Contacts of the strand formed by residues 186 - 194 (chain B) in PDB entry 3D87
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 186 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B PHE* 3.9 23.1 - - + -
136B SER* 3.2 25.6 - - - +
137B SER 3.4 7.6 - - - +
138B ARG* 2.9 60.3 - - + +
146B VAL* 4.5 4.0 - - + -
173B GLU* 4.8 4.5 - - + +
182B GLU* 5.2 0.2 - - - +
185B PRO* 1.3 75.3 - - - +
187B GLU* 1.3 69.5 + - - +
188B VAL* 4.0 0.2 - - + -
203B SER 3.5 0.5 - - - +
204B SER* 2.9 24.3 + - - -
205B PHE* 2.9 35.4 + - + +
207B ILE* 4.8 6.3 - - + -
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Residues in contact with GLU 187 (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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136B SER* 3.1 7.6 + - - -
137B SER* 2.9 42.0 + - - +
139B GLY* 4.2 4.5 - - - +
140B SER* 3.6 34.1 + - - -
185B PRO* 4.1 9.5 - - - +
186B ILE* 1.3 78.1 - - - +
188B VAL* 1.3 62.6 + - - +
189B MET* 4.0 21.8 - - + +
202B THR* 6.0 2.2 - - - -
203B SER 2.8 9.2 - - - +
204B SER* 3.8 15.5 + - - +
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Residues in contact with VAL 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 4.7 4.1 - - + +
118B PHE* 3.6 32.1 - - + -
120B CYS* 4.1 17.5 - - + -
134B VAL* 4.3 13.7 - - + -
135B LYS 3.3 7.9 - - - +
136B SER* 4.0 3.8 - - - +
148B CYS* 5.4 0.2 - - - -
169B VAL* 5.4 0.4 - - + -
186B ILE* 4.0 0.2 - - + -
187B GLU* 1.3 80.0 - - - +
189B MET* 1.3 63.4 + - - +
190B VAL* 4.1 20.6 - - + -
201B TYR 3.8 0.6 - - - +
202B THR* 3.2 6.8 - - - -
203B SER* 2.7 36.6 + - - +
205B PHE* 3.7 20.0 - - + -
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Residues in contact with MET 189 (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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134B VAL* 3.7 0.3 - - - +
135B LYS* 2.6 83.6 + - + +
136B SER* 5.3 0.9 - - - -
137B SER* 5.1 9.9 - - - +
187B GLU* 4.3 29.8 - - + +
188B VAL* 1.3 74.6 - - - +
190B VAL* 1.3 63.1 + - - +
191B ASP 4.0 0.2 - - - -
200B GLN* 3.0 25.1 - - - +
201B TYR 3.5 4.5 - - - -
202B THR* 4.0 11.2 - - + -
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Residues in contact with VAL 190 (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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95B LEU* 5.1 1.1 - - + -
107B LEU* 3.4 28.0 - - + -
122B TRP* 4.1 16.8 - - + -
132B PHE* 4.0 29.4 - - + -
133B SER 3.5 5.4 - - - +
134B VAL* 3.0 30.1 - - + -
188B VAL* 4.1 4.9 - - + -
189B MET* 1.3 74.5 - - - +
191B ASP* 1.3 61.7 - - - +
192B ALA* 3.2 6.7 + - + +
199B GLU 3.5 0.2 - - - +
200B GLN* 3.2 7.2 - - - -
201B TYR* 2.6 44.1 + - + +
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Residues in contact with ASP 191 (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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2B TRP* 5.1 2.6 - - - -
4B LEU* 3.9 25.8 - - + +
131B THR* 3.5 1.6 + - - +
132B PHE* 3.2 6.8 + - - -
133B SER* 2.6 53.1 + - - +
135B LYS* 3.4 26.4 - - - +
189B MET 4.0 0.2 + - - -
190B VAL* 1.3 68.2 - - - +
192B ALA* 1.3 59.8 + - - +
193B VAL* 3.5 4.9 + - + +
198B TYR* 2.9 14.2 + - + -
199B GLU 3.8 3.1 - - - -
200B GLN* 2.3 36.0 + - - -
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Residues in contact with ALA 192 (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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94B ILE* 3.3 19.5 - - + +
131B THR 3.6 0.2 - - - -
132B PHE* 3.6 28.5 - - + -
190B VAL* 3.2 2.5 + - + +
191B ASP* 1.3 69.6 - - - +
193B VAL* 1.3 62.1 + - - +
194B HIS 3.7 0.3 + - - -
197B LYS 3.8 0.5 - - - +
198B TYR* 4.7 0.2 - - - -
199B GLU 2.6 36.4 + - - +
201B TYR* 3.7 28.9 - - + -
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Residues in contact with VAL 193 (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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4B LEU* 4.5 11.7 - - + -
79B LEU* 5.9 0.4 - - + -
81B LEU* 4.1 23.1 - - + -
129B ASP 3.2 4.5 - - - +
130B LEU* 3.3 3.4 - - - -
131B THR* 2.7 64.7 + - + +
191B ASP 3.5 3.6 + - - +
192B ALA* 1.3 71.2 - - - +
194B HIS* 1.3 61.5 + - - +
195B LYS 3.9 20.2 - - - +
197B LYS 3.6 9.6 - - - +
198B TYR* 3.4 33.4 - - + -
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Residues in contact with HIS 194 (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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94B ILE* 3.8 26.2 - - + -
126B ILE* 3.6 31.7 - - + +
128B THR* 2.9 22.6 + - + -
129B ASP* 2.7 29.5 + - + +
130B LEU* 4.1 5.8 - - + -
192B ALA 3.7 1.4 + - - -
193B VAL* 1.3 73.5 - - - +
195B LYS* 1.3 90.9 + - + +
196B LEU 3.1 6.1 + - - -
197B LYS* 3.1 36.4 + - + +
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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