Contacts of the strand formed by residues 163 - 173 (chain B) in PDB entry 3D87
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 LYS 163 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B THR* 3.7 15.9 - - - +
156B GLU* 2.3 46.0 + - + +
157B ARG 3.7 15.3 - - - +
158B VAL* 4.3 21.5 - - + +
162B ASN* 1.3 78.9 - - - +
164B GLU* 1.3 57.7 + - - +
165B TYR* 3.3 39.9 - - + +
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Residues in contact with GLU 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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96B LYS* 2.7 40.3 + - - +
123B LEU* 2.8 45.5 - - + +
124B THR 3.6 3.8 - - - +
125B THR* 4.8 0.2 - - - +
156B GLU* 3.6 5.2 - - - +
157B ARG* 3.0 58.5 + - + +
158B VAL 5.2 0.2 - - - -
159B ARG* 4.4 13.4 - - + +
162B ASN 3.7 0.4 + - - -
163B LYS* 1.3 73.4 - - - +
165B TYR* 1.3 64.1 + - - +
166B GLU* 3.8 1.6 + - - +
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Residues in contact with TYR 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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122B TRP 3.5 1.2 - - - +
123B LEU* 3.5 6.1 - - - -
124B THR* 2.4 63.8 + - + +
125B THR 2.9 30.1 - - - -
126B ILE 3.7 8.3 - - - +
127B SER* 3.8 26.6 + - - -
153B LEU* 3.5 26.9 - - + -
155B ALA 4.5 0.7 - - - -
156B GLU* 3.7 32.3 - - + -
163B LYS* 3.3 37.7 - - + +
164B GLU* 1.3 66.8 - - - +
166B GLU* 1.3 60.4 + - - +
167B TYR* 3.8 4.1 + - + -
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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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98B GLN* 5.5 1.3 + - - +
108B ARG* 4.0 9.7 + - - -
121B TRP* 3.1 30.9 + - + +
122B TRP 3.5 4.5 - - - +
123B LEU* 3.2 25.0 - - + +
153B LEU* 3.2 4.1 - - - +
154B SER* 2.4 63.2 + - - -
155B ALA 3.0 24.5 + - - +
156B GLU* 5.2 0.2 - - - -
157B ARG* 3.4 35.0 + - + +
164B GLU* 3.8 2.6 + - - +
165B TYR* 1.3 70.7 - - - +
167B TYR* 1.3 56.6 + - - +
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Residues in contact with TYR 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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121B TRP* 3.3 20.6 - - - -
122B TRP* 2.9 42.3 + + + +
124B THR* 3.5 24.9 - - + -
126B ILE 4.3 3.6 + - - -
127B SER 4.8 6.1 + - - -
130B LEU* 3.7 19.1 - - + +
132B PHE* 3.2 35.2 - + - -
151B ALA 4.6 3.1 - - - -
152B THR 2.7 23.8 - - - +
153B LEU* 3.2 38.8 - - + +
154B SER 4.2 0.4 - - - -
165B TYR* 4.1 5.0 - - + +
166B GLU* 1.3 77.2 - - - +
168B SER* 1.3 68.4 + - - +
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Residues in contact with SER 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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119B THR* 4.0 10.1 - - - +
120B CYS 3.0 15.0 - - - -
121B TRP* 3.8 13.0 + - - -
122B TRP* 4.2 4.6 - - - -
150B ALA 3.7 0.7 - - - +
151B ALA* 3.2 2.9 - - - -
152B THR* 3.0 33.6 + - - -
154B SER* 3.5 23.2 - - - -
167B TYR* 1.3 83.7 - - - +
169B VAL* 1.3 62.7 + - - +
170B GLU* 6.0 0.7 - - - +
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Residues in contact with VAL 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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119B THR* 3.1 27.9 - - - +
120B CYS* 3.3 14.7 + - + +
122B TRP* 3.4 32.1 - - + -
134B VAL* 3.8 23.1 - - + -
149B GLY 3.5 13.9 - - - +
150B ALA 4.1 16.6 - - - +
151B ALA 4.5 0.2 - - - +
168B SER* 1.3 75.2 - - - +
170B GLU* 1.3 81.3 + - - +
171B CYS* 3.4 15.5 - - - -
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Residues in contact with GLU 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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117B ARG* 3.9 26.6 - - + +
118B PHE 3.6 2.5 - - - -
119B THR* 2.4 31.0 + - + +
147B THR 3.9 0.2 - - - +
149B GLY* 2.8 31.9 + - - +
168B SER* 6.0 0.4 - - - +
169B VAL* 1.3 80.4 - - - +
171B CYS* 1.3 65.7 + - - +
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Residues in contact with CYS 171 (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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116B GLY 4.1 1.1 - - - -
117B ARG* 3.0 28.3 - - - +
118B PHE* 2.9 50.2 + - + -
120B CYS* 4.9 1.3 - - - -
134B VAL* 4.5 0.9 - - - -
136B SER* 4.7 0.4 - - - -
146B VAL* 3.8 7.2 - - + -
147B THR 3.1 10.3 - - - +
148B CYS* 3.2 24.7 - - - -
169B VAL* 3.4 16.4 - - - -
170B GLU* 1.3 83.8 - - - +
172B GLN* 1.3 60.4 + - - +
188B VAL* 5.4 0.7 - - - -
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Residues in contact with GLN 172 (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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115B SER 3.5 14.3 + - - -
116B GLY 3.3 22.0 + - - -
117B ARG* 2.7 40.1 + - + +
146B VAL* 3.3 4.2 - - - +
147B THR* 2.7 41.1 + - - +
171B CYS* 1.3 75.5 - - - +
173B GLU* 1.3 71.9 + - - +
174B ASP* 3.3 3.8 + - - +
176B ALA* 5.3 0.2 - - - +
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Residues in contact with GLU 173 (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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116B GLY* 2.8 18.6 + - - +
118B PHE* 5.6 2.0 - - + -
138B ARG* 2.7 50.8 + - - +
144B GLN* 3.2 22.2 + - - +
145B GLY 3.6 12.5 - - - +
146B VAL* 3.9 13.0 - - + +
172B GLN* 1.3 81.3 + - - +
174B ASP* 1.3 68.9 + - - +
175B SER 3.2 5.3 + - - +
176B ALA* 3.0 46.4 + - + +
177B CYS 4.6 2.2 + - - -
186B ILE* 5.2 2.9 - - + -
207B ILE* 6.4 0.2 - - + -
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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