Contacts of the strand formed by residues 146 - 154 (chain D) in PDB entry 1RLI
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 SER 146 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111D SER 5.2 0.2 + - - -
113D LYS 3.4 10.5 + - - -
114D GLN* 3.6 3.9 - - - -
115D ALA* 2.8 32.4 + - - -
144D GLY 3.7 4.1 + - - -
145D MET* 1.3 71.4 - - - +
147D PHE* 1.3 56.2 + - - +
148D LYS* 3.2 33.3 + - - +
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Residues in contact with PHE 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B ASN* 3.7 12.0 + - - +
127B ILE* 2.8 45.2 - - + +
115D ALA 3.5 10.5 - - - -
117D VAL* 3.6 34.3 - - + -
133D ILE* 3.6 42.0 - - + -
136D PHE* 4.0 3.4 - - + -
137D GLU* 3.7 29.8 - - + +
140D PHE* 3.6 22.4 - + + -
145D MET 3.5 3.4 + - - +
146D SER* 1.3 68.9 - - - +
148D LYS* 1.3 58.5 + - - +
149D GLY 3.4 22.9 - - - -
150D TYR* 4.3 5.4 - + + -
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Residues in contact with LYS 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B ASN* 5.3 2.1 - - - +
126B LYS* 5.8 2.9 - - - +
127B ILE* 4.9 1.6 - - - -
114D GLN* 3.0 41.8 - - + +
115D ALA 2.9 10.1 + - - +
116D TYR* 3.3 31.3 - - + +
146D SER* 3.7 34.4 + - - +
147D PHE* 1.3 73.2 - - - +
149D GLY* 1.3 55.9 + - - +
176D LYS* 3.2 48.3 + - + +
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Residues in contact with GLY 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B LYS* 6.0 5.2 - - - -
127B ILE* 5.2 2.9 - - - -
166B GLN* 5.2 6.7 - - - -
116D TYR* 3.2 21.9 - - - -
117D VAL 3.1 18.9 + - - -
147D PHE* 3.4 8.3 - - - -
148D LYS* 1.3 82.1 - - - +
150D TYR* 1.3 67.5 + - - +
174D LEU* 3.9 4.5 - - - -
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Residues in contact with TYR 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B LYS* 2.9 39.6 + - + +
127B ILE* 4.3 7.6 - - + -
130B LEU* 3.4 17.8 - - + +
150B TYR* 5.0 7.0 + + - -
152B LEU* 4.5 4.0 - - - +
166B GLN* 3.6 14.8 + - - +
117D VAL* 2.9 27.4 - - + +
133D ILE* 3.9 39.7 - - + -
147D PHE* 4.3 7.6 - + + -
149D GLY* 1.3 77.3 - - - +
151D VAL* 1.3 79.9 + - - +
152D LEU* 4.2 21.8 - - + -
170D ALA* 5.6 0.2 - - - +
174D LEU* 3.7 4.9 - - - +
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Residues in contact with VAL 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B GLN* 4.2 0.7 - - - +
19D LEU* 4.5 9.4 - - + -
117D VAL* 2.9 8.4 + - - +
118D ILE* 3.6 9.1 - - + +
119D ALA* 3.0 27.0 + - - +
133D ILE* 5.5 0.2 - - - +
150D TYR* 1.3 83.1 - - - +
152D LEU* 1.3 72.7 + - - +
167D ALA* 3.8 28.5 - - + +
170D ALA* 3.7 33.0 - - + +
171D ALA* 3.8 8.3 - - + +
174D LEU* 3.7 21.1 - - + -
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Residues in contact with LEU 152 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150B TYR* 4.3 3.6 - - - +
78D ILE* 4.1 17.9 - - + -
119D ALA* 3.4 22.4 - - + -
125D PRO* 3.5 30.1 - - + +
126D LYS* 4.0 12.0 + - - +
129D GLY 4.2 5.2 - - - +
130D LEU* 3.7 27.1 - - + -
132D LEU* 5.9 0.2 - - + -
133D ILE* 4.1 20.4 - - + -
150D TYR* 4.2 18.5 - - + -
151D VAL* 1.3 80.9 - - - +
153D GLY* 1.3 59.8 + - - +
164D ASP* 4.7 1.2 - - - +
167D ALA* 4.3 4.3 - - - +
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Residues in contact with GLY 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 4.4 5.1 - - - +
119D ALA 2.8 11.2 + - - +
120D VAL* 3.2 5.9 - - - +
121D GLY 3.0 25.1 + - - +
125D PRO* 3.6 8.5 - - - +
151D VAL* 4.0 2.0 - - - +
152D LEU* 1.3 75.8 - - - +
154D GLU* 1.3 61.1 + - - -
161D ILE* 3.9 6.1 - - - -
164D ASP* 3.7 6.7 - - - -
167D ALA* 3.8 13.0 - - - -
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Residues in contact with GLU 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D VAL* 4.1 0.4 - - - -
121D GLY 3.3 9.4 - - - +
122D GLY* 4.7 7.8 - - - +
124D ASN* 4.1 11.6 + - - +
125D PRO* 3.9 20.2 - - + +
153D GLY* 1.3 74.1 - - - -
155D GLY* 1.3 61.0 + - - +
156D ASN* 6.1 1.3 - - - +
160D ASP* 4.2 3.5 - - - +
161D ILE* 3.4 22.4 - - - +
164D ASP* 2.8 25.6 + - + +
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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