Contacts of the strand formed by residues 185 - 195 (chain A) in PDB entry 2PWY
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 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A ALA* 4.0 5.2 - - - +
164A TYR* 3.5 18.6 - - - +
166A GLY* 3.6 31.6 - - - +
167A VAL* 4.0 6.3 - - + -
181A ALA 3.0 16.5 + - - +
182A ALA 3.8 6.9 + - - +
183A LEU 3.4 0.9 - - - +
184A ALA* 1.3 76.9 - - - +
186A LYS* 1.3 74.0 + - - +
187A PRO* 3.5 3.5 - - - +
189A ARG* 3.6 21.5 - - + +
190A PHE 3.5 27.4 - - - +
191A LEU* 3.7 7.2 - - + +
213A PHE* 3.7 22.2 - - + -
251A ARG* 3.5 18.5 + - + +
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Residues in contact with LYS 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ARG* 6.2 0.4 - - - +
162A ALA* 3.2 27.8 - - + +
163A ALA* 4.0 17.5 + - - +
164A TYR 2.9 17.3 + - - +
165A ASP* 2.8 33.0 + - - +
184A ALA 3.6 0.8 + - - -
185A LEU* 1.3 73.6 - - - +
187A PRO* 1.4 75.3 - - + +
188A ASP 3.4 0.2 + - - -
189A ARG* 3.1 30.6 + - + +
251A ARG* 3.4 6.3 - - - +
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Residues in contact with PRO 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ALA* 4.1 14.1 - - + -
185A LEU 3.5 4.7 - - - +
186A LYS* 1.4 88.6 - - + +
188A ASP* 1.3 65.8 + - - +
189A ARG* 3.2 8.3 + - - +
251A ARG* 3.6 8.5 - - + +
252A TRP 3.5 18.8 - - - +
253A LYS* 4.1 3.1 - - - -
254A GLY* 3.5 32.8 - - - +
44B PRO* 4.2 16.6 - - + +
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Residues in contact with ASP 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A LYS 3.4 0.2 + - - -
187A PRO* 1.3 73.8 - - - +
189A ARG* 1.3 65.7 + - + +
190A PHE* 4.0 4.3 - - - -
250A ARG* 3.1 40.0 + - - +
251A ARG 2.8 20.8 + - - +
252A TRP 4.5 1.0 - - - -
44B PRO* 3.7 18.4 - - + +
45B GLY* 3.3 21.7 + - - -
59B HIS* 2.9 49.6 + - - +
60B ARG 4.1 5.2 + - - +
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Residues in contact with ARG 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LEU 3.1 16.7 + - - -
90A ASP* 2.8 50.7 + - - +
95A MET* 3.5 21.9 - - - +
165A ASP* 3.0 32.9 + - - +
185A LEU* 3.6 12.2 - - + +
186A LYS* 3.1 33.8 + - + +
187A PRO 3.9 4.3 - - - +
188A ASP* 1.3 86.1 + - - +
190A PHE* 1.3 69.4 + - - +
250A ARG* 3.5 1.9 - - - -
251A ARG* 2.9 26.9 + - - +
60B ARG 5.6 3.2 + - - -
61B PRO 5.7 0.2 + - - -
62B THR* 4.7 6.7 - - - +
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Residues in contact with PHE 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LEU 3.9 23.3 - - - +
89A LEU* 3.4 18.1 + - + +
165A ASP 4.4 2.2 + - - -
166A GLY* 3.3 7.5 - - - -
167A VAL 3.0 21.5 + - - -
185A LEU* 3.5 8.1 - - - +
188A ASP 4.0 4.7 - - - -
189A ARG* 1.3 87.4 - - - +
191A LEU* 1.3 64.5 + - - +
192A VAL* 4.5 2.0 - - + -
216A GLU* 4.1 12.6 - - + -
217A ARG* 6.4 0.4 - - + -
248A ALA* 4.8 9.2 - - + -
249A LEU 3.3 18.8 - - - +
250A ARG* 3.4 53.8 - - + -
62B THR* 3.5 29.6 - - + -
65B GLU* 4.9 0.9 - - - -
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Residues in contact with LEU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A VAL* 3.2 20.6 - - + +
169A LEU* 3.9 24.2 - - + -
178A LEU* 3.9 16.6 - - + -
181A ALA* 3.5 32.3 - - + -
185A LEU* 3.7 1.9 - - + +
190A PHE* 1.3 73.2 - - - +
192A VAL* 1.3 75.4 + - - +
193A ALA* 4.0 9.6 - - + +
204A LEU* 5.2 2.5 - - + -
213A PHE* 4.0 20.6 - - + -
247A VAL 4.6 0.9 - - - +
248A ALA* 3.3 3.1 - - - +
249A LEU* 2.8 53.7 + - + +
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Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A MET* 3.5 32.8 - - + +
88A LEU* 3.9 31.6 - - + +
89A LEU* 3.8 27.4 - - + -
167A VAL 2.9 7.5 + - - -
168A ALA* 3.6 1.7 - - - -
169A LEU 2.9 23.0 + - - -
190A PHE* 4.5 2.7 - - + -
191A LEU* 1.3 81.9 - - - +
193A ALA* 1.3 66.6 + - - +
246A LEU* 4.4 11.2 - - + -
247A VAL 3.2 11.4 - - - +
248A ALA* 4.1 10.5 - - + -
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Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A LEU* 3.4 18.2 - - + -
174A PRO* 4.6 8.1 - - + -
191A LEU* 4.0 6.9 - - + +
192A VAL* 1.3 76.8 - - - +
194A TYR* 1.3 59.9 + - - +
195A LEU* 4.0 7.1 + - + -
204A LEU* 3.7 29.6 - - + -
245A PHE 3.5 1.2 - - - +
246A LEU* 3.3 6.0 - - - +
247A VAL* 2.8 37.2 + - + +
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Residues in contact with TYR 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A THR 6.1 0.2 - - - -
76A PRO 4.6 1.1 + - - -
77A THR* 3.7 18.6 - - + -
78A TYR* 3.4 32.1 + - - -
81A ASP* 3.3 31.8 + - + -
85A MET* 4.1 11.9 - - - -
169A LEU 2.9 15.1 + - - +
170A ASP* 3.4 45.3 - - + +
171A LEU 4.3 2.8 + - - +
193A ALA* 1.3 71.2 - - - +
195A LEU* 1.3 71.7 + - - +
196A PRO* 4.5 7.7 - - + +
243A THR* 3.7 7.1 - - - -
244A ALA* 3.5 23.8 - - + -
245A PHE 3.5 4.5 - - - -
246A LEU* 3.7 17.9 - - + -
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Residues in contact with LEU 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A LEU 3.7 18.8 - - - +
174A PRO* 3.9 17.0 - - + -
175A TRP* 5.0 0.2 - - + -
193A ALA* 4.7 2.0 - - + -
194A TYR* 1.3 84.2 - - - +
196A PRO* 1.3 68.9 - - + +
200A GLN* 3.8 50.5 - - + +
201A VAL* 3.9 19.3 - - + +
204A LEU* 3.8 30.3 - - + -
244A ALA* 3.4 4.8 - - - +
245A PHE* 2.7 42.1 + - - +
247A VAL* 4.4 4.0 - - + -
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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