.0 - - - +
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Residues in contact with GLU 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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107A ALA* 3.4 18.6 - - - +
108A ASP 3.1 14.8 + - - +
109A ASN* 2.9 25.8 - - - +
110A ILE 3.3 0.2 - - - -
111A LEU* 1.3 77.1 - - - +
113A GLY* 1.3 63.2 + - - +
115A LEU* 3.4 11.5 + - - +
116A ILE* 3.4 12.5 + - - +
146A ARG* 2.8 31.0 + - - -
226A ILE* 3.7 23.8 - - + +
245A VAL* 3.8 24.1 - - + +
246A GLU 4.6 1.4 - - - +
247A LEU* 3.5 18.5 - - - +
277A SER* 3.6 14.9 + - - +
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Residues in contact with GLY 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 ASN 3.3 4.8 + - - -
110A ILE 3.2 6.9 + - - -
112A GLU* 1.3 77.8 - - - +
114A LYS* 1.3 56.1 + - - +
116A ILE* 3.3 3.5 + - - +
117A GLY 3.0 23.4 + - - -
146A ARG* 3.8 4.9 - - - -
149A GLY* 4.3 0.2 - - - -
150A PHE* 3.4 23.5 - - - +
196A TYR* 3.4 25.8 - - - -
226A ILE* 4.2 1.2 - - - +
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Residues in contact with LYS 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 ILE* 2.9 17.0 + - + +
111A LEU* 3.1 25.1 + - + +
113A GLY* 1.3 73.9 - - - +
115A LEU* 1.3 61.1 + - + +
118A ASP* 2.8 69.2 + - - +
149A GLY* 3.5 15.3 - - - +
152A GLU* 6.4 0.2 - - + -
153A ALA* 4.0 8.7 - - + +
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Residues in contact with LEU 115 (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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111A LEU* 2.8 40.9 + - + +
112A GLU* 3.6 5.2 - - - +
113A GLY 3.3 0.2 - - - -
114A LYS* 1.3 75.6 - - + +
116A ILE* 1.3 62.6 + - - +
118A ASP* 4.0 7.9 - - + +
119A TRP* 3.1 23.7 + - - +
245A VAL* 3.8 32.1 - - + -
277A SER* 4.0 26.2 - - - +
279A LEU* 4.3 25.4 - - + +
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Residues in contact with ILE 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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112A GLU 3.4 11.4 + - - +
113A GLY 3.3 7.5 + - - +
114A LYS 3.3 0.4 - - - -
115A LEU* 1.3 75.2 - - - +
117A GLY* 1.3 59.7 + - - +
119A TRP* 3.3 8.3 + - + +
120A LEU* 2.9 26.5 + - - +
150A PHE* 4.0 2.5 - - + -
194A MET* 4.0 19.1 - - + -
196A TYR* 3.7 31.9 - - + -
224A GLY* 4.0 4.5 - - - -
225A SER 3.5 32.5 - - - +
226A ILE* 4.3 2.2 - - + -
243A ALA* 4.0 14.4 - - + +
245A VAL* 3.8 16.2 - - + -
279A LEU* 3.9 14.1 - - + -
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Residues in contact with GLY 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 GLY 3.0 11.3 + - - -
114A LYS 3.7 2.2 - - - -
116A ILE* 1.3 77.1 - - - +
118A ASP* 1.3 60.2 + - - +
120A LEU* 3.2 2.8 + - - +
121A VAL* 3.0 28.1 + - - +
150A PHE* 3.6 23.1 - - - -
153A ALA* 3.7 19.1 - - - -
154A ILE* 4.2 4.6 - - - +
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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 LYS* 2.8 55.0 + - - +
115A LEU* 4.0 9.2 - - + +
117A GLY* 1.3 71.4 - - - -
119A TRP* 1.3 64.1 + - - +
121A VAL* 3.4 7.9 + - - +
122A LYS* 3.2 30.8 + - + +
153A ALA* 3.4 20.1 - - - +
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Residues in contact with TRP 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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115A LEU 3.1 19.4 + - - +
116A ILE* 3.5 14.1 - - + +
117A GLY 3.3 0.2 - - - -
118A ASP* 1.3 76.7 - - - +
120A LEU* 1.3 90.7 + - + +
122A LYS* 3.3 10.8 + - + +
123A GLU* 2.9 61.5 + - + +
194A MET* 4.3 10.5 - - + -
222A LEU* 4.4 11.7 - - + -
223A THR 4.0 8.3 - - - -
224A GLY* 4.7 0.4 - - - -
242A ASN* 3.6 35.4 + - + -
243A ALA* 3.7 20.4 - - + -
279A LEU* 4.0 15.0 - - + -
281A LEU* 3.6 32.7 - - + +
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Residues in contact with LEU 120 (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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116A ILE 2.9 16.3 + - - +
117A GLY* 3.2 6.0 + - - +
119A TRP* 1.3 90.5 - - + +
121A VAL* 1.3 66.4 + - - +
123A GLU* 3.6 2.3 - - + +
124A VAL* 3.0 43.6 + - + +
129A CYS* 4.3 2.0 - - - -
131A VAL* 3.8 20.2 - - + -
150A PHE* 3.7 28.0 - - + -
154A ILE* 4.7 0.7 - - + -
160A ILE* 4.0 19.3 - - + -
194A MET* 3.8 29.2 - - + -
222A LEU* 4.2 5.6 - - + -
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Residues in contact with VAL 121 (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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117A GLY 3.0 19.4 + - - +
118A ASP* 3.7 9.4 - - - +
119A TRP 3.3 0.2 - - - -
120A LEU* 1.3 75.0 - - - +
122A LYS* 1.3 65.4 + - + +
124A VAL* 3.9 2.3 - - - +
125A ASN* 3.1 21.3 + - - -
126A GLY 4.4 1.6 + - - -
153A ALA 3.6 22.0 - - - +
154A ILE* 4.2 3.4 - - - -
157A ALA* 4.0 18.8 - - + -
160A ILE* 3.8 22.9 - - + -
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Residues in contact with LYS 122 (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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118A ASP* 3.2 17.7 + - + +
119A TRP* 3.6 10.5 - - + +
121A VAL* 1.3 78.8 - - + +
123A GLU* 1.3 67.8 + - - +
125A ASN* 3.4 17.8 + - - +
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Residues in contact with GLU 123 (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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119A TRP* 2.9 52.3 + - + +
120A LEU* 3.1 8.0 + - + +
122A LYS* 1.3 79.7 - - - +
124A VAL* 1.3 62.0 + - + +
125A ASN* 3.6 3.3 + - - +
127A LYS* 5.1 4.0 + - - -
222A LEU* 4.0 28.6 - - + +
242A ASN* 5.5 1.3 - - - +
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Residues in contact with VAL 124 (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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120A LEU* 3.0 39.2 + - + +
121A VAL 3.9 4.3 - - - +
123A GLU* 1.3 73.6 - - - +
125A ASN* 1.3 69.5 + - - +
127A LYS* 3.0 44.5 + - + +
128A PRO 5.4 0.4 - - - +
129A CYS* 3.9 17.9 - - + -
159A ASN* 3.7 23.3 - - - +
160A ILE* 4.0 16.6 - - + -
193A CYS* 4.1 7.2 - - - -
222A LEU* 4.3 8.7 - - + -
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Residues in contact with ASN 125 (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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121A VAL 3.1 16.3 + - - -
122A LYS* 3.7 13.2 - - - +
123A GLU 3.4 3.5 - - - +
124A VAL* 1.3 78.2 - - - +
126A GLY* 1.3 58.4 + - - +
127A LYS* 3.5 8.7 + - - +
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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