Contacts of the helix formed by residues 120 - 137 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118B LEU 3.3 5.8 - - - +
119B LYS* 1.3 87.7 - - + +
121B ILE* 1.3 67.6 + - + +
122B ALA* 4.3 7.9 - - + +
123B ASP* 2.9 43.7 + - - +
124B ARG* 3.2 9.0 + - - +
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Residues in contact with ILE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B LYS 3.6 1.6 + - - -
120B PRO* 1.3 71.5 - - + +
122B ALA* 1.3 59.0 + - + +
124B ARG* 3.0 17.9 + - - +
125B ALA* 2.7 33.7 + - + +
177B ALA* 3.6 41.5 - - + +
178B VAL* 4.2 13.2 - - + +
181B GLU* 3.3 40.4 + - + +
225B LEU* 3.5 33.4 - - + +
226B MET* 4.7 4.3 - - + -
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Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B SER* 5.9 7.4 - - - +
120B PRO* 3.1 6.3 + - + +
121B ILE* 1.3 85.6 - - + +
123B ASP* 1.3 62.6 + - - +
125B ALA* 3.8 6.4 - - - +
126B GLN* 3.0 27.4 + - - +
178B VAL* 4.7 8.5 - - + -
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Residues in contact with ASP 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B LYS* 3.7 19.0 - - + +
120B PRO* 2.9 35.7 + - - +
122B ALA* 1.3 79.0 - - - +
124B ARG* 1.3 66.0 + - - +
126B GLN* 3.4 19.1 + - - +
127B ILE* 3.6 12.5 + - - +
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Residues in contact with ARG 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B TRP* 2.7 69.5 + - + -
117B ASP* 2.9 17.4 + - - +
119B LYS* 2.7 39.0 + - + -
120B PRO 3.7 8.1 - - - +
121B ILE* 3.0 24.0 + - - +
123B ASP* 1.3 73.7 - - - +
125B ALA* 1.3 65.8 + - - +
127B ILE* 3.1 16.8 + - - +
128B PHE* 3.4 15.9 - - - -
181B GLU* 5.5 2.2 + - - -
197B TYR 4.7 9.7 + - - -
225B LEU* 2.8 35.0 + - + +
226B MET* 3.5 15.8 + - - +
227B GLY* 3.5 7.5 - - - +
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Residues in contact with ALA 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LEU* 5.0 0.9 - - + -
121B ILE* 2.7 21.9 + - + +
122B ALA* 3.8 4.5 - - - +
124B ARG* 1.3 72.2 - - - +
126B GLN* 1.3 63.4 + - - +
128B PHE* 3.0 5.9 + - - +
129B LEU* 2.9 30.0 + - + +
174B ALA* 3.9 20.8 - - + +
178B VAL* 4.2 19.3 - - + -
225B LEU* 3.7 18.2 - - + +
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Residues in contact with GLN 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ALA 3.0 15.0 + - - +
123B ASP* 3.4 13.7 - - - +
124B ARG 3.1 0.4 - - - -
125B ALA* 1.3 76.7 - - - +
127B ILE* 1.3 56.9 + - + +
129B LEU* 3.2 12.9 + - - +
130B LYS* 3.0 28.4 + - - +
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B TRP* 3.9 32.5 - - + -
119B LYS* 5.4 2.7 - - + -
123B ASP 3.7 13.9 - - - +
124B ARG* 3.1 6.5 + - - +
126B GLN* 1.3 76.4 - - + +
128B PHE* 1.3 63.7 + - + +
130B LYS* 3.4 0.7 + - - +
131B ALA* 3.0 23.0 + - - +
249B LEU* 4.1 7.6 - - + +
252B ALA* 3.4 23.5 - - + +
253B GLY* 3.3 26.5 - - - +
254B LEU* 3.4 33.0 - - + +
255B PRO* 4.0 1.1 - - + -
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Residues in contact with PHE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B TRP* 4.7 3.4 - + - -
124B ARG 3.4 16.6 - - - -
125B ALA* 3.0 7.8 + - - +
127B ILE* 1.3 77.1 - - + +
129B LEU* 1.3 63.0 + - - +
131B ALA* 3.9 3.8 - - - -
132B ALA* 3.0 26.9 + - - +
170B PHE* 3.4 43.5 - + + +
174B ALA* 5.2 0.2 - - + -
221B GLY* 3.5 36.1 - - - -
224B ALA* 4.0 11.0 - - + -
225B LEU* 3.9 35.4 - - + -
249B LEU* 3.5 31.0 - - + -
254B LEU* 4.3 18.4 - - + -
259B ILE* 5.2 0.4 - - + -
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LEU* 3.9 32.5 - - + -
32B VAL* 5.3 3.8 - - + -
125B ALA* 2.9 23.0 + - + +
126B GLN* 3.2 12.1 + - - +
128B PHE* 1.3 77.1 - - - +
130B LYS* 1.3 56.4 + - - +
132B ALA* 3.3 4.5 - - - +
133B ASP* 3.0 34.5 + - - +
171B ARG* 3.8 41.2 + - + +
174B ALA* 3.9 10.1 - - + -
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Residues in contact with LYS 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B GLN 3.0 15.5 + - - +
127B ILE 3.7 4.3 - - - +
129B LEU* 1.3 75.3 - - - +
131B ALA* 1.3 58.9 + - - +
133B ASP* 3.4 9.2 + - - +
134B MET* 3.0 36.3 + - - +
252B ALA* 4.1 19.5 - - + +
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Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B ILE 3.0 17.9 + - - +
128B PHE 3.9 4.9 - - - +
130B LYS* 1.3 77.0 - - - +
132B ALA* 1.3 56.2 + - - +
134B MET* 3.2 3.8 + - - +
135B LEU* 2.8 35.8 + - - +
170B PHE* 3.9 10.3 - - + -
248B ILE* 4.0 15.0 - - + +
249B LEU* 3.9 22.9 - - + -
252B ALA* 3.5 15.5 - - + +
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Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B PHE 3.0 19.8 + - - +
129B LEU 3.3 6.5 - - - +
131B ALA* 1.3 75.8 - - - +
133B ASP* 1.3 57.5 + - - +
135B LEU* 3.1 5.4 + - - +
136B SER* 2.8 27.5 + - - -
167B ILE* 3.6 14.8 - - + +
170B PHE* 4.0 15.2 - - + -
171B ARG* 3.6 35.9 - - + +
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Residues in contact with ASP 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B LEU* 3.0 22.5 + - - +
130B LYS* 3.8 7.9 - - - +
131B ALA 3.3 0.2 - - - -
132B ALA* 1.3 72.7 - - - +
134B MET* 1.3 66.0 + - + +
136B SER* 3.1 4.1 + - - -
137B GLY* 3.0 19.4 + - - -
138B PRO* 3.9 5.1 - - - +
171B ARG* 2.9 28.1 + - - +
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Residues in contact with MET 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B LYS* 3.0 21.5 + - + +
131B ALA 3.4 6.3 - - - +
133B ASP* 1.3 78.7 - - + +
135B LEU* 1.3 62.1 + - - +
136B SER 3.3 0.3 + - - -
138B PRO* 3.4 14.5 - - + +
139B ARG* 2.9 64.2 + - + +
248B ILE* 3.8 25.4 - - + +
251B GLU* 3.8 13.7 - - + +
252B ALA* 4.1 25.6 - - - -
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ALA 2.8 18.7 + - - +
132B ALA* 3.5 7.2 - - - +
134B MET* 1.3 76.0 - - - +
136B SER* 1.3 63.1 + - - +
139B ARG* 4.2 3.6 - - + -
140B ARG* 3.2 27.7 - - - +
143B ILE* 4.0 33.9 - - + +
162B ALA 4.3 5.6 - - - +
163B ALA* 5.0 0.3 - - - +
166B LEU* 3.7 31.6 - - + -
167B ILE* 3.7 17.3 - - + +
170B PHE* 4.0 19.5 - - + -
245B VAL* 5.2 2.9 - - + -
248B ILE* 3.6 32.5 - - + -
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Residues in contact with SER 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B GLU* 2.4 30.1 + - - -
132B ALA 2.8 13.1 + - - -
133B ASP* 3.1 10.5 + - - -
135B LEU* 1.3 78.0 - - - +
137B GLY* 1.3 58.1 + - - +
140B ARG* 3.2 26.8 + - - +
167B ILE* 3.6 10.5 - - - +
171B ARG* 3.8 15.2 + - - -
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Residues in contact with GLY 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ASP 3.0 10.7 + - - -
135B LEU 3.4 0.2 - - - -
136B SER* 1.3 75.5 - - - +
138B PRO* 1.3 73.5 - - - +
139B ARG 3.3 1.3 - - - -
140B ARG* 3.1 19.6 + - - +
141B ALA 4.6 0.7 + - - -
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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