Contacts of the helix formed by residues 126 - 136 (chain B) in PDB entry 1VLH
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 126 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B THR* 4.3 7.2 - - - -
89B ARG* 4.0 22.7 - - - +
91B VAL* 5.1 1.3 - - - -
125B ILE* 1.3 78.2 - - - +
127B SER* 1.3 63.9 + - - +
128B SER* 3.5 10.6 + - - -
129B LEU* 3.0 20.2 + - - +
130B VAL* 3.2 23.4 + - - +
39D ARG* 5.1 0.3 + - - -
99D GLN* 3.2 18.5 + - - +
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Residues in contact with SER 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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9B PHE 5.2 0.2 + - - -
10B ASP* 3.6 23.5 + - - -
11B PRO* 2.6 28.4 + - - +
13B THR* 3.7 9.2 - - - +
16B HIS* 3.4 19.1 - - - -
89B ARG* 5.1 1.2 - - - +
126B SER* 1.3 72.2 - - - +
128B SER* 1.3 56.6 + - - +
130B VAL* 3.3 6.2 + - - +
131B LYS* 2.9 37.1 + - - +
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Residues in contact with SER 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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126B SER* 3.6 9.8 - - - -
127B SER* 1.3 76.0 - - - +
129B LEU* 1.3 64.6 + - - +
131B LYS* 3.4 15.3 + - - +
132B GLU* 3.0 24.9 + - - +
39D ARG* 3.4 23.2 + - - +
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Residues in contact with LEU 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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124B PHE 4.1 18.4 - - - +
125B ILE* 4.2 15.5 - - + -
126B SER* 3.0 22.1 + - - +
128B SER* 1.3 76.6 - - - +
130B VAL* 1.3 65.4 + - - +
132B GLU* 3.8 2.6 - - - +
133B VAL* 3.0 34.9 + - + +
143B TRP* 4.2 17.3 - - + -
39D ARG* 3.8 13.0 - - - +
99D GLN* 3.9 18.2 - - + +
100D MET* 5.2 1.8 - - + -
103D ALA* 3.8 33.4 - - + -
200D PNS 3.8 19.5 - - + -
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Residues in contact with VAL 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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11B PRO* 4.3 8.3 - - + -
13B THR* 4.2 8.3 - - + -
125B ILE* 5.4 1.3 - - + -
126B SER 3.2 13.2 + - - +
127B SER* 3.3 11.0 - - - +
129B LEU* 1.3 81.1 - - + +
131B LYS* 1.3 57.6 + - - +
133B VAL 3.3 0.7 + - - -
134B ALA* 2.9 27.2 + - - +
140B VAL* 3.4 15.2 - - + +
143B TRP* 3.9 26.5 - - + -
144B VAL* 3.7 28.5 - - + -
152B LEU* 3.3 29.2 - - + -
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Residues in contact with LYS 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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10B ASP* 3.0 42.6 + - - +
11B PRO* 4.1 7.6 - - + -
40B LYS* 6.0 5.7 - - - +
41B LYS 4.7 8.3 + - - -
42B CYS* 4.9 0.2 - - - +
43B MET* 3.6 46.6 - - + +
127B SER* 2.9 25.5 + - - +
128B SER* 3.7 11.5 - - - +
130B VAL* 1.3 77.5 - - - +
132B GLU* 1.3 55.1 + - - +
134B ALA* 4.0 3.8 - - - +
135B LEU* 2.8 36.9 + - - +
152B LEU* 4.4 3.6 - - + -
156B LEU* 4.7 1.7 - - - +
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Residues in contact with GLU 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 SER 3.0 15.8 + - - +
129B LEU* 3.8 3.4 - - - +
131B LYS* 1.3 77.8 - - - +
133B VAL* 1.3 62.4 + - - +
135B LEU* 3.5 8.9 + - - +
136B TYR* 3.2 28.2 + - + -
37D ASN* 4.7 0.5 - - - +
38D PRO* 3.3 39.4 - - + +
39D ARG* 2.7 45.2 + - + +
200D PNS 3.3 42.4 + - + +
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Residues in contact with VAL 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 LEU* 3.0 25.7 + - + +
132B GLU* 1.3 75.1 - - - +
134B ALA* 1.3 64.3 + - - +
136B TYR* 3.2 9.4 + - - +
138B GLY* 2.8 44.7 + - - -
140B VAL* 3.7 19.3 - - + -
143B TRP* 3.8 18.8 - - + -
71D LEU* 4.0 8.2 - - + +
107D LEU* 3.9 22.2 - - + -
200D PNS 3.6 26.0 - - + -
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Residues in contact with ALA 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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130B VAL 2.9 18.3 + - - +
131B LYS 4.0 2.0 - - - +
133B VAL* 1.3 76.4 - - - +
135B LEU* 1.3 55.8 + - - +
137B GLY* 2.7 24.6 + - - -
138B GLY 4.0 10.8 - - - +
140B VAL* 3.8 8.9 - - + +
152B LEU* 4.1 25.4 - - + -
156B LEU* 3.3 23.6 - - + +
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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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43B MET* 5.9 1.6 - - + -
131B LYS 2.8 18.5 + - - +
132B GLU* 3.6 7.2 - - - +
133B VAL 3.2 0.2 - - - -
134B ALA* 1.3 76.8 - - - +
136B TYR* 1.3 90.2 + - + +
137B GLY 3.2 0.9 + - - -
156B LEU* 3.4 30.4 - - + +
38D PRO* 4.2 15.7 - - + -
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Residues in contact with TYR 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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132B GLU 3.2 19.2 + - - -
133B VAL 3.2 2.2 + - - +
134B ALA 3.1 0.8 - - - -
135B LEU* 1.3 94.2 - - + +
137B GLY* 1.3 60.5 + - - +
138B GLY 3.3 1.3 + - - -
36D GLU* 3.4 28.0 + - - +
38D PRO* 3.5 34.5 - - + +
69D HIS 3.2 20.6 - - - -
70D GLY* 3.6 15.6 - - - -
71D LEU* 3.7 35.4 + - + +
74D ASP* 4.5 4.9 - - - +
200D PNS 3.6 33.0 - - + -
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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