Contacts of the helix formed by residues 119 - 133 (chain A) in PDB entry 2VSH
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 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A LYS* 5.3 2.0 - - - -
117A PHE 3.7 11.2 - - - +
118A ILE* 1.3 80.4 - - - +
120A LEU* 1.3 64.1 + - - +
121A ARG* 3.5 3.1 + - - +
122A MET* 3.2 39.1 + - + +
123A ILE* 3.1 27.3 + - - +
213A GLU* 5.2 2.6 + - + +
215A SER* 6.0 1.1 - - - +
1239A PEG 3.4 44.4 - - - +
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Residues in contact with LEU 120 (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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39A LYS* 3.6 24.6 + - - +
42A LEU* 4.6 23.3 - - + -
43A GLU* 3.7 38.8 - - + +
44A PRO* 6.4 0.4 - - + -
119A THR* 1.3 71.0 - - - +
121A ARG* 1.3 59.9 + - - +
123A ILE* 4.1 7.2 - - + +
124A GLN* 2.7 49.6 + - - +
1239A PEG 3.3 23.9 + - - +
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Residues in contact with ARG 121 (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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119A THR* 3.1 2.1 + - - +
120A LEU* 1.3 78.9 - - - +
122A MET* 1.3 78.0 + - - +
124A GLN* 3.8 7.5 - - - +
125A ASP* 2.7 78.7 + - - +
211A LYS* 2.9 50.9 + - - +
212A GLY 3.5 5.9 + - - -
213A GLU* 3.1 26.1 + - - -
1239A PEG 3.3 30.0 - - - +
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Residues in contact with MET 122 (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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117A PHE 4.7 2.9 - - - +
118A ILE* 4.1 17.3 - - + -
119A THR* 3.2 37.8 + - + +
121A ARG* 1.3 93.1 - - - +
123A ILE* 1.3 65.4 + - - +
125A ASP* 3.4 2.0 + - - +
126A ASN* 3.0 33.0 + - - +
138A THR* 5.0 2.9 - - + -
170A PRO* 4.8 7.9 - - + -
211A LYS 3.9 8.7 - - - +
212A GLY* 3.9 2.7 - - - -
213A GLU* 3.0 55.4 - - + +
216A ASN* 4.2 19.7 - - + -
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Residues in contact with ILE 123 (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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39A LYS* 3.5 27.8 - - + +
40A PHE* 3.8 33.2 - - + -
43A GLU* 4.1 17.5 - - + -
46A ILE* 4.7 2.7 - - + -
109A VAL* 5.0 4.2 - - + +
118A ILE* 3.5 23.6 - - + -
119A THR 3.1 16.7 + - - +
120A LEU* 3.6 14.6 - - + +
122A MET* 1.3 75.8 - - - +
124A GLN* 1.3 63.8 + - - +
126A ASN* 3.4 6.1 + - - +
127A ILE* 3.1 41.4 + - + +
170A PRO* 5.0 2.9 - - + -
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Residues in contact with GLN 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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43A GLU* 2.8 35.4 + - - +
44A PRO* 5.2 3.8 - - - +
120A LEU* 2.7 38.9 + - - +
121A ARG* 3.8 6.0 - - - +
123A ILE* 1.3 74.6 - - - +
125A ASP* 1.3 59.2 + - - +
127A ILE* 3.3 8.5 + - + +
128A GLN* 3.0 30.1 + - - +
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Residues in contact with ASP 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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121A ARG* 2.7 60.8 + - - +
122A MET 3.7 4.0 - - - +
124A GLN* 1.3 72.5 - - - +
126A ASN* 1.3 58.3 + - - +
128A GLN* 3.3 14.5 + - - +
129A LEU* 2.9 46.3 + - + +
210A ALA* 4.8 7.2 - - + -
211A LYS* 5.0 4.2 + - - +
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Residues in contact with ASN 126 (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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109A VAL* 4.6 3.4 - - + -
122A MET* 3.0 25.0 + - - +
123A ILE* 3.5 11.0 - - - +
125A ASP* 1.3 71.8 - - - +
127A ILE* 1.3 65.3 + - - +
130A ALA* 3.0 25.5 + - - +
136A VAL* 3.6 23.3 - - - +
138A THR* 2.9 25.9 + - - +
170A PRO* 3.4 22.9 - - + +
172A THR* 2.7 32.8 + - - +
210A ALA* 3.6 11.5 - - - +
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Residues in contact with ILE 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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0A HIS* 6.0 1.1 - - + -
2A ILE* 3.4 41.3 - - + -
43A GLU* 4.5 2.9 - - + -
45A SER* 3.6 22.2 - - - +
46A ILE* 4.2 5.6 - - + -
107A ILE* 5.1 5.9 - - + +
109A VAL* 3.8 17.7 - - + -
123A ILE* 3.1 34.2 + - + +
124A GLN* 3.3 9.6 + - + +
126A ASN* 1.3 75.5 - - - +
128A GLN* 1.3 63.8 + - - +
130A ALA* 3.4 14.7 + - - +
131A GLN* 3.5 22.8 + - + +
172A THR* 4.8 2.0 - - - -
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Residues in contact with GLN 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 GLN 3.0 17.1 + - - +
125A ASP* 3.3 16.4 + - - +
127A ILE* 1.3 77.6 - - - +
129A LEU* 1.3 69.4 + - + +
131A GLN* 3.2 37.3 + - - +
132A ASN* 3.5 7.3 + - - +
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Residues in contact with LEU 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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125A ASP* 2.9 26.3 + - + +
128A GLN* 1.3 86.8 - - + +
130A ALA* 1.3 61.1 + - - +
131A GLN 3.1 0.9 + - - -
132A ASN* 3.1 10.3 + - - +
133A HIS* 3.1 37.3 + - + +
136A VAL* 3.6 16.2 - - + -
208A ALA* 4.1 14.6 - - + -
209A LEU 3.6 21.8 - - - +
210A ALA* 3.8 20.0 - - + -
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Residues in contact with ALA 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 ILE* 4.0 19.0 - - + +
126A ASN 3.0 20.0 + - - +
127A ILE* 3.6 7.2 - - - +
128A GLN 3.3 0.4 - - - -
129A LEU* 1.3 75.7 - - - +
131A GLN* 1.3 50.9 + - - +
133A HIS 3.1 12.7 - - - +
135A ALA* 5.5 1.1 - - - -
136A VAL* 3.5 9.3 - - + +
172A THR* 3.7 24.9 - - + +
173A PHE* 5.1 2.5 - - - +
174A ARG* 2.6 33.2 + - - +
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Residues in contact with GLN 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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0A HIS* 5.4 15.0 + - + +
107A ILE* 5.4 3.4 - - + -
127A ILE* 3.5 17.4 + - + +
128A GLN* 3.3 32.9 - - - +
129A LEU 3.1 1.0 + - - -
130A ALA* 1.3 78.4 - - - +
132A ASN* 1.3 63.7 + - - +
174A ARG* 3.5 14.8 + - - +
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Residues in contact with ASN 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 GLN* 3.5 11.2 + - - +
129A LEU* 3.1 16.6 - - - +
131A GLN* 1.3 82.2 + - - +
133A HIS* 1.3 85.2 + - + +
174A ARG* 5.5 0.2 - - - -
206A ASP* 4.0 2.3 - - - +
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Residues in contact with HIS 133 (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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129A LEU* 3.1 35.8 + - + +
130A ALA* 3.1 6.3 - - - +
131A GLN 3.6 0.2 - - - -
132A ASN* 1.3 99.3 + - + +
134A ASP* 1.3 64.9 + - - +
135A ALA 3.4 12.8 - - - +
174A ARG* 2.8 23.6 + - - -
206A ASP* 2.6 38.9 + - - +
208A ALA* 3.5 24.5 - - + +
153B GLN* 5.9 2.2 - - - -
154B PHE* 6.4 0.2 - - + -
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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