Contacts of the strand formed by residues 187 - 193 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A GLN* 3.1 50.3 + - + +
156A PHE* 3.6 2.9 - - - -
159A TRP* 3.9 11.2 - - + -
185A GLY 3.4 1.3 + - - +
186A GLN* 1.3 73.5 - - - +
188A TYR* 1.3 65.6 + - - +
211A GLN* 2.8 38.4 - - + +
217A ALA* 3.7 17.3 - - + +
218A SER 3.0 24.7 - - - +
219A LEU* 3.8 19.5 - - + -
310A ARG* 5.9 1.1 - - - +
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Residues in contact with TYR 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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127A ALA* 3.5 14.5 + - + +
140A PHE* 3.6 32.8 - + - -
152A VAL* 4.8 0.4 - - + -
153A VAL 3.1 15.5 - - - +
156A PHE* 3.3 12.6 - + + -
159A TRP* 3.5 8.5 - - - -
186A GLN 3.8 0.7 - - - -
187A LEU* 1.3 79.7 - - - +
189A LYS* 1.3 80.9 - - - +
190A TYR* 3.9 15.9 - + - -
204A ASP* 3.2 23.8 + - + +
206A TYR 5.3 0.3 + - - -
207A ALA* 5.0 3.5 - - - -
217A ALA 3.7 0.3 - - - -
218A SER* 2.8 62.9 + - - -
219A LEU 3.7 3.9 + - - -
220A ILE* 3.5 37.9 - - + -
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Residues in contact with LYS 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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152A VAL 4.1 0.2 - - - -
153A VAL* 3.0 38.3 + - + +
159A TRP* 3.6 18.6 - - + -
188A TYR* 1.3 93.2 - - - +
190A TYR* 1.3 76.0 + - - +
201A LEU* 3.7 34.9 + - + +
202A LYS 3.7 14.4 - - - +
203A SER* 3.7 19.5 + - - +
215A GLU* 4.0 9.3 + - + +
216A THR* 3.0 31.1 + - - +
217A ALA* 4.0 4.5 - - + -
218A SER* 4.6 0.9 - - - +
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Residues in contact with TYR 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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126A GLY 3.9 7.4 + - - -
140A PHE* 4.0 11.0 - + - -
141A SER 3.7 6.6 + - - -
142A VAL* 3.2 50.3 - - + +
150A VAL* 4.5 10.1 - - + -
151A SER 3.6 8.5 - - - +
152A VAL* 4.6 3.6 - - + -
153A VAL* 4.0 0.7 - - - -
166A MET* 4.1 15.7 - - + -
188A TYR* 3.9 15.9 - + - -
189A LYS* 1.3 86.3 - - - +
191A GLU* 1.3 60.2 - - - +
192A MET* 4.2 4.0 - - + +
200A ARG 3.7 0.2 - - - +
201A LEU* 3.1 14.5 - - - +
202A LYS* 2.9 50.9 + - + +
203A SER 4.7 0.2 - - - -
204A ASP* 3.2 45.8 + - + -
205A PRO* 5.1 0.4 - - + -
351A PHE* 5.3 0.2 - + - -
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Residues in contact with GLU 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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149A ARG* 2.6 32.9 + - - +
150A VAL* 3.0 4.4 - - - +
151A SER* 2.6 49.4 + - - +
153A VAL* 2.9 31.9 - - + +
159A TRP 5.3 0.2 - - - +
160A ASP* 4.7 0.7 - - - -
161A GLY* 3.0 21.4 + - - -
162A ARG* 4.2 1.9 + - - +
190A TYR* 1.3 72.7 - - - +
192A MET* 1.3 62.7 + - - +
199A LEU* 4.0 15.2 - - + +
200A ARG 3.6 4.5 - - - +
201A LEU* 4.1 7.3 - - + +
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Residues in contact with MET 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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142A VAL* 5.9 1.1 - - + -
144A ALA* 3.4 27.8 - - + -
147A ALA* 4.0 5.8 - - + -
149A ARG 2.9 15.0 - - - +
150A VAL* 3.3 28.5 - - + -
190A TYR* 5.5 2.7 - - + +
191A GLU* 1.3 75.7 - - - +
193A ILE* 1.3 68.5 + - - +
194A ASP* 4.6 8.5 - - - +
199A LEU* 3.3 5.4 - - - +
200A ARG* 2.9 44.1 + - + +
202A LYS* 4.9 18.2 - - + -
351A PHE* 4.4 9.9 - - + -
352A ASP* 3.7 26.9 - - - +
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Residues in contact with ILE 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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147A ALA* 2.7 19.6 - - - +
148A ARG* 3.1 24.9 - - + +
149A ARG* 3.0 54.0 + - - +
192A MET* 1.3 84.8 - - - +
194A ASP* 1.3 69.6 + - - +
197A GLY* 3.3 38.8 - - - +
198A ASN 2.8 6.5 - - - +
199A LEU* 3.4 16.6 - - + +
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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