Contacts of the strand formed by residues 169 - 178 (chain B) in PDB entry 1P5Q
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 ILE 169 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167B GLY 4.4 2.2 - - - +
168B ALA* 1.3 75.3 - - - +
170B VAL* 1.3 60.6 + - - +
189B ARG* 3.8 39.9 - - - +
190B PHE* 3.5 10.5 - - - +
191B GLU* 4.0 20.2 - - + +
252B PHE* 2.9 24.3 - - - +
253B GLU* 3.1 24.5 + - + +
276B ARG* 3.3 38.6 - - - +
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Residues in contact with VAL 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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164B PRO* 3.8 26.0 - - + -
168B ALA* 4.5 1.1 - - + -
169B ILE* 1.3 77.6 - - - +
171B GLU* 1.3 54.8 + - - +
172B VAL* 4.1 11.2 - - + -
189B ARG* 2.7 35.9 - - - +
190B PHE* 2.9 49.6 + - + +
192B ILE* 4.0 18.8 - - + -
208B ILE* 4.2 4.7 - - + -
249B LEU* 4.0 7.6 - - + -
251B SER 3.5 7.4 - - - +
252B PHE* 3.7 15.0 - - + -
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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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170B VAL* 1.3 71.6 - - - +
172B VAL* 1.3 64.9 + - - +
188B LEU 3.7 4.6 - - - -
189B ARG* 3.3 35.1 + - + +
250B LYS* 2.8 45.4 + - + -
251B SER* 2.9 38.2 + - - +
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Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B VAL* 4.1 9.0 - - + -
171B GLU* 1.3 85.9 - - - +
173B ALA* 1.3 61.1 + - - +
174B LEU* 4.5 9.0 - - + -
187B GLU* 3.6 1.3 - - - +
188B LEU* 2.9 52.6 + - + +
190B PHE* 3.8 19.3 - - + -
208B ILE* 4.6 15.9 - - + -
247B LEU* 5.2 4.9 - - + -
248B HIS 3.2 8.7 - - - +
249B LEU* 3.5 33.0 - - + +
250B LYS* 4.2 4.9 - - - +
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Residues in contact with ALA 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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172B VAL* 1.3 73.8 - - - +
174B LEU* 1.3 60.3 + - - +
186B ARG 3.5 6.3 - - - +
187B GLU* 3.4 32.8 - - + +
247B LEU* 3.0 2.6 - - - +
248B HIS* 2.6 50.4 + - + +
250B LYS* 4.6 6.0 - - + +
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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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172B VAL* 4.5 8.1 - - + -
173B ALA* 1.3 75.0 - - - +
175B GLU* 1.3 81.6 + - - +
176B GLY 4.9 0.4 - - - +
184B ASP* 4.0 22.7 - - - +
185B GLN* 4.3 0.3 - - - +
186B ARG* 3.0 46.5 + - + +
188B LEU* 3.9 23.6 - - + -
200B LEU* 3.4 33.4 - - + -
204B LEU* 4.4 7.6 - - + -
208B ILE* 5.9 1.3 - - + -
245B TYR* 4.8 8.3 - - + -
246B GLU 3.1 11.2 - - - +
247B LEU* 3.8 12.1 - - + -
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Residues in contact with GLU 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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174B LEU* 1.3 86.6 - - - +
176B GLY* 1.3 60.6 + - - +
177B TYR* 3.3 34.1 + - + -
182B LEU* 3.8 5.8 - - + -
184B ASP 2.7 7.2 - - - +
185B GLN* 3.5 38.8 + - + +
245B TYR* 3.3 5.6 - - - -
246B GLU* 2.8 43.5 + - + +
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Residues in contact with GLY 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* 4.9 0.2 - - - +
175B GLU* 1.3 72.7 - - - +
177B TYR* 1.3 56.8 + - - -
181B LYS 3.5 0.7 - - - +
182B LEU* 3.6 3.8 - - - +
183B PHE* 2.8 47.9 + - - -
184B ASP* 2.5 17.0 + - - +
244B LYS 3.8 0.2 - - - -
245B TYR* 3.5 27.1 - - - -
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Residues in contact with TYR 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 GLU* 3.3 42.8 + - + -
176B GLY* 1.3 71.4 - - - -
178B TYR* 1.3 58.7 - - - +
179B LYS 4.2 0.2 - - - -
180B ASP* 3.9 19.5 - - - +
181B LYS 3.2 17.0 - - - -
182B LEU* 3.3 29.1 - - + +
183B PHE* 3.2 10.9 - - - -
243B LEU* 3.4 2.6 - - - -
244B LYS* 2.5 77.9 + - + +
246B GLU* 3.4 25.3 + - + -
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Residues in contact with TYR 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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233A GLU* 3.3 31.7 - - - +
1002A SO4 3.8 4.7 + - - -
177B TYR* 1.3 73.6 - - - +
179B LYS* 1.3 88.9 + - + +
181B LYS* 2.9 36.1 + - + +
183B PHE* 3.5 20.4 - - + -
235B PHE 5.8 1.1 - - - -
236B GLN 4.9 2.9 - - - -
237B ILE* 4.7 8.7 - - + -
238B PRO* 3.0 36.8 - - + +
240B ASN 5.5 0.3 + - - -
241B ALA* 3.6 22.5 - - + +
242B GLU 3.3 20.6 - - - -
243B LEU* 3.5 9.0 - - + +
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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