Contacts of the helix formed by residues 153 - 164 (chain A) in PDB entry 1VH7
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 LEU 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A ILE* 3.7 31.2 - - + -
131A ALA* 4.0 12.3 - - + -
138A PHE* 2.9 44.8 + - + +
140A VAL* 3.8 10.7 - - + +
151A ILE 3.5 2.4 + - - -
152A LEU* 1.3 70.3 - - - +
154A ARG* 1.3 63.4 + - - +
156A TRP 3.2 0.9 + - - -
157A VAL* 2.9 42.4 + - + +
170A LEU* 4.1 9.2 - - + -
186A MET* 3.8 20.2 - - + -
189A PHE* 4.1 6.3 - - + -
190A VAL* 3.7 24.7 - - + -
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Residues in contact with ARG 154 (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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152A LEU* 3.8 24.9 - - + +
153A LEU* 1.3 80.9 - - - +
155A ASP* 1.3 91.1 + - - +
157A VAL* 4.0 1.9 - - - +
158A VAL* 3.3 26.0 + - + +
189A PHE* 4.0 21.0 - - + -
193A LEU* 3.7 34.2 - - + +
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Residues in contact with ASP 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ILE* 4.8 5.6 - - + -
152A LEU* 3.0 27.3 + - + +
154A ARG* 1.3 114.2 + - - +
156A TRP* 1.3 63.7 + - - +
158A VAL* 3.4 6.7 + - - +
159A GLU* 3.0 22.8 + - - +
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Residues in contact with TRP 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ALA* 3.4 29.8 - - + -
107A VAL* 3.7 38.3 - - + +
110A PRO* 3.8 23.3 - - + -
113A ILE* 4.2 4.9 - - + -
127A VAL* 4.3 4.1 - - + +
128A ALA 5.2 0.8 + - - -
129A ILE* 3.7 35.6 - - + +
140A VAL* 3.8 34.7 - - + +
151A ILE* 3.9 18.3 - - + +
152A LEU 3.0 9.1 + - - +
153A LEU 3.9 1.8 - - - +
155A ASP* 1.3 74.5 - - - +
157A VAL* 1.3 59.2 + - - +
159A GLU* 3.1 21.7 + - + -
160A VAL* 2.8 55.6 + - + +
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Residues in contact with VAL 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ILE* 4.1 13.9 - - + -
153A LEU* 2.9 41.9 + - + +
154A ARG* 4.0 4.7 - - - +
156A TRP* 1.3 76.3 - - - +
158A VAL* 1.3 64.2 + - - +
160A VAL* 3.3 7.4 + - - +
161A GLU* 3.2 21.3 + - - +
168A ILE* 4.0 8.5 - - + +
170A LEU* 5.7 0.2 - - + -
190A VAL* 4.0 19.5 - - + -
193A LEU* 4.0 17.5 - - + +
194A THR* 3.7 33.7 - - + -
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Residues in contact with VAL 158 (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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154A ARG* 3.3 17.0 + - + +
155A ASP* 3.4 9.1 + - - +
156A TRP 3.2 0.2 - - - -
157A VAL* 1.3 77.4 - - - +
159A GLU* 1.3 64.3 + - - +
161A GLU* 3.4 5.0 + - - +
162A LYS* 3.0 24.9 + - + +
193A LEU* 4.0 31.4 - - + +
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Residues in contact with GLU 159 (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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110A PRO* 4.8 2.9 - - + -
155A ASP 3.0 17.5 + - - +
156A TRP* 3.1 27.3 + - + +
158A VAL* 1.3 76.2 - - - +
160A VAL* 1.3 58.8 + - - +
162A LYS* 3.1 28.1 + - - +
163A ARG* 2.7 75.4 + - + +
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Residues in contact with VAL 160 (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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113A ILE* 4.2 10.4 - - + +
127A VAL* 3.9 22.7 - - + -
129A ILE* 4.4 2.5 - - + -
156A TRP* 2.8 64.7 + - + +
157A VAL* 3.6 5.8 - - - +
158A VAL 3.3 0.2 - - - -
159A GLU* 1.3 72.9 - - - +
161A GLU* 1.3 62.6 + - - +
163A ARG* 3.4 6.4 + - - +
164A GLY 3.4 0.5 + - - -
165A ALA* 3.2 42.1 + - + +
168A ILE* 4.1 21.3 - - + -
196A LEU* 4.7 0.2 - - + -
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Residues in contact with GLU 161 (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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157A VAL 3.2 10.3 + - - +
158A VAL* 3.9 7.6 - - - +
160A VAL* 1.3 78.4 - - - +
162A LYS* 1.3 64.6 + - - +
164A GLY* 3.0 15.1 + - - +
165A ALA 4.2 1.6 + - - +
193A LEU 4.4 1.0 - - - +
194A THR* 2.5 33.5 + - - +
195A THR* 2.7 37.8 + - - +
196A LEU* 3.8 28.3 - - + +
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Residues in contact with LYS 162 (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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158A VAL* 3.0 18.7 + - + +
159A GLU* 3.1 34.1 + - - +
161A GLU* 1.3 78.2 - - - +
163A ARG* 1.3 61.8 + - + +
164A GLY* 3.4 1.2 + - - -
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Residues in contact with ARG 163 (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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110A PRO* 3.7 40.8 - - + +
111A SER* 3.8 24.4 - - - +
113A ILE* 3.9 11.4 - - + -
114A THR* 2.7 48.3 + - - +
159A GLU* 2.7 47.5 + - + +
160A VAL 3.9 4.9 - - - +
161A GLU 3.2 0.4 - - - -
162A LYS* 1.3 78.0 - - - +
164A GLY* 1.3 57.4 + - - +
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Residues in contact with GLY 164 (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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113A ILE* 3.7 4.7 - - - -
117A ALA* 3.6 11.2 - - - +
122A SER* 2.6 34.0 + - - -
161A GLU 3.0 12.4 + - - -
162A LYS 3.2 1.5 - - - -
163A ARG* 1.3 78.6 - - - +
165A ALA* 1.3 65.5 + - - +
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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