Contacts of the helix formed by residues 157 - 164 (chain A) in PDB entry 3V3J
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 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A PHE* 3.7 29.8 - - + -
148A LEU* 4.7 5.2 - - + -
154A LYS* 3.0 18.0 + - + +
156A GLY* 1.3 75.0 - - - +
158A GLN* 1.3 65.9 + - - +
159A LYS 3.3 2.9 - - - -
160A VAL* 3.0 32.0 + - + +
161A VAL* 3.1 19.9 + - + +
184A LEU* 3.9 16.5 - - + +
216A ILE* 5.6 1.1 - - + -
218A VAL* 3.6 33.7 - - + -
222A GLN* 4.0 13.2 - - + +
226A PHE* 4.5 13.5 - - + -
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Residues in contact with GLN 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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153A ALA* 5.3 2.3 - - - +
154A LYS 3.6 2.2 + - - -
155A PRO* 3.1 17.1 + - + +
157A LEU* 1.3 79.2 - - - +
159A LYS* 1.3 57.0 + - - +
161A VAL* 3.7 18.3 - - - +
162A ASP* 2.8 67.4 + - - +
222A GLN* 2.8 35.1 + - - +
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Residues in contact with LYS 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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155A PRO 4.7 1.2 + - - -
156A GLY 4.9 1.2 + - - -
157A LEU 3.3 0.8 - - - -
158A GLN* 1.3 78.1 - - - +
160A VAL* 1.3 63.6 + - - +
162A ASP* 3.6 7.1 + - - +
163A VAL* 3.4 15.6 + - - +
175A ASP* 5.5 2.0 + - - -
176A PHE* 3.6 35.9 - - + +
177A THR* 3.4 28.3 + - - +
178A ASN* 4.8 3.7 - - - +
179A PHE* 3.9 33.2 - - + +
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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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59A ILE* 4.6 3.1 - - + -
66A PHE* 3.7 35.7 - - + -
68A VAL* 4.8 0.7 - - + -
93A PHE* 4.2 12.8 - - + -
95A PHE* 4.5 1.8 - - + -
157A LEU* 3.0 29.2 + - + +
159A LYS* 1.3 75.3 - - - +
161A VAL* 1.3 67.1 + - - +
163A VAL* 3.1 15.3 + - - +
164A LEU* 3.2 17.7 - - + +
176A PHE* 3.6 25.4 - - + -
179A PHE* 4.0 23.1 - - + -
226A PHE* 4.7 3.4 - - + -
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Residues in contact with VAL 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 LEU* 3.1 24.2 + - + +
158A GLN* 3.7 24.9 - - - +
160A VAL* 1.3 74.9 - - - +
162A ASP* 1.3 65.3 + - - +
163A VAL 3.3 0.7 + - - -
164A LEU* 3.4 16.4 + - - +
165A ASP 4.7 0.2 + - - -
221A GLU 4.8 1.1 - - - +
222A GLN* 3.7 43.1 - - + +
225A LYS* 3.4 42.4 - - + +
226A PHE* 4.3 7.9 - - + -
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Residues in contact with ASP 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 GLN* 2.8 57.1 + - - +
159A LYS* 4.0 7.0 - - - +
161A VAL* 1.3 75.5 - - - +
163A VAL* 1.3 59.6 + - - +
164A LEU 3.7 0.2 + - - -
165A ASP* 4.4 8.7 + - - +
166A SER 5.4 0.2 + - - -
225A LYS* 5.5 4.4 + - - +
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Residues in contact with VAL 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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59A ILE* 3.6 32.3 - - + -
159A LYS* 3.4 9.2 + - + +
160A VAL 3.1 14.7 + - - +
162A ASP* 1.3 76.1 - - - +
164A LEU* 1.3 61.8 + - + +
165A ASP 3.2 3.6 - - - -
166A SER* 2.7 46.3 + - - +
167A ILE* 3.8 2.8 + - + +
174A ALA* 4.0 18.2 - - + -
175A ASP 4.7 2.7 - - - +
176A PHE* 3.8 20.2 - - + -
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Residues in contact with LEU 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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59A ILE* 4.1 17.0 - - + -
66A PHE* 3.9 28.5 - - + -
160A VAL 3.2 17.7 - - - +
161A VAL* 3.4 10.7 + - - +
163A VAL* 1.3 76.8 - - - +
165A ASP* 1.3 63.0 + - - +
166A SER 3.0 0.2 - - - -
167A ILE* 3.1 29.7 + - + +
168A LYS* 3.7 1.6 + - - -
225A LYS* 3.9 20.9 - - + +
226A PHE* 3.5 43.1 - - + -
229A LEU* 3.7 21.9 - - + +
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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