Contacts of the helix formed by residues 128 - 143 (chain A) in PDB entry 3VOD
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 THR 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A ASN 4.3 0.2 + - - -
127A LEU* 1.3 75.6 - - - +
129A ALA* 1.3 63.7 + - + +
130A ASP* 3.4 22.7 - - + +
131A GLU* 3.1 27.8 + - + -
132A VAL* 2.9 27.5 + - - +
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Residues in contact with ALA 129 (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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127A LEU 3.9 0.4 + - - -
128A THR* 1.3 77.4 - - + +
130A ASP* 1.3 57.6 + - - +
132A VAL* 3.4 9.7 + - - +
133A ALA* 2.9 28.1 + - - +
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Residues in contact with ASP 130 (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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128A THR* 3.2 13.8 - - + +
129A ALA* 1.3 77.5 - - - +
131A GLU* 1.3 59.7 + - + +
133A ALA* 3.4 8.7 + - - +
134A THR* 2.9 36.9 + - - -
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Residues in contact with GLU 131 (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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126A ASN 4.2 0.9 - - - +
127A LEU* 3.5 15.6 - - + +
128A THR* 3.1 39.3 + - + +
130A ASP* 1.3 77.5 - - + +
132A VAL* 1.3 54.0 + - - +
134A THR* 3.3 5.5 + - - -
135A LEU* 2.7 36.2 + - - +
137B TYR* 4.4 8.3 + - - -
138B LEU* 3.5 31.1 - - + +
141B LYS* 3.8 25.2 + - - -
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Residues in contact with VAL 132 (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 HIS* 4.2 19.1 - - + +
124A THR* 3.7 41.3 - - + -
127A LEU* 3.8 14.1 - - + +
128A THR 2.9 24.7 + - - +
129A ALA* 3.6 10.1 - - - +
131A GLU* 1.3 75.8 - - - +
133A ALA* 1.3 55.7 - - - +
135A LEU* 3.2 7.2 + - + +
136A GLU* 2.9 41.9 + - + +
14B LEU* 5.2 3.8 - - + -
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Residues in contact with ALA 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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129A ALA 2.9 17.2 + - - +
130A ASP* 3.6 13.5 - - - +
132A VAL* 1.3 77.3 - - - +
134A THR* 1.3 61.1 + - - +
136A GLU* 3.4 9.4 + - - +
137A TYR* 3.0 24.1 + - - +
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Residues in contact with THR 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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130A ASP* 2.9 22.1 + - - -
131A GLU* 3.3 6.2 + - - -
133A ALA* 1.3 76.2 - - - +
135A LEU* 1.3 62.9 + - - +
137A TYR* 3.4 9.6 + - + +
138A LEU* 3.1 40.3 + - + +
134B THR* 4.0 10.5 - - + -
138B LEU* 3.8 17.5 - - + -
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Residues in contact with LEU 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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127A LEU* 3.7 23.8 - - + -
131A GLU 2.7 21.0 + - - +
132A VAL* 3.2 6.9 + - - +
134A THR* 1.3 74.2 - - - +
136A GLU* 1.3 61.3 + - - +
138A LEU* 3.4 2.7 + - - +
139A LEU* 3.1 32.3 + - + +
14B LEU* 3.7 26.7 - - + -
135B LEU* 3.8 22.2 - - + -
138B LEU* 3.8 23.7 - - + +
139B LEU* 3.9 22.4 - - + -
142B VAL* 3.9 18.4 - - + -
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Residues in contact with GLU 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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120A HIS* 3.6 14.6 + - - -
132A VAL* 2.9 25.6 + - - +
133A ALA* 3.9 9.1 - - - +
135A LEU* 1.3 76.9 - - - +
137A TYR* 1.3 62.6 + - - +
139A LEU* 3.4 1.9 + - - -
140A LYS* 3.0 39.8 + - - +
11B ILE* 5.3 7.6 - - - +
12B ILE 3.3 13.8 - - - +
13B PRO* 3.7 1.9 - - - +
14B LEU* 3.2 35.5 + - + +
17B LEU* 3.5 22.8 - - + +
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Residues in contact with TYR 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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133A ALA 3.0 18.4 + - - +
134A THR* 3.6 10.5 - - + +
135A LEU 3.3 0.2 - - - -
136A GLU* 1.3 77.9 - - - +
138A LEU* 1.3 80.5 + - + +
140A LYS* 3.6 15.5 - - + +
141A LYS* 2.9 58.3 + - + +
131B GLU* 4.3 3.7 + - - -
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Residues in contact with LEU 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 THR* 3.1 29.6 + - + +
135A LEU* 4.1 0.4 - - - +
137A TYR* 1.3 91.2 - - + +
139A LEU* 1.3 65.8 + - - +
141A LYS* 3.2 18.9 + - + +
142A VAL* 3.5 11.8 + - - +
127B LEU* 3.9 10.4 - - + +
131B GLU* 3.7 40.2 - - + +
134B THR* 3.9 13.5 - - + -
135B LEU* 3.6 48.9 - - + +
138B LEU* 4.9 1.8 - - + -
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Residues in contact with LEU 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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18A ILE* 4.9 3.6 - - + -
135A LEU* 3.1 27.3 + - + +
136A GLU 3.8 3.8 - - - +
138A LEU* 1.3 76.3 - - - +
140A LYS* 1.3 61.8 + - - +
142A VAL* 3.0 22.4 + - + +
143A LEU* 3.7 3.5 + - - +
14B LEU* 3.5 32.5 - - + -
17B LEU* 4.1 20.6 - - + -
18B ILE* 4.0 20.0 - - + +
21B VAL* 3.7 31.9 - - + +
135B LEU* 3.8 19.1 - - + -
139B LEU* 4.5 16.4 - - + -
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Residues in contact with LYS 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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136A GLU* 3.0 37.0 + - - +
137A TYR* 3.6 14.8 - - + +
139A LEU* 1.3 74.5 - - - +
141A LYS* 1.3 57.5 + - + +
143A LEU* 3.0 29.5 + - - +
144A PRO* 3.1 11.8 - - - +
10B GLU* 3.0 34.4 + - + +
11B ILE* 4.7 1.8 - - - +
12B ILE* 3.7 35.0 - - + +
17B LEU* 3.9 17.0 - - + +
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Residues in contact with LYS 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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137A TYR* 2.9 46.0 + - + +
138A LEU* 3.2 12.3 + - + +
139A LEU 3.1 1.0 - - - -
140A LYS* 1.3 79.2 - - + +
142A VAL* 1.3 57.5 + - - +
143A LEU 3.2 0.2 - - - -
144A PRO* 3.3 7.1 - - - +
126B ASN* 3.1 45.0 + - + +
127B LEU* 3.6 26.9 - - + -
131B GLU* 2.6 29.0 + - - +
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Residues in contact with VAL 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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14A LEU* 4.7 5.4 - - + -
18A ILE* 5.9 0.2 - - + -
138A LEU 3.5 15.5 - - - +
139A LEU* 3.0 11.8 + - + +
141A LYS* 1.3 76.5 - - - +
143A LEU* 1.3 56.0 + - - +
144A PRO 3.7 0.8 - - - +
21B VAL* 3.8 28.5 - - + -
24B LYS* 2.5 36.7 + - + +
123B LEU* 3.4 39.7 - - + +
126B ASN* 4.6 1.5 + - - +
127B LEU* 3.7 21.3 - - + -
135B LEU* 4.0 13.2 - - + -
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Residues in contact with LEU 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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139A LEU 3.9 4.9 - - - +
140A LYS* 3.0 10.5 + - - +
142A VAL* 1.3 76.1 - - - +
144A PRO* 1.3 72.1 - - + +
12B ILE* 5.8 1.3 - - + -
17B LEU* 3.8 27.1 - - + -
20B MET* 3.8 42.8 - - + +
21B VAL* 3.7 40.4 - - + +
24B LYS* 4.5 14.2 - - + +
27B ARG* 6.4 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