Contacts of the strand formed by residues 160 - 166 (chain A) in PDB entry 2RLI
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 VAL 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A TRP* 3.6 36.3 - - + +
124A VAL* 5.3 0.2 - - - +
125A LEU* 5.2 13.0 - - + -
147A VAL* 5.3 4.0 - - + +
148A VAL* 3.8 40.9 - - + +
151A LEU* 3.9 17.0 - - + -
158A PRO* 2.9 20.9 + - + +
159A PRO* 1.3 68.3 - - - +
161A GLN* 1.3 59.8 + - - +
162A PRO* 3.7 7.6 - - - +
230A LEU* 4.6 12.3 - - + -
254A VAL* 4.5 11.0 - - + -
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Residues in contact with GLN 161 (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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119A PHE* 4.3 5.6 - - - -
122A GLN* 2.9 35.1 + - - +
123A TRP 3.0 14.5 + - - +
124A VAL* 3.3 11.6 - - + +
125A LEU* 2.9 22.7 + - - -
159A PRO 3.3 4.1 + - - +
160A VAL* 1.3 70.6 - - - +
162A PRO* 1.3 89.4 + - + +
163A VAL* 3.3 21.4 - - - +
187A ARG* 5.1 5.8 - - + +
189A LEU* 3.4 20.6 - - + +
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Residues in contact with PRO 162 (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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125A LEU* 3.5 21.1 - - + +
127A TYR* 6.5 0.4 - - + -
144A LEU* 6.5 0.9 - - + -
145A VAL* 6.0 2.7 - - + -
148A VAL* 4.7 15.3 - - + -
160A VAL 3.7 8.3 - - - +
161A GLN* 1.3 100.3 + - + +
163A VAL* 1.3 61.3 + - - +
187A ARG* 3.9 29.4 - - + +
188A LEU* 4.2 26.0 - - + -
189A LEU* 3.3 13.7 + - - +
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Residues in contact with VAL 163 (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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119A PHE* 4.2 11.2 - - + -
124A VAL* 4.1 11.2 - - + -
125A LEU 2.8 18.4 + - - +
126A MET* 3.8 27.6 - - + -
127A TYR* 3.0 31.2 + - - +
161A GLN* 3.3 23.6 - - - +
162A PRO* 1.3 72.5 - - - +
164A PHE* 1.3 58.2 + - - +
165A ILE* 4.2 13.7 - - + -
188A LEU* 6.4 0.2 - - - -
189A LEU* 3.6 14.6 - - + +
191A LEU* 3.9 26.0 - - + -
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Residues in contact with PHE 164 (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 TYR* 3.4 42.0 - + + -
129A GLY* 3.8 4.7 - - - -
130A PHE 3.6 40.4 - - - -
131A THR* 4.4 1.1 - - - -
137A CYS* 4.1 6.7 - - - -
141A LEU* 3.9 18.6 - - + -
163A VAL* 1.3 71.5 - - - +
165A ILE* 1.3 60.8 + - - +
177A MET* 3.8 20.8 - - + +
180A TYR* 3.5 43.5 - + + -
181A VAL* 6.5 0.2 - - + -
188A LEU* 5.5 7.6 - - + +
189A LEU 3.0 13.3 + - - +
190A GLY* 3.7 3.3 - - - -
191A LEU* 2.9 29.1 + - - +
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Residues in contact with ILE 165 (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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106A LEU* 4.9 18.6 - - + -
126A MET* 4.3 20.9 - - + -
127A TYR 2.8 17.2 + - - +
128A PHE* 3.7 38.0 - - + -
129A GLY 2.9 30.6 + - - +
163A VAL* 4.2 23.6 - - + -
164A PHE* 1.3 78.4 - - - +
166A THR* 1.3 71.2 + - - +
167A VAL* 3.5 1.0 + - - +
191A LEU* 3.4 22.7 - - + +
192A THR* 5.8 0.4 - - - -
198A VAL* 6.0 2.5 - - + -
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Residues in contact with THR 166 (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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129A GLY 3.3 6.7 - - - +
130A PHE* 4.6 8.2 - - + -
131A THR* 3.9 3.3 + - - -
165A ILE* 1.3 77.6 - - - +
167A VAL* 1.3 60.0 + - - +
168A ASP 3.1 32.3 + - - +
169A PRO* 4.3 2.2 - - + -
172A ASP* 2.7 38.0 + - + +
177A MET* 3.0 14.6 - - - +
191A LEU 3.1 9.5 + - - -
192A THR* 3.6 16.3 - - - +
193A GLY 5.7 1.3 + - - +
198A VAL* 4.3 13.7 - - - +
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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