Contacts of the strand formed by residues 163 - 170 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A THR* 3.3 11.1 + - - +
13A LYS* 3.4 49.6 - - + +
33A LYS* 2.9 24.6 + - - +
34A ALA 5.5 0.2 - - - +
342A ILE* 4.7 13.2 - - + -
101B LEU* 5.8 2.9 - - - -
157B ILE* 3.6 4.7 - - - +
158B ASP* 3.0 31.1 + - + +
161B GLY* 3.4 8.0 - - - +
162B GLU* 1.3 78.8 - - - +
164B VAL* 1.3 74.6 + - - +
165B ILE* 3.4 4.5 + - + -
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Residues in contact with VAL 164 (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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13A LYS* 5.6 4.9 - - - +
101B LEU* 4.2 27.1 - - + +
155B TRP* 3.5 35.9 - - + +
156B VAL 3.4 5.2 - - - +
157B ILE* 4.5 3.8 - - + +
163B GLU* 1.3 82.0 + - - +
165B ILE* 1.3 60.4 + - - +
166B GLU 3.5 26.2 - - - +
167B GLN* 4.0 13.8 + - + +
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Residues in contact with ILE 165 (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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4A ILE* 4.8 13.7 - - - +
341A LEU* 4.1 41.1 - - + +
342A ILE* 4.6 15.3 - - + -
345A LYS* 5.3 5.5 - - + +
117B ARG* 3.8 34.8 - - + -
156B VAL* 2.9 25.6 + - + +
158B ASP* 4.3 11.2 - - + +
163B GLU* 4.1 10.3 - - + +
164B VAL* 1.3 75.9 - - - +
166B GLU* 1.3 73.0 + - + +
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Residues in contact with GLU 166 (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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345A LYS* 5.6 5.7 - - - +
155B TRP* 3.4 1.4 - - - -
156B VAL* 2.7 52.1 + - + +
164B VAL* 3.5 3.8 - - - +
165B ILE* 1.3 92.5 - - + +
167B GLN* 1.3 67.6 + - - +
168B PHE* 5.4 0.7 - - + -
205B TRP* 3.2 35.0 - - + -
207B ASP* 4.1 23.1 - - - +
208B GLY* 4.4 2.7 + - - -
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Residues in contact with GLN 167 (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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154B PHE 3.0 13.2 - - - +
155B TRP* 3.3 27.1 + - + +
164B VAL* 4.0 10.6 - - + +
166B GLU* 1.3 81.4 + - - +
168B PHE* 1.3 69.2 + - - +
205B TRP* 5.2 0.9 - - - -
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Residues in contact with PHE 168 (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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153B THR* 3.7 2.9 - - - +
154B PHE* 2.9 72.2 + + + +
156B VAL* 5.6 3.6 - - + -
166B GLU 5.4 0.4 - - - -
167B GLN* 1.3 81.5 - - - +
169B GLU* 1.3 70.5 + - - +
170B LYS* 4.3 9.6 - - + -
183B ILE* 4.2 13.5 - - + -
185B VAL* 4.2 14.4 - - + -
205B TRP* 3.3 69.8 - + + +
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Residues in contact with GLU 169 (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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124B LYS* 4.6 11.1 - - - +
151B LYS* 3.4 37.8 + - + +
152B THR 3.2 14.8 - - - +
153B THR* 4.5 8.3 - - + +
154B PHE* 4.8 0.7 - - - -
168B PHE* 1.3 80.5 - - - +
170B LYS* 1.3 79.9 + - - +
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Residues in contact with LYS 170 (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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151B LYS* 3.7 14.3 - - - +
152B THR 2.9 22.7 + - - +
154B PHE* 3.9 19.3 - - + -
168B PHE* 4.3 16.6 - - + -
169B GLU* 1.3 82.8 - - - +
171B PRO* 1.3 80.4 - - + +
174B SER* 3.3 19.1 - - - +
185B VAL* 4.0 18.8 - - + -
187B VAL* 4.4 5.6 - - + -
203B TYR* 4.9 8.2 - - - -
205B TRP* 4.9 3.7 - - - +
210B GLU* 2.8 37.4 + - - -
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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