Contacts of the helix formed by residues 126 - 136 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C THR* 4.3 6.7 - - - -
89C ARG* 3.9 21.8 - - - +
91C VAL* 5.2 2.0 - - - -
125C ILE* 1.3 77.2 - - - +
127C SER* 1.3 63.2 + - - +
128C SER* 3.6 10.8 + - - -
129C LEU* 3.1 20.4 + - - +
130C VAL* 3.1 25.5 + - - +
39E ARG* 5.6 0.2 + - - -
99E GLN* 3.4 17.4 + - - -
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Residues in contact with SER 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C PHE 5.2 0.3 + - - -
10C ASP* 3.5 25.7 + - - -
11C PRO* 2.8 22.8 + - - +
13C THR* 4.0 10.2 - - - +
16C HIS* 3.4 18.9 - - - -
89C ARG* 5.1 2.4 - - - +
126C SER* 1.3 70.5 - - - +
128C SER* 1.3 60.7 + - - +
130C VAL* 3.2 6.5 + - - +
131C LYS* 2.9 36.5 + - - +
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Residues in contact with SER 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C SER* 3.2 10.7 - - - -
127C SER* 1.3 79.1 - - - +
129C LEU* 1.3 61.5 + - - +
131C LYS* 3.4 14.2 + - - +
132C GLU* 3.0 20.1 + - - +
39E ARG* 3.3 33.3 + - - +
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Residues in contact with LEU 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C PHE 4.1 11.7 - - - +
125C ILE* 4.0 25.6 - - + -
126C SER* 3.1 21.2 + - - +
128C SER* 1.3 74.2 - - - +
130C VAL* 1.3 64.6 + - - +
132C GLU* 3.3 3.8 + - + +
133C VAL* 3.0 27.4 + - + +
143C TRP* 3.9 25.6 - - + -
39E ARG* 3.5 10.4 - - - +
99E GLN* 4.1 19.1 - - + +
100E MET* 5.4 0.7 - - - -
103E ALA* 3.9 26.5 - - + -
200E PNS 3.9 19.5 - - + -
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Residues in contact with VAL 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C PRO* 4.3 10.3 - - + -
13C THR* 4.2 9.0 - - + -
125C ILE* 5.3 1.8 - - + -
126C SER 3.1 13.4 + - - +
127C SER* 3.3 11.0 - - - +
129C LEU* 1.3 81.6 - - + +
131C LYS* 1.3 56.8 + - - +
134C ALA* 2.9 29.6 + - - +
140C VAL* 3.5 12.3 - - + +
143C TRP* 3.9 27.8 - - + -
144C VAL* 3.6 34.3 - - + -
152C LEU* 3.6 19.1 - - + -
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Residues in contact with LYS 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ASP* 2.8 43.8 + - - +
11C PRO* 3.8 14.1 - - + -
41C LYS 5.1 4.8 + - - -
43C MET* 3.8 42.2 - - + +
127C SER* 2.9 28.0 + - - +
128C SER* 3.8 10.8 - - - +
130C VAL* 1.3 70.8 - - - +
132C GLU* 1.3 61.1 + - - +
134C ALA* 4.0 4.4 - - - +
135C LEU* 2.9 41.4 + - + +
152C LEU* 4.2 4.5 - - + -
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Residues in contact with GLU 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C SER 3.0 17.0 + - - +
129C LEU* 3.6 5.6 - - + +
131C LYS* 1.3 78.4 - - - +
133C VAL* 1.3 62.1 + - - +
135C LEU* 3.4 6.0 + - - +
136C TYR* 3.1 31.6 + - + -
37E ASN* 4.9 1.0 - - - +
38E PRO* 3.4 37.0 - - + +
39E ARG* 3.0 35.3 + - - +
100E MET* 4.3 3.8 - - - +
200E PNS 3.0 45.8 + - - +
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Residues in contact with VAL 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C LEU* 3.0 32.2 + - + +
132C GLU* 1.3 75.8 - - - +
134C ALA* 1.3 63.9 + - - +
136C TYR* 3.3 9.4 + - - +
138C GLY* 2.8 42.5 + - - -
140C VAL* 3.6 21.5 - - + -
143C TRP* 3.7 19.5 - - + -
71E LEU* 4.1 7.7 - - + +
107E LEU* 4.0 25.8 - - + -
200E PNS 4.2 16.4 - - - -
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Residues in contact with ALA 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C VAL 2.9 20.9 + - - +
131C LYS 4.0 2.9 - - - +
133C VAL* 1.3 73.2 - - - +
135C LEU* 1.3 56.9 + - + +
137C GLY* 2.7 25.3 + - - -
138C GLY 3.9 11.0 - - - +
140C VAL* 3.8 8.5 - - + +
152C LEU* 4.1 36.3 - - + +
153C ASN* 6.3 0.2 - - - -
156C LEU* 4.0 15.4 - - + +
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Residues in contact with LEU 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C MET* 3.7 31.6 - - + -
131C LYS* 2.9 25.9 + - + +
132C GLU* 3.9 7.4 - - - +
134C ALA* 1.3 77.7 - - + +
136C TYR* 1.3 64.3 + - + +
137C GLY 3.3 1.0 + - - -
152C LEU* 5.8 0.9 - - + +
155C LYS 5.5 1.3 - - - +
156C LEU* 3.9 40.5 - - + +
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Residues in contact with TYR 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C GLU* 3.1 25.2 + - + -
133C VAL 3.3 2.2 + - - -
134C ALA 3.1 0.6 - - - -
135C LEU* 1.3 81.5 - - + +
137C GLY* 1.3 61.5 + - - +
138C GLY 3.4 1.9 + - - -
36E GLU* 3.6 30.5 + - + -
38E PRO* 3.7 33.9 - - + +
69E HIS 3.1 21.3 - - - -
70E GLY* 3.5 20.8 - - - -
71E LEU* 3.6 34.4 + - + +
74E ASP* 4.6 5.0 - - - +
200E PNS 3.6 30.3 - - + -
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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