Contacts of the strand formed by residues 123 - 129 (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 TRP 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A GLN* 1.3 79.7 - - - +
124A VAL* 1.3 63.2 + - - +
158A PRO* 3.5 39.7 - - + +
159A PRO* 3.0 23.3 + - + +
160A VAL* 3.9 14.4 - - + -
161A GLN* 3.0 23.7 + - - +
230A LEU* 3.4 33.9 - - + -
231A LEU 3.6 2.2 - - - -
232A ASN* 4.4 3.7 - - + +
233A PRO* 4.0 20.5 - - + +
238A THR* 4.8 6.1 - - + -
254A VAL* 4.2 15.7 - - + -
257A HIS* 3.9 11.7 - - + -
258A MET* 3.6 34.8 - - + -
261A PHE* 4.0 30.3 - + + -
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Residues in contact with VAL 124 (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* 4.5 19.7 - - + +
122A GLN* 3.8 29.4 - - + +
123A TRP* 1.3 79.9 - - - +
125A LEU* 1.3 61.8 + - - +
126A MET* 3.8 8.5 + - + -
160A VAL* 5.7 0.2 - - - -
161A GLN* 3.3 17.3 - - - +
163A VAL* 4.1 31.2 - - + -
229A TYR 3.6 2.3 - - - +
230A LEU* 3.7 6.9 - - - +
231A LEU* 2.8 57.3 + - + +
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Residues in contact with LEU 125 (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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124A VAL* 1.3 70.1 - - - +
126A MET* 1.3 69.3 + - - +
127A TYR* 4.4 7.4 - - + +
144A LEU* 4.1 37.5 - - + -
148A VAL* 5.5 7.9 - - + -
160A VAL* 5.2 13.4 - - + -
161A GLN 2.9 14.7 + - - +
162A PRO* 4.2 13.9 - - + -
163A VAL 2.8 31.9 + - - +
228A ILE* 4.1 24.9 - - + -
229A TYR 3.6 6.5 - - - +
230A LEU* 4.6 15.3 - - + -
250A ILE* 6.4 0.4 - - + -
254A VAL* 6.5 1.3 - - + -
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Residues in contact with MET 126 (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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104A PHE* 4.1 23.1 - - + -
106A LEU* 6.4 0.9 - - + -
124A VAL* 4.3 4.0 - - + -
125A LEU* 1.3 73.0 - - - +
127A TYR* 1.3 59.1 + - - +
128A PHE* 4.3 11.2 + - + -
163A VAL* 3.8 19.7 - - + -
165A ILE* 4.3 22.9 - - + -
191A LEU* 5.8 3.4 - - + -
228A ILE* 3.4 8.5 - - - +
229A TYR* 2.9 49.8 + - + +
231A LEU* 4.0 43.7 - - + -
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Residues in contact with TYR 127 (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* 4.4 6.1 - - + -
126A MET* 1.3 73.8 - - - +
128A PHE* 1.3 77.1 + - - +
137A CYS* 3.5 23.1 - - - -
140A GLU* 3.8 21.6 - - + +
141A LEU* 3.6 19.4 - - + +
144A LEU* 4.0 12.8 - - + -
162A PRO* 6.5 0.2 - - + -
163A VAL* 3.0 15.8 + - - +
164A PHE* 3.4 38.1 - + + -
165A ILE* 2.8 33.0 + - - +
224A HIS* 3.6 7.9 - + - -
226A ILE* 3.3 24.2 - - + +
228A ILE* 3.5 25.6 - - + +
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Residues in contact with PHE 128 (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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126A MET* 4.9 11.0 - - + -
127A TYR* 1.3 77.5 - - - +
129A GLY* 1.3 52.0 + - - +
165A ILE* 3.7 41.1 - - + -
167A VAL* 3.9 21.8 - - + -
207A VAL* 5.0 21.1 - - + -
209A TYR* 6.4 1.3 - + - -
224A HIS* 2.8 29.4 + - + +
226A ILE* 6.0 0.2 - - - -
227A ALA 4.5 12.1 + - - +
229A TYR* 3.9 35.7 - + - -
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Residues in contact with GLY 129 (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* 3.9 1.2 + - - -
128A PHE* 1.3 73.5 - - - +
130A PHE* 1.3 61.9 + - - +
137A CYS* 4.9 0.2 - - - -
164A PHE* 3.8 20.4 - - - -
165A ILE 2.9 12.2 + - - +
166A THR* 3.3 0.9 - - - -
167A VAL* 2.9 33.0 + - - +
224A HIS* 3.9 15.0 - - - -
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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