Contacts of the strand formed by residues 165 - 172 (chain A) in PDB entry 3HMX
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 TYR 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A LEU* 3.7 1.8 - - - -
124A THR* 2.9 47.1 + - - +
125A THR 3.6 12.1 - - - -
126A ILE 3.7 12.1 - - - +
127A SER* 3.4 28.8 + - - -
153A LEU* 4.2 13.5 - - + -
155A ALA 3.9 4.0 - - - -
156A GLU* 4.0 24.4 + - + -
163A LYS* 3.0 40.2 - - + +
164A GLU* 1.3 79.1 - - - +
166A GLU* 1.3 61.1 + - - +
167A TYR* 4.2 15.7 - + + -
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Residues in contact with GLU 166 (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 TRP* 4.1 28.1 - - + +
122A TRP 3.6 5.2 - - - +
123A LEU* 3.5 24.2 - - + +
153A LEU* 3.4 5.0 - - - +
154A SER* 2.8 47.5 + - - -
155A ALA* 3.7 27.6 + - + +
157A ARG* 3.6 28.4 + - + +
165A TYR* 1.3 72.3 - - - +
167A TYR* 1.3 64.2 + - - +
168A SER* 5.1 1.7 - - - -
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Residues in contact with TYR 167 (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 TRP* 3.0 5.2 - - - +
122A TRP* 2.9 59.4 + - + +
124A THR* 3.7 29.4 - - + -
126A ILE 5.1 1.8 + - - -
127A SER* 5.3 4.7 - - - -
130A LEU* 4.0 19.2 - - + +
132A PHE* 3.8 25.4 - + - -
151A ALA 4.7 3.1 - - - -
152A THR* 3.1 23.3 - - - +
153A LEU* 3.9 28.3 - - + +
165A TYR* 4.1 8.9 - - + +
166A GLU* 1.3 78.9 - - - +
168A SER* 1.3 61.1 + - - +
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Residues in contact with SER 168 (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 THR* 4.4 10.5 - - - +
120A CYS 3.1 11.9 - - - -
121A TRP* 3.8 9.6 - - - -
122A TRP* 4.9 2.0 - - - -
150A ALA 4.0 0.5 - - - +
151A ALA* 3.4 2.8 - - - -
152A THR* 2.9 38.6 + - - -
154A SER* 2.8 23.6 + - - -
166A GLU* 5.1 1.8 - - - -
167A TYR* 1.3 75.7 - - - +
169A VAL* 1.3 61.6 + - - +
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Residues in contact with VAL 169 (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 THR* 3.2 9.2 + - - -
120A CYS* 2.7 55.5 + - + +
122A TRP* 3.7 22.9 - - + -
134A VAL* 4.1 23.6 - - + -
149A GLY 4.0 25.6 - - - +
150A ALA 4.3 7.0 - - - -
151A ALA* 4.3 2.5 - - - -
168A SER* 1.3 76.4 - - - +
170A GLU* 1.3 73.0 + - - +
171A CYS* 4.5 8.1 - - - -
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Residues in contact with GLU 170 (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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112A LYS* 5.8 1.7 + - - -
117A ARG* 3.3 35.5 + - + +
118A PHE 3.7 6.7 - - - +
119A THR* 3.6 14.1 + - - +
149A GLY* 3.0 29.6 + - - +
150A ALA 5.3 0.6 + - - -
169A VAL* 1.3 77.2 - - - +
171A CYS* 1.3 71.8 + - - +
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Residues in contact with CYS 171 (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 GLY 4.2 1.1 - - - -
117A ARG* 3.2 6.9 - - - +
118A PHE* 2.8 68.5 + - + +
120A CYS* 6.0 0.2 - - - -
134A VAL* 4.9 2.9 - - - -
136A SER* 5.1 0.2 - - - -
146A VAL* 4.7 1.8 - - + -
147A THR 3.5 3.8 - - - +
148A CYS* 2.0 49.6 - - - -
169A VAL* 4.5 11.0 - - - -
170A GLU* 1.3 80.6 - - - +
172A GLN* 1.3 63.0 + - - +
188A VAL* 5.9 1.6 - - - -
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Residues in contact with GLN 172 (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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115A SER* 4.8 2.9 - - - +
116A GLY* 3.6 2.4 - - - -
117A ARG* 3.1 36.1 + - + +
145A GLY 3.2 5.9 - - - +
146A VAL* 4.1 3.6 - - - -
147A THR* 3.1 36.9 + - - +
171A CYS* 1.3 78.6 - - - +
173A GLU* 1.3 72.9 + - - +
174A ASP* 4.8 12.2 - - + +
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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