Contacts of the strand formed by residues 163 - 170 (chain A) in PDB entry 4HXG
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 GLU 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A LEU* 5.5 3.8 - - - -
157A ILE* 3.4 5.7 - - - +
158A ASP* 2.9 31.5 + - + +
161A GLY* 3.4 10.5 - - - +
162A GLU* 1.3 85.4 - - - +
164A VAL* 1.3 71.1 + - - +
165A ILE* 3.6 8.1 + - + -
12C THR* 3.5 13.6 - - - +
13C LYS* 3.3 53.1 - - + +
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Residues in contact with VAL 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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101A LEU* 4.0 22.8 - - + +
155A TRP* 3.8 26.0 - - + -
156A VAL 3.5 6.7 - - - +
157A ILE* 3.9 19.7 - - + +
163A GLU* 1.3 79.8 + - - +
165A ILE* 1.3 60.8 + - - +
166A GLU 3.4 27.8 - - - +
167A GLN* 4.2 15.9 + - - +
13C LYS* 5.9 2.4 - - - +
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Residues in contact with ILE 165 (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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117A ARG* 3.7 35.0 - - + +
156A VAL* 2.9 21.7 + - + +
158A ASP* 4.1 16.4 - - + +
163A GLU* 4.0 16.8 - - + +
164A VAL* 1.3 75.4 - - - +
166A GLU* 1.3 77.4 + - + +
4C ILE* 5.8 3.5 + - - +
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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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154A PHE 3.7 0.2 - - - +
155A TRP* 3.5 0.5 - - - -
156A VAL* 2.9 49.5 + - + -
164A VAL* 3.4 6.4 - - - +
165A ILE* 1.3 97.7 - - + +
167A GLN* 1.3 69.4 + - - +
168A PHE* 5.5 0.9 - - + -
205A TRP* 3.3 31.9 - - + -
207A ASP* 4.3 17.2 - - - +
208A GLY* 4.7 2.5 + - - -
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Residues in contact with GLN 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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154A PHE 3.2 11.7 - - - +
155A TRP* 3.2 29.0 + - + +
164A VAL* 4.2 14.2 + - + +
166A GLU* 1.3 83.4 + - - +
168A PHE* 1.3 68.9 + - - +
205A TRP* 5.2 1.4 - - - -
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Residues in contact with PHE 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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153A THR* 3.7 2.1 - - - -
154A PHE* 2.8 74.4 + + + +
156A VAL* 5.7 2.9 - - + -
166A GLU 5.5 0.2 - - - -
167A GLN* 1.3 79.3 - - - +
169A GLU* 1.3 64.4 + - - +
170A LYS* 4.2 18.2 - - + -
183A ILE* 4.5 11.2 - - + -
185A VAL* 4.2 15.0 - - + -
205A TRP* 3.3 66.6 - + + +
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Residues in contact with GLU 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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124A LYS* 5.4 4.5 - - - +
151A LYS* 3.3 42.0 + - + +
152A THR 3.0 16.2 - - - +
153A THR* 4.3 12.4 - - + +
168A PHE* 1.3 78.9 - - - +
170A LYS* 1.3 71.6 + - - +
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Residues in contact with LYS 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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151A LYS* 3.7 11.7 - - - +
152A THR 2.7 28.4 + - - +
154A PHE* 3.7 19.4 - - + -
168A PHE* 4.2 17.0 - - + -
169A GLU* 1.3 79.1 - - - +
171A PRO* 1.3 77.5 - - + +
174A SER* 3.3 20.0 - - - +
185A VAL* 3.8 21.3 - - + -
187A VAL* 4.2 7.6 - - + -
203A TYR* 4.8 8.8 - - - -
205A TRP* 5.0 1.1 - - - -
210A GLU* 2.9 40.6 + - - -
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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