Contacts of the helix formed by residues 156 - 175 (chain A) in PDB entry 6JOD
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 ASN 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A ARG* 3.2 1.4 - - - +
155A ARG* 1.3 80.2 - - - +
157A PRO* 1.3 64.7 - - - +
158A TRP* 3.1 16.3 + - - +
159A GLN* 2.7 62.3 + - - +
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Residues in contact with PRO 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LYS* 5.5 7.6 - - - +
78A VAL* 5.0 2.0 - - + -
81A ILE* 5.1 12.2 - - + +
154A ARG* 3.2 44.6 - - + +
156A ASN* 1.3 89.0 - - - +
158A TRP* 1.3 68.5 + - + +
160A ALA* 3.1 13.1 + - + +
161A SER* 2.9 23.7 + - - -
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Residues in contact with TRP 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 ASN* 2.9 11.3 + - - +
157A PRO* 1.3 86.3 - - + +
159A GLN* 1.3 59.8 + - - +
161A SER* 3.0 33.1 + - - -
162A TYR* 2.9 51.0 + + + -
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Residues in contact with GLN 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A VAL* 5.3 4.0 - - + +
155A ARG* 2.9 47.5 + - - +
156A ASN* 2.7 41.8 + - - +
158A TRP* 1.3 72.7 - - - +
160A ALA* 1.3 61.5 + - + +
162A TYR* 3.2 11.9 + - - +
163A ILE* 2.9 44.1 + - + +
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Residues in contact with ALA 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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78A VAL* 4.3 28.7 - - + -
81A ILE* 4.5 23.8 - - + -
82A TYR* 4.7 6.7 - - + +
157A PRO 3.1 11.7 + - - +
159A GLN* 1.3 79.8 - - + +
161A SER* 1.3 57.0 + - - +
162A TYR 3.0 5.2 - - - -
163A ILE* 4.1 9.4 - - - +
164A VAL* 2.9 37.2 + - - +
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Residues in contact with SER 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 5.9 0.4 - - - +
157A PRO 2.9 8.0 + - - -
158A TRP* 3.0 46.2 + - - -
160A ALA* 1.3 74.1 - - - +
162A TYR* 1.3 59.9 + - - +
164A VAL* 5.1 2.5 - - - -
165A PRO* 3.2 21.9 - - - +
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Residues in contact with TYR 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 TRP* 2.9 44.1 + + + -
159A GLN* 3.2 10.7 + - - +
160A ALA 3.0 0.2 - - - -
161A SER* 1.3 82.0 - - - +
163A ILE* 1.3 64.1 + - + +
164A VAL 3.4 0.7 - - - -
165A PRO* 3.4 6.6 - - + +
166A LEU* 3.3 20.5 + - - +
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Residues in contact with ILE 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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78A VAL* 6.3 0.2 - - + -
82A TYR* 3.3 34.8 - - + +
137A CYS* 4.2 7.6 - - - -
159A GLN* 2.9 35.9 + - + +
160A ALA* 3.1 4.9 + - - +
162A TYR* 1.3 75.4 - - + +
164A VAL* 1.3 67.0 + - - +
166A LEU* 2.9 17.5 + - + +
167A VAL* 2.8 37.2 + - + +
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Residues in contact with VAL 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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81A ILE* 4.0 12.8 - - + -
82A TYR* 4.5 12.1 - - + -
85A ASN* 3.2 37.9 - - - +
134A PHE* 4.2 4.3 - - + -
160A ALA 2.9 16.8 + - - +
161A SER* 5.1 2.0 - - - -
163A ILE* 1.3 75.6 - - - +
165A PRO* 1.3 70.6 - - + +
167A VAL* 3.2 5.9 + - - +
168A TRP* 3.0 48.3 + - + +
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Residues in contact with PRO 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 SER 3.2 26.7 - - - +
162A TYR* 3.4 10.5 - - + +
164A VAL* 1.3 94.3 - - + +
166A LEU* 1.3 54.1 + - - +
168A TRP* 3.8 7.6 - - + +
169A CYS* 2.9 40.2 + - - -
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Residues in contact with LEU 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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162A TYR 3.3 11.5 + - - +
163A ILE* 2.9 22.6 + - + +
165A PRO* 1.3 79.0 - - - +
167A VAL* 1.3 58.6 + - + +
169A CYS* 3.3 6.6 + - + +
170A MET* 2.9 44.5 + - + +
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Residues in contact with VAL 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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130A ALA* 4.7 3.6 - - - +
133A PHE* 3.7 31.3 - - + +
134A PHE* 3.6 37.9 - - + -
137A CYS* 4.7 10.3 - - + -
163A ILE* 2.8 38.2 + - + +
164A VAL 3.7 4.9 - - - +
166A LEU* 1.3 74.1 - - + +
168A TRP* 1.3 63.2 + - - +
170A MET* 3.2 8.4 + - - +
171A ALA* 2.9 22.5 + - - +
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Residues in contact with TRP 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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85A ASN* 4.4 14.8 + - + -
88A VAL* 4.9 12.1 - - + -
89A ALA* 4.2 12.3 - - + -
92A LEU* 5.5 5.2 - - + -
126A LEU* 4.1 18.7 - - + +
127A ASN* 3.8 22.0 - - - -
130A ALA* 3.7 28.0 - - + -
134A PHE* 3.7 23.9 - + - -
164A VAL* 3.0 49.1 + - + +
165A PRO* 3.9 7.9 - - + +
167A VAL* 1.3 74.7 - - - +
169A CYS* 1.3 59.7 + - - +
171A ALA* 3.3 4.3 + - - +
172A CYS* 2.9 37.3 + - - -
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Residues in contact with CYS 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 PRO* 2.9 26.9 + - - +
166A LEU* 3.8 8.5 - - + +
167A VAL 3.2 0.2 - - - -
168A TRP* 1.3 76.0 - - - +
170A MET* 1.3 60.3 + - - +
172A CYS* 3.3 8.0 + - - +
173A LEU* 2.9 38.3 + - + +
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Residues in contact with MET 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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133A PHE* 4.0 28.5 - - + -
166A LEU* 2.9 33.4 + - + +
167A VAL* 3.2 7.6 + - - +
169A CYS* 1.3 74.4 - - - +
171A ALA* 1.3 59.6 + - - +
173A LEU* 3.4 11.5 + - + +
174A SER* 2.9 35.8 + - - +
218A LEU* 6.3 2.7 - - + -
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Residues in contact with ALA 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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126A LEU* 3.5 21.6 - - + +
129A PHE* 3.7 16.2 - - + -
130A ALA* 3.6 31.0 - - + +
133A PHE* 3.9 4.2 - - + -
167A VAL 2.9 16.4 + - - +
168A TRP* 3.6 3.6 - - - +
170A MET* 1.3 76.6 - - - +
172A CYS* 1.3 57.2 + - - +
174A SER* 3.3 2.4 + - - -
175A SER* 2.9 29.3 + - - -
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Residues in contact with CYS 172 (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 LEU* 3.5 23.8 - - - -
168A TRP* 2.9 30.4 + - - +
169A CYS* 3.6 9.4 - - - +
171A ALA* 1.3 75.5 - - - +
173A LEU* 1.3 64.5 + - + +
175A SER* 2.8 24.6 + - - -
176A LEU* 3.0 17.6 + - + +
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Residues in contact with LEU 173 (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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169A CYS* 2.9 25.8 + - + +
170A MET* 3.8 10.1 - - + +
172A CYS* 1.3 77.2 - - + +
174A SER* 1.3 61.5 + - - +
176A LEU* 3.3 41.0 + - + +
177A PRO* 4.0 3.1 - - - +
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Residues in contact with SER 174 (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 THR* 4.7 0.3 - - - +
129A PHE* 3.2 39.1 - - - -
133A PHE* 3.9 13.8 - - - -
170A MET* 2.9 21.5 + - - +
171A ALA 4.4 0.2 - - - -
173A LEU* 1.3 77.1 - - - +
175A SER* 1.3 56.2 + - - +
176A LEU 3.2 0.9 - - - -
177A PRO* 3.2 17.5 - - - +
178A THR* 5.1 0.9 + - - -
218A LEU* 3.6 28.2 - - - +
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Residues in contact with SER 175 (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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122A SER* 4.0 9.0 + - - -
125A THR* 3.6 26.9 - - - -
126A LEU* 3.8 22.3 - - - +
129A PHE* 3.7 0.2 - - - -
171A ALA 2.9 13.9 + - - -
172A CYS* 2.8 19.3 + - - -
174A SER* 1.3 74.7 - - - +
176A LEU* 1.3 60.0 + - - +
177A PRO* 3.3 2.5 - - - -
178A THR* 3.2 4.9 + - - +
179A PHE* 2.7 29.2 + - - +
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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