Contacts of the helix formed by residues 120 - 137 (chain A) in PDB entry 3V9H
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 PRO 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A LEU 3.3 6.2 - - - +
119A LYS* 1.3 88.3 - - + +
121A ILE* 1.3 66.3 + - - +
122A ALA* 4.3 7.0 - - + +
123A ASP* 2.9 43.6 + - - +
124A ARG* 3.2 9.2 + - - +
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Residues in contact with ILE 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 LYS 3.6 1.6 + - - -
120A PRO* 1.3 72.0 - - + +
122A ALA* 1.3 59.7 + - + +
124A ARG* 3.1 18.4 + - + +
125A ALA* 2.7 33.7 + - + +
177A ALA* 3.5 41.7 - - + +
178A VAL* 4.3 13.0 - - + +
181A GLU* 3.3 40.2 + - + +
225A LEU* 3.5 32.8 - - + +
226A MET* 4.7 3.8 - - + -
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Residues in contact with ALA 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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120A PRO* 3.1 5.6 - - + -
121A ILE* 1.3 84.8 - - + +
123A ASP* 1.3 61.5 + - - +
125A ALA* 3.8 6.3 - - - +
126A GLN* 3.0 30.7 + - - +
178A VAL* 4.6 6.1 - - + -
24C TRP* 4.6 19.9 - - + -
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Residues in contact with ASP 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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119A LYS* 3.7 28.3 + - + +
120A PRO* 2.9 36.4 + - - +
122A ALA* 1.3 77.8 - - - +
124A ARG* 1.3 67.1 + - - +
126A GLN* 3.4 18.2 + - - +
127A ILE* 3.5 12.5 + - - +
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Residues in contact with ARG 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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116A TRP* 2.7 77.6 + - + +
117A ASP* 2.9 18.2 + - - +
119A LYS* 2.8 32.5 + - + -
120A PRO 3.7 7.6 - - - +
121A ILE* 3.1 24.8 + - + +
123A ASP* 1.3 75.4 - - - +
125A ALA* 1.3 65.1 + - - +
127A ILE* 3.1 14.6 + - - +
128A PHE* 3.4 16.3 - - - -
181A GLU* 5.5 2.8 + - - -
197A TYR 4.8 8.7 + - - -
225A LEU* 2.8 33.1 + - + +
226A MET* 3.6 14.6 + - - +
227A GLY* 3.5 7.3 - - - +
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Residues in contact with ALA 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 ILE* 2.7 20.9 + - + +
122A ALA 3.8 4.0 - - - +
124A ARG* 1.3 72.3 - - - +
126A GLN* 1.3 63.7 + - - +
128A PHE* 2.9 6.4 + - - +
129A LEU* 2.9 29.8 + - + +
174A ALA* 3.9 21.2 - - + +
178A VAL* 4.2 19.5 - - + -
225A LEU* 3.7 17.8 - - + +
24C TRP* 5.4 2.0 - - + -
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Residues in contact with GLN 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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122A ALA 3.0 14.8 + - - +
123A ASP* 3.4 13.9 - - - +
124A ARG 3.1 0.4 - - - -
125A ALA* 1.3 76.0 - - - +
127A ILE* 1.3 61.6 + - + +
129A LEU* 3.1 22.9 + - - +
130A LYS* 3.0 30.3 + - + +
24C TRP* 4.2 14.4 + - - -
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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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116A TRP* 3.8 32.5 - - + -
119A LYS* 5.4 2.9 - - + -
123A ASP 3.7 14.8 - - - +
124A ARG* 3.1 6.5 + - - +
126A GLN* 1.3 78.6 - - + +
128A PHE* 1.3 62.7 + - + +
130A LYS* 3.4 0.3 + - - +
131A ALA* 3.0 23.2 + - - +
249A LEU* 4.1 7.9 - - + +
252A ALA* 3.4 22.6 - - + +
253A GLY* 3.4 25.4 - - - +
254A LEU* 3.4 33.2 - - + +
255A PRO* 3.9 1.8 - - + -
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Residues in contact with PHE 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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116A TRP* 4.7 4.3 - + - -
124A ARG 3.4 16.2 - - - -
125A ALA* 2.9 8.0 + - - +
127A ILE* 1.3 78.5 - - + +
129A LEU* 1.3 61.9 + - - +
130A LYS 3.4 0.2 - - - -
131A ALA* 3.8 3.8 - - - -
132A ALA* 3.0 25.8 + - - +
170A PHE* 3.3 43.1 - + + +
174A ALA* 5.2 0.4 - - + -
221A GLY* 3.4 36.6 - - - -
224A ALA* 4.0 11.4 - - + -
225A LEU* 3.8 35.7 - - + -
249A LEU* 3.5 27.4 - - + -
254A LEU* 4.3 20.4 - - + -
259A ILE* 5.3 0.2 - - + -
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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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30A LEU* 4.1 24.0 - - + -
32A VAL* 5.7 0.9 - - + -
125A ALA* 2.9 21.7 + - + +
126A GLN* 3.1 27.8 + - - +
128A PHE* 1.3 76.3 - - - +
130A LYS* 1.3 60.6 + - - +
132A ALA* 3.3 4.1 - - - +
133A ASP* 3.0 35.1 + - - +
171A ARG* 3.8 42.2 + - + +
174A ALA* 3.9 11.2 - - + -
24C TRP* 4.3 15.0 - - + +
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Residues in contact with LYS 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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126A GLN* 3.0 21.5 + - + +
127A ILE 3.8 4.3 - - - +
129A LEU* 1.3 73.9 - - - +
131A ALA* 1.3 64.8 + - - +
133A ASP* 3.4 9.2 + - - +
134A MET* 2.9 32.1 + - + +
252A ALA* 4.2 19.3 - - + +
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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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127A ILE 3.0 17.4 + - - +
128A PHE 3.9 0.9 - - - +
130A LYS* 1.3 75.6 - - - +
132A ALA* 1.3 58.2 + - - +
134A MET* 3.2 4.3 + - - +
135A LEU* 2.8 36.0 + - - +
170A PHE* 3.9 13.0 - - + -
248A ILE* 4.0 15.7 - - + -
249A LEU* 3.9 22.7 - - + -
252A ALA* 3.6 15.8 - - + +
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Residues in contact with ALA 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 PHE 3.0 19.4 + - - +
129A LEU 3.3 6.5 - - - +
131A ALA* 1.3 76.7 - - - +
133A ASP* 1.3 50.8 + - - +
135A LEU* 3.1 5.9 + - - +
136A SER* 2.8 33.4 + - - -
167A ILE* 3.6 15.4 - - + +
170A PHE* 4.0 14.7 - - + -
171A ARG* 3.7 34.5 - - + +
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Residues in contact with ASP 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* 3.0 23.6 + - - +
130A LYS* 3.8 7.1 - - - +
132A ALA* 1.3 70.8 - - - +
134A MET* 1.3 65.4 + - + +
136A SER* 3.2 7.9 + - - -
137A GLY 3.1 19.2 + - - -
138A PRO* 3.8 4.7 - - - +
171A ARG* 2.9 24.0 + - - -
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Residues in contact with MET 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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130A LYS* 2.9 21.6 + - + +
131A ALA 3.4 6.1 - - - +
133A ASP* 1.3 77.4 - - + +
135A LEU* 1.3 61.6 + - - +
136A SER 3.3 0.5 + - - -
138A PRO* 3.4 14.3 - - + +
139A ARG* 2.9 64.6 + - + +
248A ILE* 3.8 25.4 - - + +
251A GLU* 3.8 14.6 - - + +
252A ALA* 4.0 26.9 - - - -
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Residues in contact with LEU 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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131A ALA 2.8 19.0 + - - +
132A ALA 3.5 5.8 - - - +
134A MET* 1.3 76.1 - - - +
136A SER* 1.3 62.2 + - - +
139A ARG* 4.3 3.6 - - + -
140A ARG* 3.2 27.0 - - - +
143A ILE* 4.0 34.2 - - + +
162A ALA 4.3 4.9 - - - +
163A ALA* 4.9 0.9 - - - +
166A LEU* 3.6 33.4 - - + -
167A ILE* 3.7 18.2 - - + +
170A PHE* 3.9 19.3 - - + -
245A VAL* 5.3 2.9 - - + -
248A ILE* 3.6 31.9 - - + -
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Residues in contact with SER 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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35A GLU* 2.7 28.8 + - - -
38A LEU* 5.6 0.7 - - - +
132A ALA 2.8 13.9 + - - -
133A ASP* 3.3 10.5 - - - -
134A MET 3.1 0.2 - - - -
135A LEU* 1.3 77.6 - - - +
137A GLY* 1.3 58.2 + - - +
140A ARG* 3.2 25.2 + - - +
167A ILE* 3.7 10.5 - - - +
171A ARG* 3.9 15.5 + - - -
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Residues in contact with GLY 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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133A ASP 3.1 9.9 + - - -
136A SER* 1.3 77.1 - - - +
138A PRO* 1.3 71.8 - - - +
139A ARG 3.3 1.3 - - - -
140A ARG* 3.1 19.8 + - - +
141A ALA 4.6 1.0 + - - -
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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