Contacts of the strand formed by residues 146 - 153 (chain X) in PDB entry 5CQM
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 ARG 146 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110X ARG* 4.6 4.5 - - - +
113X ASN* 2.8 50.9 + - - +
114X THR 3.7 8.0 + - - +
115X THR* 3.1 37.6 + - + +
116X ILE* 2.9 31.1 + - - +
145X HIS* 1.3 72.7 - - - +
147X VAL* 1.3 58.9 + - - +
167X GLY* 3.4 18.6 - - - +
203X GLU 5.5 2.6 + - - -
205X ASP* 5.7 0.2 + - - -
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Residues in contact with VAL 147 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115X THR* 5.0 1.3 - - - -
116X ILE* 3.3 9.4 - - + +
118X LEU* 5.0 1.1 - - + -
141X PHE* 4.2 13.5 - - + +
142X MET* 3.6 26.7 - - + -
145X HIS 3.4 2.8 + - - +
146X ARG* 1.3 79.2 - - - +
148X HIS* 1.3 61.4 + - - +
149X TYR* 4.1 34.1 - - + -
167X GLY 3.3 7.8 + - - +
168X ARG* 3.2 37.2 - - - +
169X GLN* 2.8 32.2 + - - +
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Residues in contact with HIS 148 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115X THR* 4.7 5.1 - - + +
116X ILE 2.9 8.3 + - - -
117X GLY* 3.2 4.7 - - - -
118X LEU 2.9 24.0 + - - -
147X VAL* 1.3 73.9 - - - +
149X TYR* 1.3 83.9 + - - +
150X TYR* 3.2 28.8 + + + +
169X GLN* 3.4 44.2 + - + +
171X SER* 2.7 26.0 + - - -
199X ARG* 4.1 3.4 - - - -
203X GLU* 3.4 30.5 + - - +
204X VAL* 4.0 11.8 - - + +
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Residues in contact with TYR 149 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118X LEU* 3.4 30.5 - - + +
120X VAL* 6.5 0.4 - - + -
133X PHE* 5.0 1.1 - + - -
134X LEU* 3.7 22.2 - - + -
137X ALA* 3.4 29.5 - - + +
138X GLU* 2.6 34.1 + - + +
147X VAL* 4.1 14.1 - - + -
148X HIS* 1.3 78.4 - - - +
150X TYR* 1.3 59.5 + - - +
151X VAL* 4.0 3.4 - - + -
164X LEU* 4.0 13.7 - - + -
168X ARG* 3.0 22.8 + - + -
169X GLN 2.8 27.8 + - - +
170X LEU* 3.9 23.6 - - + -
171X SER 2.8 26.7 + - - -
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Residues in contact with TYR 150 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117X GLY* 4.0 5.8 - - - -
118X LEU 2.8 10.9 + - - +
119X THR* 3.4 12.8 - - + -
120X VAL* 3.0 27.0 + - - +
148X HIS* 3.2 48.7 + + + -
149X TYR* 1.3 74.3 - - - +
151X VAL* 1.3 61.6 + - - +
152X PHE* 3.8 15.5 + - + -
171X SER* 3.6 6.7 - - - -
173X LEU* 4.0 22.9 - - + -
199X ARG* 3.9 13.2 - - - -
200X PHE* 3.5 35.2 - + - -
203X GLU* 2.6 41.3 + - - +
204X VAL* 3.5 11.9 - - + +
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Residues in contact with VAL 151 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120X VAL* 3.6 18.6 - - + +
122X ALA* 4.7 1.8 - - + -
130X LEU* 3.9 30.1 - - + -
134X LEU* 4.7 6.3 - - + -
149X TYR* 4.9 2.7 - - + -
150X TYR* 1.3 74.4 - - - +
152X PHE* 1.3 56.8 + - - +
153X THR* 3.8 9.4 + - + -
159X VAL* 4.1 22.7 - - + -
170X LEU* 3.8 29.6 - - + -
171X SER 2.9 13.1 + - - +
172X VAL* 3.5 8.3 - - + +
173X LEU* 2.8 31.5 + - - +
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Residues in contact with PHE 152 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119X THR* 4.3 9.9 - - - -
120X VAL 2.9 16.7 + - - +
121X PHE* 3.4 42.9 - + + -
122X ALA* 2.8 28.8 + - - +
123X ILE* 4.2 3.4 - - - +
150X TYR* 4.0 20.9 - - + -
151X VAL* 1.3 68.5 - - - +
153X THR* 1.3 60.8 + - - +
173X LEU* 3.3 38.4 - - + -
175X VAL* 4.0 19.1 - - + -
200X PHE* 3.9 27.4 - + - -
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Residues in contact with THR 153 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122X ALA* 2.7 22.6 + - - -
123X ILE* 4.1 2.2 - - - -
127X VAL* 3.5 13.3 - - - +
151X VAL* 4.3 9.6 - - + +
152X PHE* 1.3 74.6 - - - +
154X ASP* 1.3 60.8 + - - +
155X GLN* 3.1 10.9 + - - -
156X PRO* 3.8 21.1 - - + -
159X VAL* 3.9 10.0 - - + +
172X VAL* 3.8 25.8 - - + -
173X LEU 3.0 5.3 + - - +
174X GLU* 3.2 7.6 - - - +
175X VAL* 3.0 25.4 + - - +
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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