Contacts of the strand formed by residues 170 - 179 (chain B) in PDB entry 2DH3
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 ASP 170 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B GLN* 2.8 36.1 + - - +
168B LYS 3.0 4.2 + - - +
169B ASP* 1.3 75.9 - - - +
171B VAL* 1.3 56.3 + - - +
172B ALA* 3.2 11.8 + - - +
173B GLN* 2.9 35.5 + - + +
174B THR* 2.6 33.0 + - - -
218B PHE* 3.8 1.7 - - - -
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Residues in contact with VAL 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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169B ASP 3.8 4.7 + - - +
170B ASP* 1.3 71.2 + - - +
172B ALA* 1.3 66.5 + - - +
174B THR* 3.3 10.9 + - - +
218B PHE* 3.9 31.6 - - + -
220B THR* 3.9 23.6 - - - +
221B GLN 5.5 0.7 - - - +
224B THR* 4.1 20.2 - - + -
225B VAL* 4.5 15.9 - - + -
228B LYS* 3.5 31.6 - - + -
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Residues in contact with ALA 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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170B ASP* 3.2 8.6 + - - +
171B VAL* 1.3 80.0 - - - +
173B GLN* 1.3 63.4 + - + +
174B THR 3.3 5.4 + - - +
175B ASP* 5.9 0.2 - - - +
228B LYS* 4.5 4.9 + - - +
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Residues in contact with GLN 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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165B LYS* 4.3 8.7 - - - +
167B GLN* 3.0 53.5 + - + +
170B ASP* 2.9 21.6 + - + +
172B ALA* 1.3 74.0 - - + +
174B THR* 1.3 61.5 + - - +
175B ASP* 3.5 6.5 + - - +
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Residues in contact with THR 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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164B HIS* 4.4 0.2 - - + -
165B LYS 3.4 17.7 - - - +
166B ASN* 3.1 29.0 + - + +
167B GLN 3.8 1.4 + - - -
170B ASP 2.6 20.7 + - - -
171B VAL 3.3 8.8 + - - +
172B ALA 3.2 3.8 - - - +
173B GLN* 1.3 77.4 - - - +
175B ASP* 1.3 59.0 + - - +
176B LEU* 4.2 17.7 - - + -
209B PRO* 4.1 9.4 - - + +
218B PHE* 3.3 17.6 - - + -
228B LYS* 2.8 33.8 + - + +
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Residues in contact with ASP 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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165B LYS* 2.9 41.7 + - + -
172B ALA 5.9 0.2 - - - +
173B GLN 3.5 5.9 + - - +
174B THR* 1.3 73.4 - - - +
176B LEU* 1.3 63.3 + - - +
177B LEU* 2.7 40.7 + - - +
178B GLN* 2.6 44.1 + - - +
228B LYS* 4.9 1.8 - - - +
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Residues in contact with LEU 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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164B HIS* 3.4 49.2 - - + +
174B THR* 4.3 8.3 - - + -
175B ASP* 1.3 72.7 + - - +
177B LEU* 1.3 63.1 + - + +
178B GLN 3.4 1.0 + - - -
207B LEU* 4.4 17.4 - - + +
209B PRO* 4.1 18.8 - - + -
228B LYS* 3.9 40.9 - - + +
229B VAL* 4.0 15.3 - - + +
232B ALA* 3.8 20.0 - - + -
236B TRP* 3.2 22.3 + - - -
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Residues in contact with LEU 177 (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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175B ASP* 2.7 21.7 + - - +
176B LEU* 1.3 76.8 - - + +
178B GLN* 1.3 61.7 + - + +
186B LYS* 6.2 0.2 - - - +
228B LYS 5.1 1.3 - - - +
231B ASP* 3.9 15.9 - - + +
232B ALA* 3.5 37.2 - - + +
235B PHE* 3.6 40.2 - - + -
236B TRP* 4.1 11.0 - - - +
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Residues in contact with GLN 178 (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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164B HIS* 3.5 6.4 - - - +
165B LYS* 2.7 62.0 + - + +
175B ASP* 2.6 29.3 + - - +
176B LEU 3.4 0.8 - - - -
177B LEU* 1.3 84.8 - - + +
179B ILE* 1.3 61.5 + - - +
236B TRP* 5.2 1.1 - - - -
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Residues in contact with ILE 179 (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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140B LEU* 4.4 6.3 - - + -
163B ILE* 3.7 29.4 - - + +
164B HIS* 4.5 0.7 - - - +
165B LYS* 3.8 10.1 + - - -
178B GLN* 1.3 74.2 - - - +
180B ASP* 1.3 76.9 + - - +
181B PRO* 3.4 7.3 - - - +
183B PHE* 4.6 3.6 - - + -
184B GLY 3.8 17.4 - - - +
185B SER* 3.8 8.3 - - - +
186B LYS* 3.7 34.3 - - + -
189B PHE* 4.0 15.0 - - + -
236B TRP* 3.8 30.3 - - + -
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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