Contacts of the strand formed by residues 175 - 181 (chain A) in PDB entry 3M6L
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 PHE 175 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A VAL* 4.3 3.6 - - + -
123A ALA* 3.5 37.0 - - + -
124A VAL* 3.7 29.4 - - + -
127A ALA* 4.0 15.9 - - + -
146A ILE* 3.6 10.5 - - + -
148A CYS* 4.1 11.0 - - + -
164A CYS* 4.8 0.7 - - - -
167A ALA* 4.3 4.5 - - + -
172A LEU* 3.2 15.5 + - + +
173A ASP 3.5 1.3 - - - -
174A ASN* 1.3 76.0 - - - +
176A ILE* 1.3 69.4 + - - +
177A LEU* 3.9 24.5 - - + -
207A PHE* 4.0 22.4 - + - -
232A LYS 4.6 0.7 - - - +
233A PRO* 3.6 16.8 - - + +
234A CYS* 2.9 26.3 + - - +
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Residues in contact with ILE 176 (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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145A LYS* 4.3 12.8 - - + +
146A ILE 2.9 9.9 + - - +
147A TYR* 3.3 41.5 - - + +
148A CYS* 2.9 24.6 + - - +
175A PHE* 1.3 84.6 - - - +
177A LEU* 1.3 60.8 + - - +
178A ILE* 4.0 7.1 + - + +
224A LEU* 4.7 2.0 - - + +
227A ALA* 3.9 41.3 - - + +
228A LYS* 3.9 21.1 - - + -
234A CYS* 3.5 8.3 - - + +
236A ILE* 4.2 16.4 - - + -
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Residues in contact with LEU 177 (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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120A VAL* 4.3 11.0 - - + -
148A CYS* 3.6 37.0 - - + +
150A CYS* 3.8 19.5 - - + -
155A LEU* 4.4 7.4 - - + -
164A CYS* 4.2 14.4 - - - -
175A PHE* 3.9 19.0 - - + -
176A ILE* 1.3 72.2 - - - +
178A ILE* 1.3 60.0 + - - +
202A PHE* 3.7 32.5 - - + -
207A PHE* 4.7 1.8 - - + -
234A CYS 2.8 14.3 + - - +
235A LEU* 3.3 17.3 - - + +
236A ILE* 2.8 27.0 + - - +
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Residues in contact with ILE 178 (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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35A LEU* 5.7 1.9 - - + +
38A ILE* 4.2 31.4 - - + -
42A LEU* 4.3 14.4 - - + -
147A TYR* 4.6 10.1 - - + -
148A CYS 2.7 10.8 + - - +
149A LEU* 3.4 33.2 - - + -
150A CYS* 2.9 29.6 + - - +
176A ILE* 4.4 5.6 - - + +
177A LEU* 1.3 74.5 - - - +
179A TYR* 1.4 60.9 + - - +
180A ASP* 3.7 1.1 + - - +
212A ILE* 6.3 0.2 - - + -
224A LEU* 4.0 24.2 - - + -
236A ILE* 3.6 26.5 - - + +
238A ALA* 4.4 8.5 - - + -
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Residues in contact with TYR 179 (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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150A CYS* 3.6 10.8 - - - -
151A GLY 3.7 10.3 - - - -
152A ASP* 2.7 41.4 + - - -
155A LEU* 3.7 26.9 - - + +
177A LEU 3.9 1.4 + - - -
178A ILE* 1.4 70.4 - - - +
180A ASP* 1.3 73.0 + - - +
181A SER* 3.1 22.3 + - - -
190A VAL* 5.5 0.2 - - - +
194A PHE* 4.5 14.4 - + - -
198A VAL* 4.2 22.7 - - + +
235A LEU* 3.9 14.1 - - + -
236A ILE 2.8 14.7 + - - +
237A ILE* 4.0 26.2 - - + -
238A ALA* 2.9 32.0 + - - +
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Residues in contact with ASP 180 (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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31A ALA* 4.6 10.0 - - - +
34A GLY* 4.8 3.7 - - - -
35A LEU* 3.7 40.2 - - + +
38A ILE* 5.6 0.2 - - - -
150A CYS 2.9 18.5 + - - +
151A GLY* 4.0 8.9 - - - -
152A ASP* 4.1 4.7 - - - +
178A ILE* 3.7 2.2 + - - +
179A TYR* 1.3 78.0 - - - +
181A SER* 1.3 57.4 + - - +
182A ASN* 3.3 22.4 + - - -
238A ALA* 3.8 4.3 - - - -
240A THR* 2.3 40.8 + - - +
5001A TPP 4.9 1.9 + - - -
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Residues in contact with SER 181 (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 ASP* 4.7 1.6 + - - -
179A TYR* 3.1 34.6 + - - -
180A ASP* 1.3 68.5 - - - +
182A ASN* 1.3 60.0 + - - +
183A ASN* 3.6 3.0 + - - -
237A ILE* 4.0 16.3 - - - +
238A ALA 2.9 16.0 + - - -
239A LYS* 3.3 12.9 - - - +
240A THR 3.0 22.2 + - - +
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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