Contacts of the helix formed by residues 135 - 150 (chain A) in PDB entry 3RK6
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 PHE 135 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LEU* 3.7 31.2 - - + -
90A LEU* 4.2 4.9 - - + -
91A THR* 3.4 36.8 - - + -
125A ILE* 5.2 1.6 - - + -
128A GLN* 3.5 31.6 - - + +
129A ALA* 3.8 18.1 - - + -
132A ILE* 3.4 23.6 + - + +
133A PRO 3.2 0.6 - - - -
134A ASN* 1.3 81.3 - - - +
136A SER* 1.3 56.7 + - - +
137A TYR 3.5 2.0 - - - -
138A MET* 3.5 33.4 - - + +
139A GLY* 2.8 47.7 + - - -
142A LEU* 5.2 2.0 - - + -
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Residues in contact with SER 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ALA 4.5 3.3 + - - -
134A ASN* 3.6 4.0 + - - -
135A PHE* 1.3 77.7 + - - +
137A TYR* 1.3 65.3 + - - +
140A ALA* 3.1 25.8 + - - +
190A ALA* 3.9 8.3 + - - -
193A LEU* 3.4 39.7 - - - +
194A PHE* 3.6 18.5 + - - +
197A GLU* 3.7 9.7 - - - +
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Residues in contact with TYR 137 (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 ASN 5.3 1.7 + - - +
135A PHE 3.5 0.2 - - - -
136A SER* 1.3 77.6 - - - +
138A MET* 1.3 78.7 + - + +
140A ALA* 3.3 2.9 + - - +
141A ARG* 2.9 71.0 + - + +
197A GLU* 3.7 33.9 - - - +
201A ASN* 4.7 10.1 - - - -
94B PRO* 3.7 36.9 + - + -
95B GLY* 3.4 33.9 - - - -
98B GLU* 5.0 8.1 + - - -
141B ARG* 5.9 0.9 + - - -
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Residues in contact with MET 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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90A LEU* 4.1 18.4 - - + +
94A PRO* 3.5 43.5 - - + +
97A PHE* 3.6 31.0 - - + -
134A ASN 5.2 2.8 + - - +
135A PHE* 3.5 39.7 + - + +
136A SER 3.4 0.2 - - - -
137A TYR* 1.3 92.5 - - + +
139A GLY* 1.3 54.0 + - - +
141A ARG* 3.6 20.1 - - - +
142A LEU* 2.8 36.7 + - - +
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Residues in contact with GLY 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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125A ILE* 4.5 3.3 - - - +
129A ALA* 4.2 4.5 - - - -
135A PHE* 2.8 41.0 + - - -
136A SER 3.9 0.9 - - - -
138A MET* 1.3 74.2 - - - +
140A ALA* 1.3 54.8 + - - +
142A LEU* 3.7 3.9 - - - +
143A CYS* 2.8 33.4 + - - -
194A PHE* 3.7 11.7 - - - -
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Residues in contact with ALA 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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136A SER 3.1 17.8 + - - +
137A TYR 3.8 1.8 - - - +
139A GLY* 1.3 72.6 - - - +
141A ARG* 1.3 61.7 + - - +
143A CYS* 3.6 1.2 - - - +
144A ASN* 2.9 30.0 + - - +
194A PHE* 3.5 11.5 - - + -
197A GLU* 3.5 27.6 - - + +
198A LEU* 3.6 26.7 - - + +
201A ASN* 4.6 7.2 - - + +
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Residues in contact with ARG 141 (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 PRO 4.5 2.6 + - - -
97A PHE* 3.4 50.2 - - + +
98A GLU* 2.5 42.4 + - - +
137A TYR* 2.9 53.6 + - + +
138A MET* 3.6 16.4 - - - +
140A ALA* 1.3 76.9 - - - +
142A LEU* 1.3 58.5 + - - +
144A ASN* 3.4 6.3 + - - +
145A TYR* 3.0 28.8 + - - +
201A ASN* 5.2 7.8 - - + +
98B GLU* 5.8 1.8 + - - -
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Residues in contact with LEU 142 (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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86A PHE* 4.4 4.3 - - + -
87A LEU* 3.7 30.1 - - + -
90A LEU* 4.5 9.4 - - + -
97A PHE* 3.9 13.2 - - + -
101A ILE* 3.5 29.8 - - + -
104A PHE* 4.0 15.5 - - + -
125A ILE* 3.8 25.8 - - + -
135A PHE* 5.2 2.0 - - + -
138A MET 2.8 18.6 + - - +
139A GLY 3.7 2.7 - - - +
141A ARG* 1.3 75.5 - - - +
143A CYS* 1.3 64.2 + - - +
145A TYR* 3.2 2.3 + - - +
146A LEU* 2.9 42.4 + - + +
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Residues in contact with CYS 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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125A ILE* 3.8 22.9 - - - -
139A GLY 2.8 25.1 + - - +
140A ALA 3.6 4.9 - - - +
142A LEU* 1.3 76.2 - - - +
144A ASN* 1.3 62.3 + - - +
147A SER* 3.0 25.7 + - - -
159A PHE* 3.5 17.5 - - + -
163A LEU* 3.7 36.1 - - + -
194A PHE* 3.9 14.8 - - - -
198A LEU* 3.9 8.5 - - + -
202A LEU* 4.4 2.4 - - + +
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Residues in contact with ASN 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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140A ALA 2.9 17.1 + - - +
141A ARG* 3.8 6.5 + - - +
143A CYS* 1.3 75.1 - - - +
145A TYR* 1.3 65.3 + - - +
147A SER* 2.8 20.7 + - - -
148A HIS* 3.0 31.6 + - - -
201A ASN* 3.2 23.0 + - + +
202A LEU* 3.6 11.9 - - - +
203A GLU* 3.0 45.1 + - - -
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Residues in contact with TYR 145 (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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97A PHE* 4.0 17.7 - + + -
101A ILE* 3.3 44.0 - - + -
102A GLU* 3.4 28.3 + - + +
105A ALA* 3.8 13.7 - - + +
141A ARG 3.0 18.2 + - - +
142A LEU 3.6 4.7 - - - +
144A ASN* 1.3 79.5 - - - +
146A LEU* 1.3 64.7 + - + +
148A HIS* 3.1 3.4 + - - -
149A HIS* 2.8 84.1 + + + -
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Residues in contact with LEU 146 (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* 4.3 13.5 - - + -
105A ALA* 4.4 18.4 - - + -
108A LEU* 4.1 19.5 - - + -
121A LEU* 4.6 2.0 - - + -
125A ILE* 3.4 33.0 - - + -
142A LEU* 2.9 33.1 + - + +
143A CYS 4.1 2.2 - - - +
145A TYR* 1.3 78.6 - - + +
147A SER* 1.3 67.1 + - - +
149A HIS 4.2 1.3 - - - +
150A LEU* 3.0 54.8 + - + +
159A PHE* 4.1 15.5 - - + +
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Residues in contact with SER 147 (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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143A CYS 3.0 16.9 + - - -
144A ASN* 2.8 19.3 + - - -
146A LEU* 1.3 79.8 - - - +
148A HIS* 1.3 67.1 + - - +
150A LEU 4.9 3.1 - - - +
159A PHE* 4.1 17.3 - - - +
160A ARG* 3.6 49.5 + - - +
202A LEU* 3.9 8.7 - - - +
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Residues in contact with HIS 148 (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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144A ASN* 3.0 43.2 + - - -
145A TYR* 3.1 2.9 + - - +
147A SER* 1.3 84.4 + - - +
149A HIS* 1.3 76.9 + - + +
150A LEU 3.8 3.8 - - - +
160A ARG* 3.2 16.3 + - - -
203A GLU* 3.1 39.6 + - + +
204A ILE* 5.2 0.2 - - - -
205A LYS 5.5 2.0 + - - -
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Residues in contact with HIS 149 (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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105A ALA* 4.2 10.5 - - + +
109A ASN* 3.4 17.5 + - - -
145A TYR* 2.8 85.9 + + + +
146A LEU* 4.8 0.4 - - - -
148A HIS* 1.3 88.7 - - + +
150A LEU* 1.3 65.6 + - - +
151A THR* 3.6 4.4 + - - +
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Residues in contact with LEU 150 (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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105A ALA* 4.3 3.6 - - - +
108A LEU* 3.7 30.1 - - + -
109A ASN* 3.3 13.2 - - - +
112A VAL* 5.6 3.6 - - + -
118A LEU* 4.1 10.8 - - + -
121A LEU* 3.7 15.3 - - + -
146A LEU* 3.0 39.6 + - + +
147A SER 4.9 3.5 - - - +
148A HIS 4.5 4.0 - - - +
149A HIS* 1.3 79.4 + - - +
151A THR* 1.3 62.3 + - - +
152A ILE* 3.5 15.6 - - + +
159A PHE* 3.6 34.8 - - + -
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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