Contacts of the helix formed by residues 157 - 171 (chain A) in PDB entry 3K6R
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 ASP 157 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A GLU* 2.9 16.9 + - - +
156A LYS* 1.3 77.7 - - - +
158A PRO* 1.4 69.0 - - - +
159A TYR* 3.7 10.9 + - - +
160A THR* 2.6 33.2 + - - +
161A PHE* 2.9 30.1 + - - +
181A ASN* 3.8 0.9 - - - -
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Residues in contact with PRO 158 (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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156A LYS 3.4 8.9 - - - +
157A ASP* 1.4 91.7 - - - +
159A TYR* 1.3 62.0 + - - +
161A PHE* 3.4 4.9 + - + +
162A LYS* 3.2 32.8 + - - +
181A ASN* 3.8 24.0 - - - +
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Residues in contact with TYR 159 (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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89A VAL* 4.5 5.0 - - - +
102A ASP* 2.6 45.2 + - + +
105A LYS* 4.1 18.4 - - + -
106A ILE* 4.6 6.3 - - + -
157A ASP* 3.4 12.2 + - - +
158A PRO* 1.3 78.8 - - - +
160A THR* 1.3 62.4 + - - +
162A LYS* 3.3 33.9 + - + +
163A PHE* 3.3 38.8 - + - -
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Residues in contact with THR 160 (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 ILE* 3.9 29.0 - - + +
135A GLY* 3.5 34.0 - - - +
136A ILE* 3.9 10.0 - - + +
155A GLU* 3.9 7.6 - - + -
157A ASP* 2.6 34.2 + - - +
159A TYR* 1.3 73.8 - - - +
161A PHE* 1.3 66.7 + - - +
163A PHE* 3.2 7.4 + - - +
164A LEU* 3.0 18.5 + - - +
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Residues in contact with PHE 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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155A GLU* 3.9 8.8 - - - +
157A ASP 2.9 17.7 + - - +
158A PRO 3.5 7.2 - - - +
160A THR* 1.3 76.4 - - - +
162A LYS* 1.3 60.0 + - + +
164A LEU* 3.2 16.8 + - + +
165A VAL* 2.9 49.1 + - + +
179A ALA* 3.7 20.2 - - + -
180A TYR* 3.4 17.9 - - - -
181A ASN* 3.4 56.3 - - + +
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Residues in contact with LYS 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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158A PRO* 3.2 21.8 + - - +
159A TYR* 3.5 26.7 - - + +
160A THR 3.3 0.6 - - - -
161A PHE* 1.3 80.6 - - + +
163A PHE* 1.3 61.2 + - + +
165A VAL* 3.4 6.3 + - - +
166A GLU* 3.0 43.2 + - - +
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Residues in contact with PHE 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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89A VAL* 4.0 20.6 - - + -
100A LYS* 3.5 34.1 - - + +
101A LEU* 3.7 23.1 - - - -
102A ASP* 3.8 13.9 - - + -
106A ILE* 3.5 14.1 - - + -
136A ILE* 3.8 9.0 - - + -
159A TYR* 3.3 63.9 - + - -
160A THR 3.2 6.1 + - - +
162A LYS* 1.3 76.2 - - + +
164A LEU* 1.3 55.8 + - - +
166A GLU* 3.2 12.1 + - - +
167A ASN* 2.7 41.5 + - - -
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Residues in contact with LEU 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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134A ALA* 3.9 22.7 - - + -
135A GLY 3.4 14.1 - - - +
136A ILE* 3.6 10.3 - - - +
137A GLY* 3.5 31.9 - - - +
141A LEU* 5.5 0.4 - - + -
153A ALA* 4.0 6.7 - - + +
155A GLU* 4.1 12.8 - - + -
160A THR 3.0 8.2 + - - +
161A PHE* 3.3 15.7 - - + +
163A PHE* 1.3 74.1 - - - +
165A VAL* 1.3 63.3 + - - +
167A ASN* 3.2 2.4 + - - +
168A ILE* 3.0 27.4 + - + +
177A MSE 3.9 20.6 - - + -
179A ALA* 3.6 28.3 - - + -
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Residues in contact with VAL 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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161A PHE* 2.9 58.0 + - + +
162A LYS* 3.7 6.1 - - - +
164A LEU* 1.3 71.9 - - - +
166A GLU* 1.3 63.1 + - + +
168A ILE* 3.2 17.5 + - + +
169A HIS* 3.1 38.1 + - + +
179A ALA* 4.4 8.3 - - + -
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Residues in contact with GLU 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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100A LYS* 2.8 46.5 + - + +
162A LYS* 3.0 32.8 + - - +
163A PHE* 3.7 14.2 - - - +
165A VAL* 1.3 76.6 - - + +
167A ASN* 1.3 57.9 + - - +
169A HIS* 3.3 8.4 + - - +
170A LEU* 2.9 33.4 + - + +
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Residues in contact with ASN 167 (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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98A LYS 3.6 10.4 - - - +
99A TYR* 3.9 4.4 - - - +
100A LYS* 2.7 54.4 + - - +
136A ILE* 2.9 26.7 + - - +
141A LEU* 3.6 20.7 - - + +
163A PHE 2.7 21.3 + - - +
164A LEU 3.2 3.8 + - - +
166A GLU* 1.3 69.6 - - - +
168A ILE* 1.3 64.8 + - - +
170A LEU* 3.8 6.2 - - - +
171A ASN* 2.8 33.4 + - - +
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Residues in contact with ILE 168 (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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141A LEU* 4.3 1.1 - - + -
164A LEU* 3.0 15.9 + - + +
165A VAL* 3.2 11.0 + - + +
167A ASN* 1.3 75.3 - - - +
169A HIS* 1.3 66.4 + - + +
172A LYS 3.3 3.3 + - - -
173A VAL* 3.1 38.2 + - + +
174A GLU* 3.6 30.8 - - + +
177A MSE 3.7 55.2 - - + +
179A ALA* 3.6 31.4 - - + +
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Residues in contact with HIS 169 (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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165A VAL* 3.1 36.1 + - + +
166A GLU* 3.3 9.0 + - - +
167A ASN 3.3 0.4 - - - -
168A ILE* 1.3 79.9 - - + +
170A LEU* 1.3 64.9 + - - +
172A LYS* 3.2 17.0 + - - +
174A GLU* 4.1 39.3 - - + +
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Residues in contact with LEU 170 (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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91A VAL* 4.4 14.1 - - + -
98A LYS* 4.2 40.6 + - + +
100A LYS* 4.0 21.8 - - + -
166A GLU* 2.9 23.2 + - + +
167A ASN* 3.4 24.8 + - - +
169A HIS* 1.3 74.0 - - + +
171A ASN* 1.3 58.7 + - - +
172A LYS* 3.4 12.5 + - - +
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Residues in contact with ASN 171 (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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96A GLY 4.4 3.3 - - - +
97A ILE* 3.6 14.3 - - - +
98A LYS* 2.7 52.5 + - - +
141A LEU* 3.7 12.7 - - + +
145A VAL* 3.9 22.6 - - + +
167A ASN* 2.8 28.5 + - - +
168A ILE 4.3 1.6 - - - +
170A LEU* 1.3 75.3 - - - +
172A LYS* 1.3 71.8 + - - +
173A VAL* 3.4 16.2 + - + +
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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