Contacts of the helix formed by residues 124 - 139 (chain A) in PDB entry 2VGL
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 ASN 124 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A SER* 3.0 13.2 + - - +
123A ARG* 1.3 75.8 - - - +
125A PRO* 1.3 68.7 - - - +
126A THR* 3.0 18.9 + - - -
127A PHE* 3.0 41.2 + - + +
128A MET* 2.8 28.3 + - - +
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Residues in contact with PRO 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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123A ARG 3.6 8.5 - - - +
124A ASN* 1.3 87.8 - - - +
126A THR* 1.3 55.9 + - - +
128A MET* 3.3 5.1 + - + +
129A GLY* 2.7 32.4 + - - -
161A MET* 3.7 32.8 - - + -
163A SER* 4.4 8.2 + - - +
164A VAL* 3.7 28.9 - - + +
137S MET* 6.5 0.2 - - + -
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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
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88A TYR* 3.7 24.2 - - + -
124A ASN* 3.0 10.2 + - - -
125A PRO* 1.3 80.6 - - - +
127A PHE* 1.3 69.2 + - + +
129A GLY* 2.9 12.3 + - - -
130A LEU* 2.9 16.2 + - + +
134S GLN* 5.0 5.3 + - - +
137S MET* 3.8 21.1 - - - +
138S LEU* 3.4 29.5 - - + +
141S LEU* 4.1 10.7 - - + +
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Residues in contact with PHE 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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86A ASN* 3.7 40.8 - - - -
88A TYR* 4.2 20.0 - - + -
91A LYS* 3.7 26.2 - - + -
119A ASP* 3.4 33.3 - - + +
122A SER* 4.1 11.2 - - - +
124A ASN* 3.0 36.9 + - + +
126A THR* 1.3 79.6 - - + +
128A MET* 1.3 66.9 + - - +
130A LEU* 3.5 11.1 + - + +
131A ALA* 3.0 26.0 + - - +
141S LEU* 5.7 1.8 - - + -
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Residues in contact with MET 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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119A ASP 3.7 17.9 + - - +
120A LEU* 3.5 23.1 - - + +
122A SER* 4.4 0.2 - - - +
123A ARG* 4.4 17.9 - - - +
124A ASN 2.8 25.3 + - - +
125A PRO* 3.5 8.7 - - - +
127A PHE* 1.3 71.7 - - - +
129A GLY* 1.3 51.7 + - - +
131A ALA* 3.1 6.3 + - - +
132A LEU* 2.8 42.6 + - + +
154A ILE* 3.8 33.4 - - + -
160A THR* 4.4 12.6 - - + -
164A VAL* 4.1 31.2 - - + -
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Residues in contact with GLY 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 PRO 2.7 19.8 + - - -
126A THR* 2.9 6.1 + - - -
128A MET* 1.3 68.9 - - - +
130A LEU* 1.3 65.1 + - - -
132A LEU* 3.1 7.4 + - - +
133A HIS* 2.8 40.9 + - - -
164A VAL* 5.0 2.6 - - - +
167A SER* 5.4 3.8 - - - -
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Residues in contact with LEU 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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88A TYR* 4.1 27.4 - - + +
91A LYS* 4.2 25.8 - - + -
92A GLN* 4.1 28.7 - - + +
95A TYR* 3.7 28.0 - - + +
126A THR* 2.9 22.3 + - + +
127A PHE* 4.0 14.4 - - + +
129A GLY* 1.3 71.0 - - - +
131A ALA* 1.3 65.5 + - - +
133A HIS* 3.2 8.2 + - - +
134A CYS* 2.8 24.6 + - - +
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Residues in contact with ALA 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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95A TYR* 4.1 15.0 - - - +
116A ILE* 4.3 10.1 - - + +
119A ASP* 3.9 15.9 - - + -
120A LEU* 3.5 22.7 - - + +
127A PHE 3.0 18.9 + - - +
128A MET 3.3 4.3 - - - +
130A LEU* 1.3 79.8 - - - +
132A LEU* 1.3 57.7 + - - +
134A CYS* 3.2 3.8 + - - +
135A ILE* 3.1 32.2 + - - +
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Residues in contact with LEU 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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120A LEU* 4.1 11.9 - - + -
128A MET* 2.8 25.2 + - + +
129A GLY* 3.8 4.5 - - - +
131A ALA* 1.3 71.0 - - - +
133A HIS* 1.3 67.3 + - - +
135A ILE* 3.4 8.2 + - + +
136A ALA* 3.0 21.7 + - - +
151A ILE* 3.5 33.0 - - + -
154A ILE* 4.9 5.4 - - + -
164A VAL* 3.7 39.3 - - + +
167A SER* 4.4 13.9 - - - +
168A ALA* 4.2 19.1 - - + +
171A CYS* 3.9 17.8 - - - +
119S LEU* 5.1 0.2 - - - +
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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 GLY* 2.8 28.0 + - - +
130A LEU* 3.7 8.4 - - + +
132A LEU* 1.3 73.2 - - - +
134A CYS* 1.3 58.5 + - - +
136A ALA* 3.0 1.9 + - - +
137A ASN* 2.7 40.1 + - - +
167A SER* 3.1 27.7 + - - -
115S ASP* 3.9 47.8 + - + +
116S GLU* 5.1 10.5 - - - -
119S LEU* 3.6 32.6 - - + +
124S ARG* 4.2 2.6 + - - -
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Residues in contact with CYS 134 (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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95A TYR* 3.4 38.1 - - + -
98A ILE* 4.0 18.2 - - - -
99A SER* 4.0 21.3 - - - +
116A ILE* 4.3 1.3 - - + -
130A LEU 2.8 7.0 + - - +
131A ALA 3.5 8.1 - - - +
133A HIS* 1.3 76.3 - - - +
135A ILE* 1.3 61.4 + - - +
137A ASN* 3.7 0.9 - - - +
138A VAL* 3.0 28.7 + - - +
143A MET* 3.4 26.0 - - + -
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Residues in contact with ILE 135 (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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116A ILE* 4.0 19.5 - - + -
120A LEU* 4.6 3.6 - - + -
131A ALA 3.1 16.0 + - - +
132A LEU* 3.6 9.9 - - - +
133A HIS 3.1 0.4 - - - -
134A CYS* 1.3 76.5 - - - +
136A ALA* 1.3 56.4 + - - +
139A GLY* 2.6 36.6 + - - -
143A MET* 4.2 19.1 - - + +
147A PHE* 3.5 40.6 - - + -
151A ILE* 4.5 13.9 - - + -
171A CYS* 3.6 17.5 - - - -
174A ARG* 4.7 0.2 - - - +
175A LEU* 4.2 22.4 - - + -
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Residues in contact with ALA 136 (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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132A LEU 3.0 14.8 + - - +
133A HIS 3.5 5.8 - - - +
135A ILE* 1.3 74.8 - - - +
137A ASN* 1.3 67.4 + - - +
171A CYS* 4.2 14.5 - - - +
174A ARG* 3.1 34.1 + - - +
119S LEU* 3.8 31.6 - - + -
120S ALA* 4.6 13.1 - - + +
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Residues in contact with ASN 137 (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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99A SER* 4.2 30.0 + - - +
133A HIS* 2.7 24.7 + - - +
134A CYS 3.7 3.4 - - - +
136A ALA* 1.3 77.9 - - - +
138A VAL* 1.3 62.4 + - - +
174A ARG* 3.3 12.8 + - - -
18S LYS* 3.9 24.2 - - - +
19S TRP 5.6 3.0 - - - +
20S TYR* 4.8 10.3 - - - -
115S ASP* 3.3 24.5 + - - -
119S LEU* 3.9 14.7 - - - +
120S ALA 5.2 0.7 + - - -
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Residues in contact with VAL 138 (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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98A ILE* 3.8 24.2 - - + +
99A SER* 4.0 12.8 - - - +
102A VAL* 3.9 29.8 - - + -
134A CYS* 3.0 24.2 + - - +
137A ASN* 1.3 74.3 - - - +
139A GLY* 1.3 66.3 + - - +
140A SER* 3.1 25.2 + - - +
143A MET* 3.9 14.1 - - + -
174A ARG* 3.7 9.4 + - - -
22S GLN* 4.0 11.1 + - - +
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Residues in contact with GLY 139 (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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135A ILE 2.6 27.2 + - - -
138A VAL* 1.3 75.2 - - - +
140A SER* 1.3 64.7 + - - +
143A MET* 4.2 5.4 - - - -
174A ARG* 4.3 11.9 - - - -
175A LEU* 4.6 16.7 - - - +
178A THR* 3.5 26.7 - - - +
179A SER* 5.1 0.5 + - - -
22S GLN* 5.2 1.1 + - - -
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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