Contacts of the helix formed by residues 129 - 144 (chain A) 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 GLY 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A ILE* 4.9 10.5 - - - -
81A PHE 5.3 1.6 - - - -
125A PRO* 2.8 23.5 + - - +
128A LYS* 1.3 77.3 - - - +
130A LEU* 1.3 66.5 + - - +
131A PRO 3.3 2.2 - - - -
132A LEU* 3.1 22.2 + - - +
133A ILE* 3.2 14.7 + - - +
152A LEU* 4.4 10.6 - - - +
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Residues in contact with LEU 130 (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 LYS 3.6 11.4 - - - +
127A ILE* 3.3 17.9 - - + +
129A GLY* 1.3 75.6 - - - +
131A PRO* 1.4 74.6 - - + +
133A ILE* 3.1 8.5 + - + +
134A GLN* 3.0 24.4 + - - +
150A TYR* 4.9 3.1 - - - +
152A LEU* 3.8 13.7 - - + -
130C LEU* 3.8 30.5 - - + +
133C ILE* 3.6 36.3 - - + -
134C GLN* 4.0 24.0 - - + +
150C TYR* 3.5 17.5 - - - +
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Residues in contact with PRO 131 (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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81A PHE 5.3 1.3 - - - +
127A ILE 4.4 0.7 - - - +
128A LYS 3.6 14.8 - - - +
129A GLY 3.6 0.4 - - - -
130A LEU* 1.4 93.0 - - + +
132A LEU* 1.3 55.6 + - - +
134A GLN* 3.1 14.5 + - - +
135A GLN* 2.9 33.8 + - - +
134C GLN* 3.6 17.0 - - - +
131D PRO* 3.6 22.5 - - + +
134D GLN* 3.8 17.5 - - + -
135D GLN* 4.1 11.9 - - + +
138D HIS* 3.9 20.2 - - + +
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Residues in contact with LEU 132 (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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76A THR* 4.8 1.3 - - + -
78A ILE* 4.2 21.1 - - + -
81A PHE 3.9 15.7 + - - +
82A GLY* 3.8 22.0 - - - +
83A MET* 3.8 28.0 - - + +
119A ALA* 4.4 11.9 - - + -
129A GLY* 3.1 12.0 + - - +
130A LEU 3.1 0.6 - - - -
131A PRO* 1.3 80.6 - - - +
133A ILE* 1.3 63.9 + - + +
135A GLN* 3.2 21.4 + - + +
136A PHE* 3.0 48.8 + - + -
152A LEU* 5.5 1.3 - - + -
135D GLN* 4.8 0.2 - - - +
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Residues in contact with ILE 133 (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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117A VAL* 4.1 20.6 - - + -
119A ALA* 5.4 0.4 - - + -
129A GLY 3.2 12.8 + - - +
130A LEU* 3.1 11.3 + - + +
132A LEU* 1.3 79.2 - - + +
134A GLN* 1.3 58.0 + - - +
136A PHE* 3.2 7.2 + - + +
137A GLU* 2.9 26.7 + - - +
147A PHE* 3.8 9.4 - - + -
150A TYR* 3.8 54.7 - - + -
151A VAL 5.8 0.4 - - - +
152A LEU* 3.9 30.1 - - + -
127C ILE* 4.1 2.5 - - + -
130C LEU* 3.9 15.7 - - + -
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Residues in contact with GLN 134 (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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130A LEU 3.0 13.7 + - - +
131A PRO* 3.4 10.4 - - - +
133A ILE* 1.3 76.0 - - - +
135A GLN* 1.3 65.6 + - - +
137A GLU* 3.2 10.1 + - - +
138A HIS* 3.0 29.8 + - + +
134B GLN* 3.4 28.6 + - - +
138B HIS* 5.8 1.0 + - - -
127C ILE* 5.1 4.2 + - + +
130C LEU* 3.9 28.3 - - + +
131C PRO* 4.0 8.7 - - - +
134C GLN* 3.5 25.6 + - - +
131D PRO* 3.6 15.3 - - + +
134D GLN* 3.4 13.2 - - - +
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Residues in contact with GLN 135 (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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83A MET* 5.7 2.2 - - + -
131A PRO 2.9 16.5 + - - +
132A LEU* 3.2 21.2 + - + +
134A GLN* 1.3 76.6 - - - +
136A PHE* 1.3 57.6 + - - +
138A HIS* 3.0 11.2 + - - +
139A ILE* 2.8 38.9 + - + +
601A PT 4.0 5.5 - - - -
80D TRP 5.1 0.2 - - - +
81D PHE* 2.9 33.3 + - + +
82D GLY* 3.4 13.0 - - - -
131D PRO* 3.8 13.2 - - + -
132D LEU* 4.0 9.9 - - - +
135D GLN* 2.9 42.7 + - - +
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Residues in contact with PHE 136 (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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74A PHE* 4.4 9.4 - - + -
76A THR* 4.6 5.8 - - + -
83A MET* 3.7 24.5 - - + -
87A LEU* 4.0 17.3 - - + -
91A ILE* 4.1 13.9 - - + -
117A VAL* 3.7 37.7 - - + -
132A LEU* 3.0 49.2 + - + -
133A ILE* 3.5 9.2 - - - +
135A GLN* 1.3 76.0 - - - +
137A GLU* 1.3 57.7 + - - +
139A ILE* 3.1 12.2 + - + +
140A PHE* 2.8 66.8 + + + -
147A PHE* 4.3 3.8 - - + -
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Residues in contact with GLU 137 (chain A).
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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133A ILE 2.9 13.2 + - - +
134A GLN* 3.4 12.3 - - - +
135A GLN 3.2 0.2 - - - -
136A PHE* 1.3 77.5 - - - +
138A HIS* 1.3 77.6 + - - +
140A PHE* 4.0 1.7 - - - +
141A HIS* 2.9 42.1 + - - +
147A PHE* 3.7 28.7 - - + +
127C ILE* 3.7 34.6 - - + +
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Residues in contact with HIS 138 (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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134A GLN* 3.0 20.6 + - - +
135A GLN* 3.0 6.5 + - - +
137A GLU* 1.3 87.1 + - - +
139A ILE* 1.3 61.4 + - - +
141A HIS* 3.4 6.9 + - - +
142A PHE* 2.9 24.8 + - - +
81D PHE* 3.3 39.3 - + + -
127D ILE* 4.7 6.1 + - + -
128D LYS* 3.8 46.4 - - + +
131D PRO* 4.0 21.0 - - + +
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Residues in contact with ILE 139 (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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83A MET* 4.2 24.9 - - + -
91A ILE* 4.3 12.3 - - + -
94A TRP* 4.0 21.5 - - + -
135A GLN* 2.8 25.0 + - + +
136A PHE* 3.5 13.9 - - + +
138A HIS* 1.3 77.9 - - - +
140A PHE* 1.3 73.2 + - + +
142A PHE* 3.3 4.1 + - - +
143A MET* 3.2 21.8 + - - +
80D TRP* 3.5 50.6 - - + +
81D PHE* 3.9 10.1 - - + -
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Residues in contact with PHE 140 (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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74A PHE* 3.6 43.5 - + - -
91A ILE* 6.2 0.7 - - + -
94A TRP* 4.9 0.9 - + - -
115A ALA* 3.8 19.5 - - + -
117A VAL* 3.7 21.5 - - + -
136A PHE* 2.8 46.9 + + + +
137A GLU 4.1 2.0 - - - +
139A ILE* 1.3 79.1 - - + +
141A HIS* 1.3 57.5 + - - +
143A MET* 3.1 3.1 + - - +
144A GLY 2.9 8.3 + - - -
145A MET* 2.8 65.6 + - + +
147A PHE* 3.6 32.1 - + + -
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Residues in contact with HIS 141 (chain A).
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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137A GLU* 2.9 34.8 + - - +
138A HIS* 3.8 9.0 - - - +
140A PHE* 1.3 75.1 - - - +
142A PHE* 1.3 64.7 + - - +
144A GLY* 3.1 13.9 + - - +
145A MET 4.2 4.2 + - - -
128D LYS* 5.3 12.6 - - - -
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Residues in contact with PHE 142 (chain A).
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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98A LEU* 4.2 15.9 - - + -
107A LYS* 3.6 33.6 + - - -
138A HIS 2.9 19.0 + - - +
139A ILE* 3.5 4.7 - - - +
140A PHE 3.2 0.2 - - - -
141A HIS* 1.3 79.6 - - - +
143A MET* 1.3 64.8 + - - +
144A GLY 3.6 0.2 + - - -
80D TRP* 3.7 34.8 - + - -
81D PHE* 4.0 13.9 - + + -
123D ASP* 3.9 23.1 - - + -
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Residues in contact with MET 143 (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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94A TRP* 4.1 12.6 - - + -
98A LEU* 4.5 8.1 - - - -
106A PHE* 3.6 33.0 - - + -
107A LYS* 4.0 22.4 - - - +
110A MET* 3.8 23.6 - - + -
111A SER* 3.2 25.1 + - - -
139A ILE 3.2 7.6 + - - +
140A PHE 3.1 1.2 + - - -
142A PHE* 1.3 84.1 - - - +
144A GLY* 1.3 56.3 + - - +
145A MET* 3.0 39.3 - - + -
80D TRP* 3.8 28.5 - - + -
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Residues in contact with GLY 144 (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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111A SER* 3.0 23.1 - - - +
140A PHE 2.9 3.0 + - - -
141A HIS* 3.1 15.0 + - - -
142A PHE 3.3 0.8 + - - -
143A MET* 1.3 77.8 - - - +
145A MET* 1.3 61.9 + - - +
146A SER 3.7 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