Contacts of the helix formed by residues 123 - 140 (chain B) in PDB entry 2VGB
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 SER 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B GLY* 1.3 73.8 - - - -
124B HIS* 1.3 66.4 + - - +
125B GLU* 3.0 21.6 + - - +
126B TYR* 3.2 18.0 + - - +
127B HIS* 2.9 29.1 + - - -
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Residues in contact with HIS 124 (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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119B PHE* 3.9 14.8 - + - -
123B SER* 1.3 73.4 - - - +
125B GLU* 1.3 78.8 + - - +
127B HIS* 3.2 3.2 + - - +
128B ALA* 2.9 20.1 + - - +
267B GLN* 3.6 12.7 + - - -
270B ARG* 4.0 16.9 + - - +
271B ASP* 2.8 35.2 + - - -
274B PHE* 3.3 46.4 - + + +
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Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B SER* 3.0 23.7 + - - +
124B HIS* 1.3 86.8 + - - +
126B TYR* 1.3 63.0 + - - +
128B ALA* 3.2 8.7 + - - +
129B GLU* 3.1 32.5 + - - +
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Residues in contact with TYR 126 (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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94B ILE* 5.5 4.7 - - + -
95B GLY* 4.0 16.8 - - - -
96B PRO* 4.2 6.6 - - - +
99B ARG* 2.9 72.2 + - - +
121B HIS 4.8 1.8 - - - -
122B GLY* 4.0 13.9 - - - -
123B SER* 3.2 24.0 + - - +
124B HIS 3.1 0.4 - - - -
125B GLU* 1.3 80.0 - - - +
127B HIS* 1.3 84.8 + + - +
129B GLU* 3.5 5.5 + - - -
130B SER* 3.3 15.6 + - - -
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Residues in contact with HIS 127 (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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117B LEU* 3.9 13.6 - - + +
118B ASN 3.6 23.3 - - - -
119B PHE* 3.5 52.8 - + + -
121B HIS 2.9 28.2 + - - -
122B GLY 3.5 7.9 + - - -
123B SER 2.9 24.9 + - - +
124B HIS 3.2 3.3 + - - +
126B TYR* 1.3 91.5 - + - +
128B ALA* 1.3 60.9 + - - +
130B SER* 3.2 8.5 + - - -
131B ILE* 3.0 32.2 + - - +
274B PHE* 4.2 5.6 - - + -
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Residues in contact with ALA 128 (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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124B HIS 2.9 12.9 + - - +
125B GLU* 3.4 11.9 - - - +
127B HIS* 1.3 77.7 - - - +
129B GLU* 1.3 56.8 + - + +
131B ILE* 3.2 8.0 + - - +
132B ALA* 2.9 30.5 + - - +
274B PHE* 3.8 14.9 - - + -
278B HIS* 4.1 16.4 - - + -
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Residues in contact with GLU 129 (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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99B ARG* 2.8 41.0 + - - +
125B GLU* 3.1 23.3 + - - +
126B TYR* 3.6 6.2 - - - +
127B HIS 3.3 0.2 - - - -
128B ALA* 1.3 74.7 - - + +
130B SER* 1.3 56.5 + - - +
132B ALA* 3.4 6.2 + - - +
133B ASN* 2.9 42.2 + - - +
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Residues in contact with SER 130 (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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94B ILE* 3.9 12.3 - - - +
99B ARG* 3.3 31.4 + - - +
104B LEU* 5.5 0.2 - - - +
117B LEU* 4.1 20.4 - - - -
126B TYR* 3.3 13.1 + - - -
127B HIS* 3.2 13.6 + - - -
128B ALA 3.2 0.2 - - - -
129B GLU* 1.3 76.4 - - - +
131B ILE* 1.3 66.0 + - - +
133B ASN* 3.2 5.7 + - - +
134B VAL* 2.9 29.6 + - - +
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Residues in contact with ILE 131 (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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117B LEU* 3.8 24.7 - - + -
127B HIS 3.0 18.8 + - - +
128B ALA* 3.6 7.2 - - - +
130B SER* 1.3 74.4 - - - +
132B ALA* 1.3 66.1 + - - +
134B VAL* 3.1 5.4 + - - +
135B ARG* 2.9 63.4 + - - +
153B ILE* 4.2 18.2 - - + -
274B PHE* 4.0 14.4 - - + -
278B HIS* 3.8 29.8 - - + +
280B VAL* 4.4 10.5 - - + -
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Residues in contact with ALA 132 (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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128B ALA 2.9 17.7 + - - +
129B GLU* 3.5 8.7 - - - +
131B ILE* 1.3 77.2 - - - +
133B ASN* 1.3 64.0 + - - +
135B ARG* 3.5 6.6 + - - +
136B GLU* 3.0 29.9 + - - +
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Residues in contact with ASN 133 (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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99B ARG* 2.9 35.5 + - - +
100B SER* 4.6 1.4 - - - -
101B VAL* 3.8 27.5 + - + +
104B LEU* 4.1 5.6 - - + -
129B GLU* 2.9 26.9 + - - +
130B SER* 3.2 4.9 + - - +
132B ALA* 1.3 78.9 - - - +
134B VAL* 1.3 66.3 + - - +
136B GLU* 3.3 7.8 + - - +
137B ALA* 2.9 24.3 + - - +
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Residues in contact with VAL 134 (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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94B ILE* 4.4 11.2 - - + -
104B LEU* 4.4 22.0 - - + +
108B ILE* 5.9 0.2 - - + -
112B MET* 5.3 3.4 - - + -
115B ALA* 4.1 20.4 - - + -
117B LEU* 5.4 2.0 - - + -
130B SER 2.9 20.3 + - - +
131B ILE* 3.5 7.6 - - - +
133B ASN* 1.3 74.9 - - - +
135B ARG* 1.3 56.0 + - + +
137B ALA* 2.9 4.4 + - - +
138B VAL* 2.7 53.2 + - + +
151B VAL* 4.1 17.3 - - + +
153B ILE* 4.1 21.3 - - + -
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Residues in contact with ARG 135 (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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131B ILE* 2.9 39.9 + - - +
132B ALA* 3.8 5.6 - - - +
134B VAL* 1.3 76.5 - - + +
136B GLU* 1.3 57.2 + - - +
138B VAL* 3.3 6.5 + - - +
139B GLU* 2.9 44.8 + - + +
153B ILE* 4.1 18.3 - - + +
278B HIS* 2.5 34.9 + - - +
279B GLY* 3.3 18.0 + - - -
280B VAL* 4.3 1.0 - - - +
281B ASP* 5.1 1.2 + - - -
504B ARG* 6.0 2.2 - - - +
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Residues in contact with GLU 136 (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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101B VAL* 3.8 29.1 - - + +
105B LYS* 6.1 0.4 - - - -
132B ALA 3.0 19.6 + - - +
133B ASN* 3.6 9.1 + - - +
135B ARG* 1.3 73.0 - - - +
137B ALA* 1.3 66.7 + - - +
139B GLU* 3.2 5.3 + - - +
140B SER* 3.1 23.9 + - - -
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Residues in contact with ALA 137 (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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101B VAL* 3.9 15.4 - - + +
104B LEU* 3.5 33.2 - - + -
105B LYS* 4.0 14.5 - - + +
108B ILE* 4.0 8.1 - - + -
133B ASN 2.9 13.4 + - - +
134B VAL 3.4 7.0 - - - +
136B GLU* 1.3 72.2 - - - +
138B VAL* 1.3 60.8 + - - +
140B SER* 2.7 22.6 + - - -
141B PHE* 3.3 11.6 - - - -
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Residues in contact with VAL 138 (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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108B ILE* 3.7 16.6 - - + -
134B VAL* 2.7 33.6 + - + +
135B ARG* 3.7 6.3 - - + +
137B ALA* 1.3 79.1 - - - +
139B GLU* 1.3 72.0 + - - +
140B SER 3.1 5.2 + - - -
141B PHE* 3.3 18.9 + - + +
148B TYR* 3.8 16.2 - - + +
149B ARG 3.7 23.3 - - - +
151B VAL* 3.6 33.0 - - + +
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Residues in contact with GLU 139 (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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135B ARG* 2.9 30.6 + - + +
136B GLU* 3.7 3.6 - - - +
138B VAL* 1.3 78.9 - - - +
140B SER* 1.3 59.7 + - - +
141B PHE 3.1 5.8 - - - -
142B ALA* 3.2 28.2 + - + +
148B TYR* 3.1 30.5 + - - -
518B ARG* 5.1 5.2 + - - -
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Residues in contact with SER 140 (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 LYS* 3.4 30.8 - - - +
136B GLU* 3.1 11.9 + - - -
137B ALA 2.7 19.9 + - - -
138B VAL 3.1 0.6 - - - -
139B GLU* 1.3 77.2 - - - +
141B PHE* 1.3 69.2 + - - +
142B ALA 3.4 0.8 + - - -
143B GLY* 4.7 2.6 + - - -
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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