Contacts of the helix formed by residues 126 - 136 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D THR* 4.1 7.2 - - - -
16D HIS* 6.0 0.2 - - - -
89D ARG* 3.9 24.0 - - - +
91D VAL* 5.1 1.1 - - - -
125D ILE* 1.3 76.6 - - - +
127D SER* 1.3 63.9 + - - +
128D SER* 3.6 10.7 + - - -
129D LEU* 3.1 19.6 + - - +
130D VAL* 3.2 24.6 + - - +
39F ARG* 5.5 0.2 + - - -
99F GLN* 3.4 18.0 + - - +
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Residues in contact with SER 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D SER* 6.5 0.4 - - - -
9D PHE* 4.8 0.3 + - - -
10D ASP* 3.6 24.5 + - - -
11D PRO* 2.6 26.1 + - - -
13D THR* 3.7 9.8 - - - +
16D HIS* 3.4 17.7 - - - -
40D LYS* 6.4 0.2 - - - -
89D ARG* 5.2 0.8 - - - +
126D SER* 1.3 70.9 - - - +
128D SER* 1.3 58.0 + - - +
130D VAL* 3.3 4.5 + - - +
131D LYS* 2.9 39.5 + - - +
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Residues in contact with SER 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D SER* 3.6 10.3 - - - -
127D SER* 1.3 77.9 - - - +
129D LEU* 1.3 64.8 + - - +
131D LYS* 3.4 14.6 + - - +
132D GLU* 3.0 19.6 + - - +
39F ARG* 3.0 35.7 + - - -
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Residues in contact with LEU 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D PHE 3.9 20.4 - - - +
125D ILE* 4.2 13.5 - - + -
126D SER* 3.1 18.9 + - - +
127D SER 3.3 0.2 - - - -
128D SER* 1.3 78.2 - - - +
130D VAL* 1.3 65.3 + - - +
132D GLU* 3.3 6.6 + - - +
133D VAL* 3.0 43.7 + - + +
143D TRP* 4.1 18.4 - - + -
39F ARG* 3.8 8.0 - - - +
99F GLN* 4.0 15.9 - - + +
103F ALA* 3.8 22.2 - - + -
200F PNS 3.8 22.4 - - - -
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Residues in contact with VAL 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D PRO* 4.5 7.4 - - + -
13D THR* 3.9 14.6 - - + -
125D ILE* 5.1 1.8 - - + -
126D SER 3.2 16.4 - - - +
127D SER* 3.4 10.3 - - - +
129D LEU* 1.3 77.3 - - + +
131D LYS* 1.3 57.5 + - - +
133D VAL 3.3 0.2 + - - -
134D ALA* 2.9 31.4 + - - +
140D VAL* 3.5 9.2 - - + +
143D TRP* 3.9 38.4 - - + -
144D VAL* 3.4 22.4 - - + -
152D LEU* 3.6 19.7 - - + -
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Residues in contact with LYS 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ASP* 2.8 46.0 + - - +
11D PRO* 3.9 10.3 - - + -
40D LYS* 5.8 6.5 - - - +
41D LYS 5.0 5.3 + - - -
43D MET* 4.0 42.7 - - + +
127D SER* 2.9 28.6 + - - +
128D SER* 3.7 10.7 - - - +
130D VAL* 1.3 75.7 - - - +
132D GLU* 1.3 57.7 + - - +
134D ALA* 3.9 4.6 - - - +
135D LEU* 2.9 33.4 + - - +
152D LEU* 4.3 5.2 - - + -
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Residues in contact with GLU 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D SER 3.0 16.2 + - - +
129D LEU* 3.3 8.0 + - - +
131D LYS* 1.3 76.5 - - - +
133D VAL* 1.3 62.0 + - + +
135D LEU* 3.6 9.7 + - - +
136D TYR* 3.1 32.1 + - + -
38F PRO* 3.5 39.7 - - + +
39F ARG* 2.7 42.3 + - - +
100F MET* 5.7 0.9 - - - +
200F PNS 2.8 48.6 + - - +
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Residues in contact with VAL 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D LEU* 3.0 30.7 + - + +
130D VAL 3.7 3.1 - - - +
132D GLU* 1.3 72.8 - - - +
134D ALA* 1.3 65.6 + - - +
136D TYR* 3.1 10.4 + - - +
138D GLY* 2.9 40.7 + - - -
140D VAL* 3.6 17.0 - - + -
143D TRP* 3.7 23.8 - - + -
71F LEU* 4.4 7.2 - - + +
107F LEU* 4.1 21.5 - - + -
200F PNS 4.1 16.6 - - - -
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Residues in contact with ALA 134 (chain D).
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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130D VAL 2.9 17.1 + - - +
131D LYS 3.9 3.4 - - - +
133D VAL* 1.3 76.1 - - - +
135D LEU* 1.3 55.1 + - - +
137D GLY* 2.6 25.8 + - - -
138D GLY 4.0 11.0 - - - +
140D VAL* 4.0 11.2 - - + -
152D LEU* 4.3 34.8 - - + +
153D ASN* 5.6 4.0 - - - +
156D LEU* 3.8 15.0 - - + +
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Residues in contact with LEU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D MET* 5.8 6.1 - - + -
131D LYS 2.9 16.4 + - - +
132D GLU* 3.6 18.8 - - - +
133D VAL 3.2 0.2 - - - -
134D ALA* 1.3 77.1 - - - +
136D TYR* 1.3 82.3 + - + +
137D GLY 3.3 0.4 - - - -
156D LEU* 3.5 28.2 - - + +
38F PRO* 4.4 13.9 - - + -
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Residues in contact with TYR 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D GLU* 3.1 29.8 + - + -
133D VAL 3.1 6.0 + - - +
135D LEU* 1.3 99.8 - - + +
137D GLY* 1.3 60.8 + - - +
138D GLY 3.4 1.9 + - - -
36F GLU* 2.8 26.2 + - + -
38F PRO* 3.4 24.9 - - + +
69F HIS 3.3 19.5 - - - -
70F GLY* 3.6 17.4 - - - -
71F LEU* 3.7 31.0 + - + +
74F ASP* 4.7 5.0 - - - +
200F PNS 3.3 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