Contacts of the strand formed by residues 160 - 167 (chain X) in PDB entry 5LMQ
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 ASP 160 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89X LYS* 5.5 4.1 + - - -
119X THR* 5.1 4.3 - - + -
120X ILE 3.3 12.8 - - - +
121X MET* 3.9 19.0 - - - +
122X PHE* 3.7 7.6 - - - -
156X MET* 3.4 25.8 - - - +
157X LEU* 3.7 40.7 + - + +
158X GLY 3.2 1.0 - - - +
159X ARG* 1.3 100.5 + - - +
161X MET* 1.3 62.9 + - - +
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Residues in contact with MET 161 (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* 3.2 7.3 - - - +
120X ILE* 2.8 38.8 + - + +
122X PHE* 3.7 18.8 - - + -
130X PRO* 4.2 35.9 - - + +
133X GLY* 4.9 3.4 - - - -
134X GLU* 6.1 0.4 - - + -
137X LEU* 4.8 14.4 - - + -
154X PRO* 3.8 35.2 - - + +
155X GLU 3.4 20.9 - - - +
156X MET* 4.0 25.1 - - + +
160X ASP* 1.3 75.5 - - - +
162X ASN* 1.3 64.3 + - - +
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Residues in contact with ASN 162 (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 LYS* 3.3 32.8 + - + +
118X VAL 3.8 4.3 - - - -
119X THR* 3.9 10.1 - - + -
137X LEU* 5.7 0.7 - - - -
152X MET* 5.5 4.0 - - - +
153X LYS 3.0 18.0 - - - +
155X GLU* 2.8 48.3 + - - +
156X MET 4.4 1.6 + - - -
157X LEU* 3.3 30.9 - - + +
161X MET* 1.3 77.3 - - - +
163X MET* 1.3 63.5 + - - +
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Residues in contact with MET 163 (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 LYS* 3.3 10.4 - - - +
118X VAL* 2.8 46.7 + - + +
137X LEU* 3.4 40.2 - - + -
138X ASN* 4.0 7.2 - - - +
141X THR* 3.9 22.2 - - + +
150X VAL* 3.8 18.4 - - + -
152X MET* 3.6 18.8 - - - +
153X LYS* 3.5 17.0 - - + +
154X PRO* 3.6 24.7 - - + -
162X ASN* 1.3 73.9 - - - +
164X LEU* 1.3 60.8 + - - +
165X LEU* 5.1 1.3 - - + -
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Residues in contact with LEU 164 (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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85X VAL* 4.9 18.6 - - + -
115X LYS* 4.0 24.9 - - + -
116X VAL 3.3 11.9 - - - +
117X LYS* 4.8 7.9 - - + +
150X VAL* 3.8 0.7 - - - -
151X GLU* 2.8 48.3 + - + +
152X MET* 3.3 33.4 + - + +
163X MET* 1.3 76.5 - - - +
165X LEU* 1.3 74.1 + - - +
166X ALA 3.5 16.6 - - - +
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Residues in contact with LEU 165 (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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106X ILE* 4.5 8.3 - - + -
110X LEU* 3.7 3.6 - - + +
115X LYS* 3.5 1.9 - - - -
116X VAL* 2.8 47.7 + - + +
118X VAL* 3.7 22.0 - - + -
140X VAL* 4.8 3.4 - - + -
141X THR* 3.7 30.3 - - + -
144X LEU* 3.6 31.2 - - + -
148X ALA* 4.1 16.2 - - + -
149X VAL 3.6 5.4 - - - +
150X VAL* 3.9 23.1 - - + +
163X MET* 5.1 2.0 - - + -
164X LEU* 1.3 84.0 - - - +
166X ALA* 1.3 62.0 + - - +
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Residues in contact with ALA 166 (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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110X LEU* 4.3 1.1 - - - -
115X LYS* 3.8 27.1 - - + -
148X ALA* 3.5 1.7 - - - -
149X VAL* 2.8 39.0 + - + +
151X GLU* 4.2 14.8 - - + +
164X LEU* 3.5 5.7 - - - +
165X LEU* 1.3 74.6 - - - +
167X PRO* 1.4 75.1 - - + +
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Residues in contact with PRO 167 (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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110X LEU* 3.9 22.2 - - + +
113X GLY* 3.7 23.3 - - - +
114X HIS 3.5 20.9 - - - +
115X LYS* 4.4 2.7 - - + +
147X LEU 3.4 12.6 - - - +
148X ALA* 4.1 1.3 - - - -
149X VAL* 3.3 10.3 - - - +
166X ALA* 1.4 94.7 - - + +
168X VAL* 1.3 67.4 + - - +
169X LYS 4.3 15.9 - - - +
170X VAL* 6.0 0.9 - - - -
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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