Contacts of the strand formed by residues 169 - 175 (chain B) in PDB entry 2PG0
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 LEU 169 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ILE* 4.3 8.1 - - + -
114B TRP* 3.7 45.8 - - + +
118B CYS* 4.4 2.2 - - - -
123B LEU* 3.8 26.7 - - + -
124B ILE 3.3 3.4 + - - +
125B THR* 3.3 27.8 - - + -
126B ALA 3.0 23.2 + - - +
167B ALA* 4.0 0.3 - - - +
168B ASP* 1.3 80.3 - - - +
170B ILE* 1.3 65.0 + - - +
171B VAL* 4.2 2.2 - - + -
191B VAL* 4.0 12.8 - - + -
192B VAL 3.7 2.5 - - - -
193B GLU* 3.5 31.0 - - + +
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Residues in contact with ILE 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ALA* 3.4 15.9 - - + +
128B ALA* 3.9 12.6 - - + -
161B ILE* 5.0 0.2 - - + -
164B GLY* 6.4 0.4 - - - -
167B ALA* 3.8 32.5 - - + +
168B ASP 4.4 1.6 - - - -
169B LEU* 1.3 80.2 - - - +
171B VAL* 1.3 63.5 + - - +
172B VAL* 3.4 21.3 + - + +
190B LEU 3.4 2.8 - - - +
191B VAL* 3.4 2.6 - - - +
192B VAL* 2.8 51.6 + - + +
194B ARG 5.1 0.4 - - - +
199B PHE* 3.7 28.3 - - + -
201B ARG* 4.0 2.9 - - - +
218B LEU* 3.8 25.6 - - + -
220B PHE* 6.0 0.2 - - + -
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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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98B VAL* 3.6 24.0 - - + +
101B TYR* 4.8 7.2 - - + -
102B ILE* 5.1 7.4 - - + -
125B THR* 6.3 0.2 - - + -
126B ALA 2.9 11.9 + - - +
127B ILE* 3.4 21.2 - - + +
128B ALA 2.8 30.8 + - - +
169B LEU* 5.7 2.0 - - + +
170B ILE* 1.3 69.8 - - - +
172B VAL* 1.3 57.2 + - - +
173B ALA 4.0 0.2 + - - -
189B LEU* 4.2 36.1 - - + -
190B LEU 3.9 4.9 - - - +
191B VAL* 4.5 10.8 - - + +
231B LEU* 4.3 19.3 - - + -
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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
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128B ALA* 3.7 5.2 - - + +
143B THR* 4.7 3.8 - - + -
154B VAL* 5.3 3.8 - - + -
158B LYS* 3.9 16.2 - - + -
170B ILE* 3.6 28.3 - - + +
171B VAL* 1.3 72.5 - - - +
173B ALA* 1.3 73.8 + - - +
174B CYS* 3.6 11.6 + - + -
188B SER 3.6 1.2 - - - +
189B LEU* 3.4 5.3 - - - -
190B LEU* 2.8 43.2 + - + +
192B VAL* 3.7 21.1 - - + -
220B PHE* 3.9 25.1 - - + -
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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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127B ILE* 6.0 0.6 - - + +
128B ALA 3.0 15.0 + - - +
129B MET* 4.3 12.8 - - + -
138B LEU* 5.7 1.3 - - + -
141B ILE* 3.7 16.5 - - + +
143B THR* 4.3 0.3 - - - -
158B LYS* 2.8 32.2 + - - -
171B VAL 4.0 1.0 + - - -
172B VAL* 1.3 71.4 - - - +
174B CYS* 1.3 60.2 + - - +
187B ILE* 4.5 2.5 - - + -
188B SER 3.5 6.7 - - - +
189B LEU* 4.0 15.3 - - + +
241B LEU* 4.2 17.5 - - + -
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Residues in contact with CYS 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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141B ILE* 4.0 7.1 - - - +
143B THR* 3.4 25.1 - - + +
144B THR 4.5 0.2 - - - -
145B ALA* 3.6 29.4 - - + -
154B VAL* 5.1 2.0 - - + -
172B VAL* 3.9 14.4 - - + +
173B ALA* 1.3 74.8 - - - +
175B LYS* 1.3 63.7 + - - +
176B THR* 3.5 5.3 + - - -
187B ILE* 3.3 3.1 - - - +
188B SER* 2.8 44.4 + - - +
190B LEU* 4.0 18.2 - - - -
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Residues in contact with LYS 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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139B ALA 3.1 25.3 + - - -
140B ASN* 4.3 3.4 + - - +
141B ILE* 2.8 37.0 + - + +
142B SER* 4.8 2.5 - - - -
143B THR 2.7 17.5 + - - +
144B THR* 3.4 8.4 - - + -
145B ALA 3.1 20.2 + - - +
146B VAL* 5.7 0.5 - - - +
174B CYS* 1.3 71.6 - - - +
176B THR* 1.3 63.2 + - - +
177B ASP 3.3 6.3 - - - +
178B PRO* 4.2 28.9 + - + +
183B PRO* 3.6 30.2 + - + +
186B GLY 3.3 11.4 - - - +
187B ILE* 3.7 22.0 - - + -
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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