Contacts of the strand formed by residues 187 - 193 (chain B) in PDB entry 1M7X
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 187 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B GLY* 3.2 1.7 - - - -
155B GLN* 2.6 54.8 + - - +
156B PHE* 4.1 1.2 - - - -
159B TRP* 3.4 10.6 - - + -
185B GLY 5.1 1.3 - - - +
186B GLN* 1.3 73.5 - - - +
188B TYR* 1.3 61.2 + - - +
211B GLN* 3.5 40.4 - - + +
217B ALA* 3.9 15.5 - - + -
218B SER 3.3 8.7 - - - +
219B LEU* 3.6 37.0 - - + -
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Residues in contact with TYR 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ALA* 3.6 19.2 + - + +
140B PHE* 3.4 24.2 - + - -
152B VAL* 4.3 1.3 - - + -
153B VAL 3.1 13.0 - - - +
156B PHE* 3.6 19.5 - - + -
159B TRP* 3.7 4.0 - - - -
187B LEU* 1.3 76.1 - - - +
189B LYS* 1.3 87.0 + - - +
190B TYR* 3.9 10.3 - + - -
204B ASP* 2.7 35.5 + - + +
206B TYR 5.4 0.2 + - - -
207B ALA* 4.9 4.3 - - - -
217B ALA* 3.6 1.6 - - - +
218B SER* 2.7 66.6 + - - +
219B LEU 3.9 7.0 + - - -
220B ILE* 3.5 30.7 - - + -
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Residues in contact with LYS 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B VAL* 3.4 9.0 - - - +
153B VAL* 2.6 47.0 + - + -
159B TRP* 4.0 9.2 - - + -
188B TYR* 1.3 88.4 - - - +
190B TYR* 1.3 65.4 + - - +
201B LEU* 4.0 43.2 + - + +
202B LYS 3.4 14.1 - - - +
203B SER* 3.9 18.6 - - - +
215B GLU* 2.7 39.1 + - + +
216B THR* 4.0 4.7 + - - -
217B ALA* 4.2 8.7 - - + +
218B SER* 5.3 1.1 - - - -
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Residues in contact with TYR 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B GLY 4.2 1.4 + - - -
140B PHE* 3.9 20.6 - + + +
141B SER 3.6 19.4 + - - -
142B VAL* 3.6 31.0 - - + -
150B VAL* 3.7 11.9 - - + -
151B SER 3.2 4.3 - - - -
152B VAL* 4.2 4.7 - - + -
166B MET* 3.8 31.6 - - + -
188B TYR* 3.9 10.5 - + - -
189B LYS* 1.3 80.2 - - - +
191B GLU* 1.3 61.3 + - - +
192B MET* 3.5 5.5 + - + -
200B ARG 3.5 0.3 - - - +
201B LEU* 3.5 2.0 - - - -
202B LYS* 2.9 49.3 + - + +
203B SER 4.7 1.8 - - - -
204B ASP* 2.7 48.4 + - + -
351B PHE* 5.9 0.2 - - + -
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Residues in contact with GLU 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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149B ARG* 2.9 39.3 + - - +
150B VAL* 3.3 0.4 - - - -
151B SER* 2.6 39.4 + - - +
153B VAL* 3.6 26.6 - - + +
159B TRP 5.3 2.3 - - - +
161B GLY* 4.4 12.2 + - - -
162B ARG 4.9 1.0 + - - -
189B LYS 4.0 1.2 + - - -
190B TYR* 1.3 71.8 - - - +
192B MET* 1.3 57.0 + - - +
199B LEU* 3.6 28.5 - - + +
200B ARG 3.7 4.0 - - - -
201B LEU* 4.2 15.6 - - + +
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Residues in contact with MET 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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142B VAL* 5.9 1.1 - - + -
144B ALA* 4.1 15.0 - - + -
147B ALA* 4.4 5.4 - - + -
149B ARG 3.0 11.7 - - - +
150B VAL* 3.4 24.0 - - + +
190B TYR* 3.5 3.1 + - + +
191B GLU* 1.3 75.6 - - - +
193B ILE* 1.3 63.7 + - - +
194B ASP* 4.4 11.0 - - - +
199B LEU* 3.4 7.8 - - - +
200B ARG* 2.8 48.6 + - + +
202B LYS* 3.8 27.4 - - + -
351B PHE* 4.1 11.7 - - + -
352B ASP* 3.4 38.4 - - - +
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Residues in contact with ILE 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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147B ALA 2.1 30.5 - - - +
148B ARG* 3.2 21.6 - - + +
149B ARG* 2.6 55.5 + - + +
192B MET* 1.3 77.8 - - - +
194B ASP* 1.3 59.2 + - - +
197B GLY* 3.8 19.3 - - - +
198B ASN 3.3 1.6 - - - -
199B LEU* 3.9 26.2 - - + +
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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