Contacts of the helix formed by residues 123 - 133 (chain A) in PDB entry 2VLH
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 PHE 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A MET 4.0 0.4 + - - -
122A TYR* 1.3 81.0 - - - +
124A THR* 1.3 84.1 + - - +
125A THR* 3.6 11.7 - - - -
126A THR* 3.5 25.4 - - - +
127A ARG* 2.8 36.3 + - - +
185A ASN* 3.2 29.6 - - + -
186A LEU* 3.9 17.0 - - + -
214A ASP* 5.3 0.7 - - - +
381A ARG* 3.6 16.2 - - - -
1457A PM9 3.1 70.7 - + + -
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Residues in contact with THR 124 (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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122A TYR* 3.7 17.9 - - + +
123A PHE* 1.3 94.0 - - + +
125A THR* 1.3 66.0 + - - +
127A ARG* 4.0 1.6 - - - +
128A TYR* 3.1 23.9 + - - +
186A LEU* 4.6 5.2 - - + -
381A ARG* 4.2 6.7 - - - +
385A SER* 3.3 33.9 - - - +
446A LEU* 3.6 8.0 - - - +
448A PHE* 3.5 35.4 - - + -
1457A PM9 3.6 3.1 - - - +
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Residues in contact with THR 125 (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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100A ARG* 3.9 37.2 - - - +
103A GLU* 2.8 22.0 + - - -
123A PHE* 3.6 5.7 - - - -
124A THR* 1.3 79.4 + - - +
126A THR* 1.3 65.8 + - - +
128A TYR* 3.3 3.4 + - - +
129A HIS* 3.0 31.3 + - - -
446A LEU* 4.1 21.5 - - + -
449A PHE* 4.7 0.9 - - + -
1457A PM9 3.5 35.2 - - + -
284B VAL 5.3 0.4 - - - +
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Residues in contact with THR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLU* 2.7 33.7 + - + +
107A SER* 4.8 0.2 + - - -
123A PHE* 3.5 30.3 - - - +
124A THR 3.4 0.2 - - - -
125A THR* 1.3 80.1 + - - +
127A ARG* 1.3 56.2 + - - +
129A HIS* 3.3 2.6 + - - +
130A GLN* 3.0 51.7 + - + +
177A TYR* 6.0 0.4 - - - +
179A CYS* 4.1 19.3 - - - -
214A ASP* 3.9 8.8 + - - +
252A THR* 5.9 1.3 - - - +
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Residues in contact with ARG 127 (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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122A TYR* 4.1 35.4 - - + +
123A PHE 2.8 21.0 + - - +
124A THR 4.1 2.5 - - - +
126A THR* 1.3 70.6 - - - +
128A TYR* 1.3 62.1 + - - +
130A GLN* 3.2 13.1 + - - +
131A GLU* 2.8 59.1 + - + +
137A PHE* 3.8 44.7 + - + +
386A ALA 5.3 1.3 + - - -
396A HIS* 3.5 43.1 + - - -
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Residues in contact with TYR 128 (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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124A THR 3.1 18.9 + - - +
125A THR* 3.8 4.5 - - - +
126A THR 3.2 0.2 - - - -
127A ARG* 1.3 78.0 - - - +
129A HIS* 1.3 59.8 + + - +
131A GLU* 3.8 11.1 - - + -
132A LYS* 2.9 62.6 + - + +
445A GLN* 3.5 41.6 + - + +
446A LEU* 4.3 15.3 - - + -
281B LEU* 5.5 1.7 - - - +
284B VAL* 3.5 41.8 - - + +
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Residues in contact with HIS 129 (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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100A ARG* 3.7 18.9 + - + -
103A GLU* 4.0 15.3 - - + +
104A ASN* 3.7 34.2 + - + -
107A SER* 3.3 21.4 - - - +
125A THR* 3.0 27.0 + - - +
126A THR 3.9 2.7 - - - +
128A TYR* 1.3 75.8 - + - +
130A GLN* 1.3 65.2 + - - +
132A LYS* 4.2 7.4 - - - +
133A ASN* 2.7 33.2 + - - -
284B VAL* 2.9 47.4 + - + +
285B TYR* 4.1 8.7 - + - -
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Residues in contact with GLN 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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107A SER* 4.5 2.0 - - - +
111A ILE* 3.9 8.0 - - + +
117A VAL* 3.4 32.0 - - + +
126A THR* 3.0 36.5 + - + +
127A ARG* 3.3 20.7 - - - +
129A HIS* 1.3 78.6 - - - +
131A GLU* 1.3 61.4 + - + +
133A ASN* 3.3 8.1 + - - +
134A GLY 3.4 0.3 + - - -
135A ALA* 3.1 34.1 + - + +
137A PHE* 3.3 36.2 - - + +
177A TYR* 4.1 14.6 + - - +
179A CYS* 4.1 9.4 - - - +
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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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127A ARG* 2.8 63.1 + - + +
128A TYR* 3.9 11.7 - - + +
130A GLN* 1.3 70.8 - - + +
132A LYS* 1.3 58.9 + - - +
133A ASN 3.1 1.6 - - - -
134A GLY* 2.9 20.3 + - - -
135A ALA 3.5 16.7 - - - +
136A VAL* 5.6 0.4 - - - -
137A PHE* 4.8 8.1 + - - +
388A ARG 5.3 3.1 - - - +
390A ASN* 3.5 41.5 + - - +
396A HIS* 4.8 4.1 + - - -
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Residues in contact with LYS 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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128A TYR* 2.9 54.2 + - + +
129A HIS* 4.0 11.7 - - - +
131A GLU* 1.3 75.7 - - - +
133A ASN* 1.3 69.9 + - - +
134A GLY 3.3 0.9 + - - -
108B GLN* 3.2 21.4 + - - +
281B LEU* 4.5 6.7 - - - +
284B VAL* 4.9 1.3 - - + -
285B TYR* 2.9 34.0 + - + +
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Residues in contact with ASN 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ASN* 4.9 1.0 + - - -
107A SER* 3.4 32.9 - - - +
108A GLN* 3.3 28.8 - - - +
111A ILE* 3.6 17.6 - - + +
113A PRO* 4.0 16.0 - - - +
129A HIS* 2.7 32.5 + - - +
130A GLN 3.3 4.7 + - - +
131A GLU 3.1 0.6 - - - -
132A LYS* 1.3 88.4 - - - +
134A GLY* 1.3 59.0 + - - +
135A ALA 3.5 2.5 - - - -
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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