Contacts of the helix formed by residues 132 - 147 (chain A) in PDB entry 1VGX
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 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A ASP* 5.0 5.0 - - - +
54A ALA* 3.6 16.5 + - + -
55A ALA* 4.1 8.5 - - + +
58A THR* 2.9 12.4 + - - -
131A HIS* 1.3 76.9 - - - +
133A LEU* 1.3 61.4 + - - +
134A ALA* 3.4 8.8 + - - +
135A ALA* 2.9 32.4 + - + +
136A ALA* 3.1 21.5 + - - +
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Residues in contact with LEU 133 (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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58A THR* 3.9 5.8 - - - -
62A LEU* 3.9 27.6 - - + -
113A HIS* 3.7 22.4 - - + +
114A ASP* 4.9 2.9 - - - -
115A GLN 3.5 24.9 - - - +
116A PRO* 5.3 0.7 - - + -
117A ILE* 4.1 24.2 - - + +
131A HIS 4.2 0.2 - - - -
132A ASP* 1.3 70.5 + - - +
134A ALA* 1.3 67.1 + - - +
136A ALA* 3.3 1.0 + - - +
137A ARG* 2.9 48.7 + - + +
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Residues in contact with ALA 134 (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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132A ASP* 3.3 6.5 + - - +
133A LEU* 1.3 82.2 - - - +
135A ALA* 1.3 57.8 + - - +
137A ARG* 3.4 8.8 + - - +
138A GLN* 3.0 28.6 + - - +
141A ARG* 4.7 2.1 + - - -
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Residues in contact with ALA 135 (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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52A ASP* 6.0 1.8 - - + -
55A ALA* 3.8 15.9 - - + -
132A ASP* 2.9 30.3 + - - +
134A ALA* 1.3 74.0 - - - +
136A ALA* 1.3 60.5 + - - +
138A GLN* 3.3 5.9 + - - +
139A HIS* 2.9 41.5 + - + +
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Residues in contact with ALA 136 (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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55A ALA* 3.9 7.9 - - - +
58A THR* 3.6 22.9 - - + -
59A LEU* 3.7 37.3 - - + +
62A LEU* 4.5 7.2 - - + -
110A THR* 4.6 1.3 - - - -
132A ASP 3.1 18.8 + - - +
133A LEU 3.3 2.7 + - - +
135A ALA* 1.3 75.0 - - - +
137A ARG* 1.3 63.2 + - - +
139A HIS* 3.3 3.0 + - - +
140A ALA* 3.0 20.3 + - - +
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Residues in contact with ARG 137 (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 THR* 3.4 17.3 - - + +
111A ALA* 2.9 33.3 + - - +
112A GLY* 3.9 9.1 + - - -
113A HIS 3.3 25.1 + - - +
114A ASP* 3.7 23.4 - - - +
133A LEU* 2.9 40.3 + - + +
134A ALA* 3.7 7.4 - - - +
136A ALA* 1.3 78.3 - - - +
138A GLN* 1.3 55.9 + - - +
140A ALA* 3.3 3.8 + - - +
141A ARG* 2.9 53.8 + - - +
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Residues in contact with GLN 138 (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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134A ALA 3.0 18.4 + - - +
135A ALA* 3.3 6.3 + - - +
137A ARG* 1.3 73.2 - - - +
139A HIS* 1.3 61.0 + - - +
141A ARG* 3.0 38.2 + - - +
142A ASP* 2.8 66.3 + - - +
145A ASP* 4.9 3.2 + - - -
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Residues in contact with HIS 139 (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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43A PHE* 4.2 18.5 - - + -
44A LEU* 4.6 19.7 - - + +
50A ALA 5.2 0.9 - - - -
51A ILE* 3.8 49.4 - - + +
52A ASP* 4.8 2.0 + - - +
55A ALA* 4.3 7.1 - - + +
59A LEU* 4.5 4.3 - - + -
135A ALA* 2.9 34.4 + - + +
136A ALA* 3.7 5.8 - - - +
138A GLN* 1.3 76.3 - - + +
140A ALA* 1.3 62.1 + - - +
142A ASP* 3.3 13.7 + - - +
143A VAL* 3.0 27.2 + - - +
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Residues in contact with ALA 140 (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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43A PHE* 4.6 1.6 - - - -
59A LEU* 5.1 0.7 - - + -
107A LEU* 3.6 41.6 - - + +
110A THR* 3.7 17.7 - - + -
111A ALA* 3.9 3.1 - - + +
136A ALA 3.0 14.0 + - - +
137A ARG 3.5 7.9 - - - +
139A HIS* 1.3 74.3 - - - +
141A ARG* 1.3 65.5 + - - +
143A VAL* 3.3 4.2 + - - +
144A LEU* 3.1 27.6 + - - +
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Residues in contact with ARG 141 (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 ALA* 3.5 34.8 + - + +
134A ALA 4.7 1.6 + - - -
137A ARG* 2.9 44.4 + - - +
138A GLN* 3.0 52.2 + - - +
140A ALA* 1.3 76.2 - - - +
142A ASP* 1.3 57.8 + - - +
144A LEU* 3.3 10.1 + - - +
145A ASP* 2.8 41.0 + - - +
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Residues in contact with ASP 142 (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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44A LEU* 6.4 1.8 - - + -
138A GLN* 2.8 55.4 + - - +
139A HIS* 3.5 17.1 + - - +
140A ALA 3.2 0.2 - - - -
141A ARG* 1.3 72.0 - - - +
143A VAL* 1.3 63.4 + - + +
145A ASP* 3.3 8.7 + - - +
146A GLN* 3.0 42.9 + - - +
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Residues in contact with VAL 143 (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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20A PRO* 3.8 15.1 - - + +
43A PHE* 3.5 52.9 - - + +
44A LEU* 6.3 0.2 - - + -
103A PHE* 4.9 1.3 - - + -
107A LEU* 3.5 26.0 - - + -
139A HIS 3.0 12.0 + - - +
140A ALA 3.3 7.1 + - - +
142A ASP* 1.3 74.8 - - + +
144A LEU* 1.3 56.9 + - - +
146A GLN* 3.2 5.7 + - - +
147A GLY* 2.8 27.4 + - - -
148A LEU* 3.7 28.7 - - + -
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Residues in contact with LEU 144 (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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104A GLU* 3.9 39.3 - - + +
107A LEU* 3.8 19.5 - - + +
108A LYS* 3.8 38.1 - - + +
111A ALA* 4.5 4.9 - - + -
140A ALA 3.1 18.4 + - - +
141A ARG* 3.7 8.7 - - - +
143A VAL* 1.3 76.7 - - - +
145A ASP* 1.3 65.2 + - - +
147A GLY* 3.5 12.8 + - - +
148A LEU* 5.3 4.3 - - + +
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Residues in contact with ASP 145 (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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138A GLN* 4.9 2.3 + - - -
141A ARG* 2.8 35.3 + - - +
142A ASP* 3.6 11.5 + - - +
144A LEU* 1.3 79.9 - - - +
146A GLN* 1.3 63.1 + - + +
147A GLY* 4.7 0.2 - - - -
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Residues in contact with GLN 146 (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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19A ALA 4.3 4.2 - - - +
20A PRO* 3.5 27.3 - - + +
43A PHE 5.0 7.7 + - - +
44A LEU* 5.7 4.9 - - - +
142A ASP* 3.0 34.5 + - - +
143A VAL* 3.7 5.1 - - - +
145A ASP* 1.3 79.6 - - + +
147A GLY* 1.3 62.0 + - - +
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Residues in contact with GLY 147 (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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20A PRO* 3.5 17.8 - - - +
143A VAL 2.8 14.5 + - - -
144A LEU* 3.5 9.6 + - - -
145A ASP 3.4 1.8 - - - -
146A GLN* 1.3 80.8 - - - +
148A LEU* 1.3 63.9 + - - -
149A LYS* 4.0 7.8 + - - -
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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