Contacts of the helix formed by residues 155 - 162 (chain A) in PDB entry 1PJJ
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 LYS 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A THR 5.1 2.7 - - - +
154A LYS* 1.3 75.0 - - - +
156A ILE* 1.3 66.3 + - - +
157A LYS 3.4 0.2 - - - -
158A PRO* 3.1 24.1 - - + +
159A TYR* 3.1 20.3 + - - +
185A PRO 3.9 6.7 - - - +
186A GLU* 3.7 43.6 + - + +
187A LYS 3.5 6.3 - - - -
188A GLU* 5.2 4.3 - - + -
189A THR* 4.2 0.2 - - - -
257A VAL* 4.6 10.7 - - + +
258A ALA* 5.7 4.3 - - + +
18E A 4.8 16.7 + - - +
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Residues in contact with ILE 156 (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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149A LEU* 3.9 13.5 - - + -
154A LYS 3.7 1.0 + - - -
155A LYS* 1.3 72.4 - - - +
157A LYS* 1.3 66.6 + - - +
159A TYR* 3.4 0.4 + - - -
160A LEU* 3.0 49.7 + - + +
165A LEU* 5.1 1.6 - - + -
178A LEU* 4.0 11.9 - - + -
183A ILE* 4.0 12.1 - - + -
184A HIS 3.4 25.6 - - - +
185A PRO* 3.5 8.1 - - + +
187A LYS 2.8 18.4 + - - +
189A THR* 3.7 22.4 - - + -
192A LEU* 4.1 11.4 - - + -
200A LEU* 3.9 19.5 - - + -
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Residues in contact with LYS 157 (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 ILE* 1.3 81.6 - - - +
158A PRO* 1.3 74.6 - - + +
160A LEU* 3.2 2.4 + - - +
161A LEU* 3.0 36.0 + - + +
171A ASN* 2.8 29.2 + - - -
174A VAL* 3.7 18.7 - - + +
175A ASP* 2.8 28.3 + - - +
178A LEU* 3.9 11.0 - - + -
185A PRO* 3.2 21.4 + - + +
257A VAL* 4.7 7.0 - - + +
260A ARG* 4.3 6.9 - - - +
261A GLY 3.0 8.7 + - - -
262A THR* 2.9 34.9 + - + +
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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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154A LYS* 6.0 1.8 - - + -
155A LYS* 3.1 33.4 - - + +
157A LYS* 1.3 96.9 - - + +
159A TYR* 1.3 60.1 + - - +
161A LEU* 3.3 19.7 + - + +
162A GLU* 3.3 18.1 + - - +
185A PRO 4.0 1.6 - - - +
257A VAL* 4.0 9.6 - - + +
258A ALA* 3.8 29.2 - - + -
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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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148A LYS* 4.1 20.9 + - - +
149A LEU* 4.4 0.9 - - + -
152A SER* 3.6 30.3 - - - -
154A LYS* 3.9 20.2 + - + +
155A LYS 3.1 19.1 + - - +
156A ILE* 3.8 5.4 - - - +
158A PRO* 1.3 78.6 - - - +
160A LEU* 1.3 61.2 + - - +
162A GLU* 3.1 44.2 + - - +
163A GLN 4.4 0.7 + - - -
164A THR* 3.7 12.7 + - - -
165A LEU* 3.6 41.1 - - + +
189A THR* 3.9 19.3 - - + -
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Residues in contact with LEU 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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145A PHE* 4.3 10.5 - - + -
156A ILE* 3.0 42.5 + - + +
157A LYS 3.7 3.8 - - - +
159A TYR* 1.3 76.9 - - - +
161A LEU* 1.3 61.5 + - - +
162A GLU 3.3 0.7 + - - -
163A GLN* 3.6 14.4 + - - -
165A LEU* 4.0 20.8 + - + -
166A VAL* 4.4 11.9 + - + +
169A LEU* 4.1 24.8 - - + +
174A VAL* 4.0 22.7 - - + -
177A VAL* 5.1 2.2 - - + -
178A LEU* 4.1 13.7 - - + -
200A LEU* 4.4 10.1 - - + -
204A ILE* 4.0 22.4 - - + -
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Residues in contact with LEU 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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57A LYS* 5.1 1.0 + - - +
157A LYS* 3.0 44.0 + - + +
158A PRO* 3.6 12.6 - - + +
159A TYR 3.2 0.4 - - - -
160A LEU* 1.3 76.0 - - - +
162A GLU* 1.3 61.3 + - - +
163A GLN* 3.2 17.6 + - - +
169A LEU 4.0 4.5 - - - +
170A GLY* 3.6 38.1 - - - +
171A ASN* 4.0 3.4 - - - +
174A VAL* 4.0 9.9 - - + -
257A VAL 6.1 0.2 - - - +
258A ALA* 6.6 0.4 - - + -
260A ARG* 4.1 31.9 - - + +
8D T 5.2 0.4 - - - +
9D T 4.5 5.2 + - + +
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Residues in contact with GLU 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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154A LYS* 2.7 42.5 + - - +
158A PRO 3.3 13.0 + - - +
159A TYR* 3.1 22.4 + - - +
161A LEU* 1.3 76.8 - - - +
163A GLN* 1.3 65.0 + - - +
164A THR* 3.1 37.0 + - + +
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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