Contacts of the strand formed by residues 164 - 176 (chain B) in PDB entry 3O7O
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 164 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A LYS* 3.1 44.1 + - + +
160B VAL* 3.7 2.6 - - - +
161B LEU 2.8 39.4 + - - +
162B ASN 3.3 4.5 - - - +
163B GLY* 1.3 81.5 - - - +
165B SER* 1.3 68.1 + - - +
166B VAL* 3.4 12.0 + - + +
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Residues in contact with SER 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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158B PRO* 6.6 0.4 - - - -
159B PHE 3.9 5.4 - - - -
160B VAL* 4.1 15.6 - - - +
163B GLY 4.2 1.4 + - - -
164B GLU* 1.3 74.5 - - - +
166B VAL* 1.3 63.0 + - - +
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Residues in contact with VAL 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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158B PRO* 3.3 5.8 - - - +
159B PHE* 3.0 74.4 + - + +
161B LEU* 4.0 19.1 - - + -
164B GLU* 3.7 17.9 - - + +
165B SER* 1.3 80.1 - - - +
167B GLU* 1.3 65.3 + - - +
168B GLY 3.9 0.5 + - - -
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Residues in contact with GLU 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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156B THR* 3.6 26.3 - - + +
157B ILE 4.3 2.9 - - - -
158B PRO* 4.4 15.9 - - + +
166B VAL* 1.3 76.4 - - - +
168B GLY* 1.3 61.9 + - - +
169B THR* 4.2 1.7 + - - -
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Residues in contact with GLY 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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156B THR* 3.3 6.3 - - - -
157B ILE 2.9 39.9 + - - -
159B PHE* 4.0 14.1 - - - -
166B VAL 3.9 2.2 + - - -
167B GLU* 1.3 73.9 - - - +
169B THR* 1.3 61.9 + - - -
170B TRP* 3.2 11.4 - - - -
186B LEU* 4.0 0.9 - - - -
265B BR 3.9 9.6 - - - -
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Residues in contact with THR 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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154B GLU* 3.5 37.5 - - + +
155B PHE 3.5 7.6 - - - +
156B THR* 4.6 9.2 + - - +
167B GLU 4.2 1.9 + - - -
168B GLY* 1.3 71.4 - - - -
170B TRP* 1.3 61.0 - - - +
186B LEU* 3.7 3.1 - - - -
187B LYS* 3.0 40.3 + - + +
265B BR 3.2 16.5 - - - +
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Residues in contact with TRP 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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138B VAL* 3.6 17.5 - - + -
139B TRP 3.5 19.1 - - - -
140B PHE* 3.5 34.8 - + - -
154B GLU* 3.4 4.1 - - - -
155B PHE* 2.7 42.6 + - - +
157B ILE* 3.2 38.2 + - + +
159B PHE* 3.9 18.2 - + + -
168B GLY* 3.2 29.7 + - - -
169B THR* 1.3 72.7 - - - +
171B GLU* 1.3 63.4 + - - +
172B LEU 3.7 0.5 + - - -
184B PHE* 3.8 27.5 - - + -
185B ARG 3.5 4.0 - - - -
186B LEU* 3.5 33.2 - - + -
202B PHE* 3.7 27.6 - + + -
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Residues in contact with GLU 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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151B LYS* 3.1 34.9 + - + +
153B GLU 3.9 4.9 - - - -
154B GLU* 4.2 4.0 - - - +
169B THR 4.1 0.2 - - - -
170B TRP* 1.3 72.3 - - - +
172B LEU* 1.3 59.5 + - - +
173B TRP* 2.8 22.8 + - + +
183B ALA 3.3 2.3 - - - +
184B PHE* 3.2 6.2 - - - -
185B ARG* 2.7 75.0 + - + +
187B LYS* 3.5 33.1 + - + +
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Residues in contact with LEU 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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151B LYS* 3.4 2.8 - - - -
152B ILE* 2.9 45.3 + - + +
153B GLU* 2.9 18.1 + - + +
155B PHE* 3.7 28.7 - - + -
170B TRP 3.7 1.0 + - - -
171B GLU* 1.3 72.5 - - - +
173B TRP* 1.3 74.8 + - - +
182B LEU* 3.9 18.6 - - + -
183B ALA 3.8 9.0 - - - +
184B PHE* 3.6 35.2 - - + -
209B ALA* 3.5 31.6 - - + -
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Residues in contact with TRP 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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146B THR* 3.5 23.3 - - + -
147B PRO* 3.6 39.6 - - + +
148B GLY 3.5 12.6 - - - +
149B GLY 3.6 22.9 - - - -
150B GLU* 3.3 4.9 - - - -
151B LYS* 3.6 36.7 - - + +
171B GLU* 2.8 35.5 + - + +
172B LEU* 1.3 78.5 - - - +
174B LEU* 1.3 59.0 + - - +
181B TYR* 3.6 2.3 - - - +
182B LEU* 3.3 6.8 - - - -
183B ALA* 2.9 40.3 + - + +
185B ARG* 3.7 20.4 - - + -
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Residues in contact with LEU 174 (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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148B GLY 4.6 0.4 - - - -
149B GLY* 3.3 1.6 - - - -
150B GLU* 2.8 36.0 + - - +
152B ILE* 3.7 40.6 - - + +
172B LEU* 4.1 0.8 + - + -
173B TRP* 1.3 73.7 - - - +
175B ALA* 1.3 65.5 + - - +
176B GLU* 3.9 29.6 - - + +
180B ASP* 4.5 3.1 - - - +
181B TYR 3.4 7.0 - - - +
182B LEU* 3.9 26.0 - - + -
209B ALA* 4.8 5.8 - - + +
210B LEU* 4.0 16.8 - - + -
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Residues in contact with ALA 175 (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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149B GLY* 3.7 12.3 - - - -
174B LEU* 1.3 78.7 - - - +
176B GLU* 1.3 64.2 + - - +
177B TRP* 3.4 45.4 + - + +
180B ASP* 3.6 3.3 - - - +
181B TYR* 2.8 44.6 + - + +
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Residues in contact with GLU 176 (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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174B LEU* 3.9 15.7 - - + +
175B ALA* 1.3 72.3 - - - +
177B TRP* 1.4 68.2 + - - +
180B ASP* 3.9 13.2 - - - +
210B LEU* 5.9 0.2 - - - +
213B SER* 4.8 9.5 + - - -
214B ALA 5.8 0.5 + - - -
215B ARG* 3.3 45.2 + - - +
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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