Contacts of the helix formed by residues 150 - 162 (chain A) in PDB entry 2J6U
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 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A MET* 4.6 6.7 - - + -
6A VAL* 3.5 11.0 - - - -
148A SER* 3.4 1.4 + - - -
149A LYS* 1.3 89.5 - - - +
151A LYS* 1.3 63.5 + - - +
152A VAL* 3.1 5.5 + - - +
153A PHE* 2.8 48.1 + - - -
154A ALA* 3.0 20.8 + - - +
234A ASP* 5.8 1.8 + - - +
236A TYR* 3.5 48.3 + - + +
238A GLU 5.4 0.2 - - - +
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Residues in contact with LYS 151 (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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6A VAL* 3.7 6.1 - - + +
103A GLU* 2.9 37.3 + - - +
111A TYR* 3.1 53.8 - - + -
150A ASN* 1.3 73.9 - - - +
152A VAL* 1.3 65.1 + - + +
154A ALA* 3.2 1.2 + - - +
155A LYS* 3.0 19.1 + - - +
236A TYR* 4.4 10.2 + - + +
238A GLU* 3.3 38.6 + - - +
239A PRO 3.0 21.9 + - - +
240A ILE* 4.1 15.3 - - + -
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Residues in contact with VAL 152 (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 TYR* 5.4 1.1 - - - -
150A ASN* 3.1 6.7 + - - +
151A LYS* 1.3 76.0 - - + +
153A PHE* 1.3 60.0 + - + +
155A LYS* 3.3 6.0 + - - +
156A ILE* 3.0 39.2 + - + +
186A VAL* 4.7 0.7 - - + -
187A PRO* 3.8 29.1 - - + +
227A TYR* 3.6 24.9 - - + +
231A LEU* 3.9 22.0 - - + -
236A TYR* 3.3 32.3 - - + +
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Residues in contact with PHE 153 (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 SER* 3.2 24.2 - - - +
149A LYS* 5.3 0.2 - - + -
150A ASN* 2.8 39.8 + - - +
152A VAL* 1.3 70.5 - - - +
154A ALA* 1.3 59.4 + - - +
156A ILE* 4.0 22.0 - - + -
157A ALA* 2.8 29.6 + - - +
169A ILE* 3.5 7.4 - - + +
174A VAL* 3.8 36.1 - - + -
177A LEU* 4.4 29.4 - - + -
178A ILE* 4.2 7.0 - - + -
181A LEU* 5.0 0.9 - - + -
205A LEU* 4.2 20.6 - - + -
231A LEU* 3.6 31.6 - - + -
234A ASP* 6.1 2.0 - - - -
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Residues in contact with ALA 154 (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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6A VAL* 3.8 22.9 - - + +
8A PHE* 3.7 13.8 - - + -
146A GLY* 3.4 32.6 - - - +
148A SER* 3.7 10.9 - - - +
150A ASN 3.0 16.6 + - - +
151A LYS 3.2 4.5 + - - +
153A PHE* 1.3 76.9 - - - +
155A LYS* 1.3 63.1 + - - +
157A ALA* 3.3 1.5 + - - -
158A ALA* 3.0 18.4 + - - +
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Residues in contact with LYS 155 (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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8A PHE* 3.5 22.0 - - + -
10A ASP* 4.6 3.0 + - - -
109A GLU* 3.3 31.0 + - - +
111A TYR* 3.6 21.3 - - + +
151A LYS 3.0 13.0 + - - +
152A VAL* 3.5 9.2 - - - +
154A ALA* 1.3 74.9 - - - +
156A ILE* 1.3 65.4 + - - +
158A ALA* 2.9 5.9 + - - +
159A ASP* 2.9 38.5 + - - +
162A LYS* 5.8 0.6 - - - +
187A PRO* 3.7 29.4 - - + -
13P C 4.9 16.6 + - - -
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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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152A VAL* 3.0 26.8 + - + +
153A PHE* 3.6 23.1 - - + +
155A LYS* 1.3 74.9 - - - +
157A ALA* 1.3 65.0 + - - +
159A ASP* 3.1 12.3 + - + +
160A MET* 3.0 43.1 + - + +
169A ILE* 4.2 4.9 - - + -
177A LEU* 4.5 8.3 - - + -
181A LEU* 3.7 33.9 - - + -
185A ASP 4.4 6.3 - - - +
186A VAL* 4.9 2.5 - - + -
187A PRO* 4.0 27.4 - - + -
205A LEU* 6.0 0.7 - - + -
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Residues in contact with ALA 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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146A GLY* 3.9 6.3 - - - -
147A ILE 3.9 6.5 - - - +
153A PHE 2.8 18.4 + - - +
154A ALA 3.4 6.5 - - - +
155A LYS 3.2 0.2 - - - -
156A ILE* 1.3 76.8 - - - +
158A ALA* 1.3 61.2 + - - +
160A MET* 3.4 9.4 + - - +
161A ALA* 3.3 15.6 + - - +
167A LYS* 3.8 32.2 - - + +
169A ILE* 3.5 26.7 - - + -
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Residues in contact with ALA 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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8A PHE* 3.5 31.4 - - + -
10A ASP* 4.9 4.7 - - + -
144A THR* 3.6 19.8 - - + +
145A VAL 4.4 0.7 - - - -
146A GLY* 3.9 11.0 - - - +
154A ALA 3.0 5.7 + - - +
155A LYS 2.9 9.8 + - - +
157A ALA* 1.3 73.3 - - - +
159A ASP* 1.3 68.7 + - - +
160A MET 3.0 1.3 - - - -
161A ALA* 2.8 12.8 + - - -
162A LYS* 3.1 17.6 + - - +
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Residues in contact with ASP 159 (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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8A PHE* 5.7 0.2 - - - -
10A ASP* 4.9 0.3 - - - +
155A LYS* 2.9 40.8 + - - +
156A ILE* 3.6 14.7 - - + +
158A ALA* 1.3 72.4 - - - +
160A MET* 1.3 62.2 + - + +
161A ALA 3.5 0.2 + - - -
162A LYS* 3.6 40.8 + - + +
185A ASP 5.0 6.9 - - - +
187A PRO* 5.2 2.8 - - - +
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Residues in contact with MET 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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156A ILE* 3.0 20.3 + - + +
157A ALA* 3.6 10.3 - - - +
158A ALA 2.9 1.0 + - - -
159A ASP* 1.3 79.6 - - + +
161A ALA* 1.3 57.5 + - - +
162A LYS 3.6 2.9 + - - +
167A LYS* 3.5 30.1 - - + -
169A ILE* 3.2 35.7 - - + -
173A GLU* 4.5 1.8 - - - +
177A LEU* 4.4 16.2 - - + -
181A LEU* 6.1 2.5 - - - -
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Residues in contact with ALA 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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144A THR* 3.7 9.4 - - + -
145A VAL 4.8 0.2 - - - +
157A ALA 3.3 13.0 + - - +
158A ALA 2.8 3.4 + - - -
160A MET* 1.3 77.0 - - - +
162A LYS* 1.3 63.8 + - - +
163A PRO 3.2 12.5 - - - +
165A GLY* 3.4 9.5 - - - -
166A ILE 3.6 26.0 - - - +
167A LYS* 4.0 14.8 - - + +
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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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10A ASP* 3.1 29.5 + - - -
12A ASP* 5.1 1.6 - - - +
51A TYR* 3.9 8.3 - - - +
144A THR* 3.7 12.6 - - - +
155A LYS* 5.8 0.8 - - - +
158A ALA* 3.1 17.2 + - - +
159A ASP* 3.6 34.8 + - - +
160A MET 3.6 3.8 - - - +
161A ALA* 1.3 79.8 - - - +
163A PRO* 1.3 67.2 - - + +
1002A CA 4.1 0.4 - - - -
1016P DGT 2.5 48.3 + - - +
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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