Contacts of the helix formed by residues 128 - 143 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127B LEU* 1.3 73.3 - - - +
129B ALA* 1.3 56.8 + - + +
130B ASP* 3.0 23.1 - - + +
131B GLU* 2.9 27.2 + - - -
132B VAL* 2.7 36.4 + - - +
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Residues in contact with ALA 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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127B LEU 3.9 0.8 + - - -
128B THR* 1.3 75.0 - - + +
130B ASP* 1.3 60.8 + - - +
132B VAL* 3.7 12.9 - - - +
133B ALA* 3.3 21.7 + - - +
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Residues in contact with ASP 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B THR* 3.6 18.7 - - + +
129B ALA* 1.3 79.3 - - - +
131B GLU* 1.3 62.9 + - + +
133B ALA* 3.4 13.4 + - - +
134B THR* 3.2 18.3 + - - -
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Residues in contact with GLU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A TYR* 4.3 4.7 + - - -
138A LEU* 3.7 19.6 - - + +
141A LYS* 2.6 33.4 + - - +
126B ASN 4.5 0.7 - - - +
127B LEU* 3.6 25.9 - - + +
128B THR* 2.9 42.8 + - - +
130B ASP* 1.3 79.4 - - + +
132B VAL* 1.3 61.4 + - - +
134B THR* 3.4 5.9 + - - -
135B LEU* 3.0 30.2 + - - +
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 5.8 2.0 - - + -
120B HIS* 4.1 17.7 - - + +
124B THR* 3.7 31.2 - - + +
127B LEU* 4.0 13.0 - - + +
128B THR 2.7 26.7 + - - +
129B ALA* 3.7 13.0 - - - +
130B ASP 3.3 0.2 - - - -
131B GLU* 1.3 74.2 - - - +
133B ALA* 1.3 56.1 + - - +
135B LEU* 3.4 7.1 + - - +
136B GLU* 3.0 51.0 + - + +
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Residues in contact with ALA 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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129B ALA 3.3 11.5 + - - +
130B ASP* 3.5 10.8 - - - +
131B GLU 3.2 0.2 - - - -
132B VAL* 1.3 78.8 - - - +
134B THR* 1.3 60.1 + - - +
136B GLU* 3.4 8.9 + - - +
137B TYR* 2.9 31.2 + - - +
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Residues in contact with THR 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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134A THR* 4.0 26.9 - - + -
138A LEU* 3.9 6.3 - - + -
130B ASP 3.2 14.1 + - - -
131B GLU* 3.7 8.3 - - - -
132B VAL 3.4 0.4 - - - -
133B ALA* 1.3 78.7 - - - +
135B LEU* 1.3 57.1 + - - +
137B TYR* 3.3 11.0 + - + +
138B LEU* 2.9 44.2 + - + +
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Residues in contact with LEU 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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14A LEU* 3.6 27.8 - - + -
18A ILE* 5.7 0.2 - - + -
135A LEU* 3.8 23.3 - - + -
138A LEU* 3.6 26.8 - - + +
139A LEU* 3.8 19.3 - - + -
142A VAL* 4.0 15.3 - - + -
127B LEU* 3.9 26.2 - - + -
131B GLU 3.0 17.9 + - - +
132B VAL* 3.6 6.3 - - - +
134B THR* 1.3 77.2 - - - +
136B GLU* 1.3 61.5 + - - +
138B LEU* 3.4 2.7 + - - +
139B LEU* 3.0 32.5 + - + +
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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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11A ILE* 4.6 13.0 - - - +
12A ILE 3.9 13.2 - - - +
13A PRO* 4.4 1.8 - - - +
14A LEU* 3.7 19.0 + - + +
17A LEU* 3.6 26.1 - - + +
120B HIS* 3.3 29.5 - - - -
132B VAL* 3.0 27.9 + - + +
133B ALA* 3.8 8.1 - - - +
135B LEU* 1.3 76.3 - - - +
137B TYR* 1.3 62.5 + - - +
139B LEU* 4.6 0.7 - - - -
140B LYS* 3.0 37.9 + - - +
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Residues in contact with TYR 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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131A GLU* 4.4 8.5 + - - -
133B ALA 2.9 17.5 + - - +
134B THR* 3.4 11.2 - - + +
136B GLU* 1.3 77.2 - - - +
138B LEU* 1.3 84.1 + - + +
140B LYS* 3.3 19.1 - - + +
141B LYS* 3.2 51.8 + - + +
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Residues in contact with LEU 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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127A LEU* 4.2 3.7 - - + +
131A GLU* 3.5 53.4 - - + +
134A THR* 3.8 26.2 - - + -
135A LEU* 3.8 25.7 - - + +
138A LEU* 4.9 1.6 - - + -
134B THR* 2.9 26.2 + - + +
135B LEU 4.2 2.0 - - - +
137B TYR* 1.3 95.8 - - + +
139B LEU* 1.3 64.7 + - - +
141B LYS* 3.2 22.0 + - + +
142B VAL* 3.5 13.0 + - - +
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Residues in contact with LEU 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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14A LEU* 3.9 26.2 - - + -
17A LEU* 4.3 18.4 - - + -
18A ILE* 4.1 19.3 - - + +
21A VAL* 3.7 39.9 - - + +
135A LEU* 3.9 23.3 - - + -
139A LEU* 4.5 9.6 - - + -
18B ILE* 4.6 9.2 - - + -
135B LEU* 3.0 28.4 + - + +
136B GLU 3.8 3.8 - - - +
138B LEU* 1.3 75.2 - - - +
140B LYS* 1.3 63.3 + - - +
142B VAL* 3.2 18.8 + - + +
143B LEU* 3.8 3.7 + - - +
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Residues in contact with LYS 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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9A ASN* 4.8 14.5 - - - +
10A GLU 3.2 33.4 + - - +
11A ILE* 5.1 3.4 - - - +
12A ILE* 4.3 18.7 + - + +
17A LEU* 4.1 16.1 - - + +
136B GLU* 3.0 31.6 + - - +
137B TYR* 3.3 19.5 - - + +
138B LEU 3.3 0.2 - - - -
139B LEU* 1.3 76.4 - - - +
141B LYS* 1.3 55.5 + - + +
143B LEU* 3.3 13.8 + - + +
144B PRO* 3.1 23.9 - - - +
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Residues in contact with LYS 141 (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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126A ASN* 3.2 47.4 + - + +
127A LEU* 3.6 13.7 - - + -
131A GLU* 3.8 31.8 + - - -
137B TYR* 3.2 45.3 + - + +
138B LEU* 3.2 16.3 + - + +
139B LEU 3.2 0.8 - - - -
140B LYS* 1.3 76.4 - - + +
142B VAL* 1.3 57.5 + - - +
143B LEU 3.3 0.2 - - - -
144B PRO* 3.8 5.0 - - - +
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Residues in contact with VAL 142 (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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21A VAL* 3.8 23.1 - - + -
24A LYS* 3.1 24.8 + - + -
123A LEU* 3.5 51.4 - - + +
126A ASN* 4.7 1.7 + - - +
127A LEU* 3.8 12.3 - - + -
135A LEU* 3.9 19.5 - - + -
14B LEU* 4.6 7.2 - - + -
138B LEU 3.7 13.2 - - - +
139B LEU* 3.2 11.3 + - - +
141B LYS* 1.3 76.9 - - - +
143B LEU* 1.3 58.1 + - - +
144B PRO 3.8 1.9 - - - +
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Residues in contact with LEU 143 (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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12A ILE* 5.4 3.1 - - + -
17A LEU* 4.1 24.7 - - + -
20A MET* 3.8 52.0 - - + +
21A VAL* 3.8 21.8 - - + -
24A LYS* 3.6 20.2 + - + +
139B LEU 3.8 11.7 - - - +
140B LYS* 3.3 9.2 + - + +
142B VAL* 1.3 76.0 - - - +
144B PRO* 1.4 74.7 - - + +
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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