Contacts of the helix formed by residues 144 - 155 (chain B) in PDB entry 6J7Z
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 VAL 144 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B VAL 3.9 13.5 - - - +
139B LEU* 4.3 21.3 - - + +
140B ALA 3.6 24.7 - - - +
141B GLY* 3.9 13.9 - - - +
142B ASN 3.2 1.3 - - - -
143B SER* 1.3 73.1 - - - +
145B HIS* 1.3 60.5 + - - +
146B GLU 3.3 0.9 - - - -
147B ASP* 3.4 17.4 + - + +
148B LYS* 2.9 26.9 + - - +
166B ILE* 3.8 34.8 - - + -
167B ILE 4.3 10.1 - - - +
168B ASP* 3.9 3.6 + - - -
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Residues in contact with HIS 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A HIS* 3.8 25.6 - - + +
148A LYS* 4.3 17.9 + - + +
164A TYR* 3.4 26.2 + + - -
166A ILE* 3.5 30.4 + - + +
143B SER* 3.7 23.3 + - - -
144B VAL* 1.3 80.5 - - - +
146B GLU* 1.3 70.9 + - + +
148B LYS* 3.3 9.4 + - + +
149B LYS* 2.9 27.4 + - - +
166B ILE* 4.3 7.6 - - + -
168B ASP* 3.4 25.9 + - - -
11C U 5.5 2.7 - - - -
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Residues in contact with GLU 146 (chain B).
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* 4.8 10.0 + - - -
50B MET* 4.2 10.1 - - + -
53B LEU* 3.3 27.1 - - + +
143B SER 3.3 7.1 + - - +
144B VAL 3.3 0.4 - - - -
145B HIS* 1.3 82.1 + - - +
147B ASP* 1.3 65.3 + - - +
149B LYS* 3.1 41.9 + - - +
150B PHE* 3.0 37.6 + - + -
11C U 3.5 44.5 - - - +
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Residues in contact with ASP 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B VAL* 4.4 7.0 - - + +
47B ASP* 3.8 7.4 - - - +
48B LEU* 3.0 56.3 + - + +
50B MET* 5.2 2.6 - - - +
139B LEU* 5.2 0.2 - - + -
142B ASN 4.2 5.2 - - - +
143B SER 3.6 6.2 - - - +
144B VAL* 3.4 34.4 + - + +
146B GLU* 1.3 75.0 - - - +
148B LYS* 1.3 55.9 + - - +
150B PHE* 3.3 1.5 + - - -
151B LEU* 2.9 40.4 + - + +
11C U 4.1 11.9 + - - +
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Residues in contact with LYS 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A HIS* 4.8 9.8 - - + -
146A GLU* 3.6 22.4 + - - -
149A LYS* 4.7 2.8 - - - +
139B LEU* 4.0 14.3 - - + +
144B VAL 2.9 18.0 + - - +
145B HIS* 3.5 8.1 - - - +
146B GLU 3.2 0.2 - - - -
147B ASP* 1.3 75.2 - - - +
149B LYS* 1.3 61.0 + - - +
151B LEU* 3.9 2.6 - - - +
152B ASP* 2.8 60.2 + - - +
159B MET* 3.7 22.4 - - + -
163B HIS 5.4 0.7 - - - -
164B TYR* 3.9 24.9 - - - +
166B ILE* 3.8 22.0 - - + -
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Residues in contact with LYS 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A LYS* 4.6 30.6 + - + +
152A ASP* 4.4 18.8 + - + +
53B LEU 4.5 5.5 + - - -
55B ILE* 3.9 37.2 - - + +
145B HIS 2.9 13.9 + - - +
146B GLU* 3.1 45.0 + - - +
148B LYS* 1.3 77.5 - - - +
150B PHE* 1.3 66.2 + - - +
152B ASP* 3.3 7.1 + - - +
153B LYS* 3.0 22.3 + - - +
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Residues in contact with PHE 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU* 3.8 20.0 - - + -
50B MET* 3.6 34.3 - - + -
52B GLY 3.4 19.5 - - - -
53B LEU 3.8 13.7 - - - -
54B ASP 4.1 2.0 - - - -
55B ILE* 3.8 27.6 - - + -
58B ASP 3.6 25.8 - - - -
60B ILE* 4.1 10.4 - - + +
146B GLU* 3.0 46.3 + - - +
149B LYS* 1.3 78.5 - - - +
151B LEU* 1.3 58.0 + - - +
153B LYS 3.4 0.5 + - - -
154B TYR* 2.9 45.1 + + - +
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Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B VAL* 3.9 25.4 - - + -
48B LEU* 4.1 13.5 - - + -
60B ILE* 4.4 3.8 - - + -
63B MET* 3.8 28.7 - - + -
139B LEU* 4.0 11.4 - - + -
147B ASP 2.9 21.5 + - - +
148B LYS 3.9 0.7 - - - +
150B PHE* 1.3 74.6 - - - +
152B ASP* 1.3 61.3 + - - +
155B MET* 2.6 56.6 + - + +
158B PHE* 4.0 10.3 - - + -
159B MET* 3.6 31.6 - - + -
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Residues in contact with ASP 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A LYS* 3.4 21.8 + - - +
148B LYS* 2.8 53.8 + - - +
149B LYS 3.7 4.3 - - - +
151B LEU* 1.3 75.2 - - - +
153B LYS* 1.3 63.3 + - - +
156B PRO* 3.9 16.9 - - - +
159B MET* 3.2 30.0 - - - +
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Residues in contact with LYS 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ILE* 2.5 51.0 + - + +
56B GLU* 3.7 22.2 + - - +
149B LYS 3.0 16.4 + - - +
150B PHE 3.8 3.8 - - - +
152B ASP* 1.3 80.7 - - - +
154B TYR* 1.3 98.7 + - + +
156B PRO* 4.4 6.3 - - - +
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Residues in contact with TYR 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ILE 3.9 0.8 + - - -
56B GLU 4.9 0.3 + - - -
57B LYS 4.8 0.9 + - - -
58B ASP 3.4 17.8 + - - -
59B GLN* 3.0 42.3 + - - -
60B ILE* 4.2 19.3 - - + -
117B LEU* 3.8 34.2 - - + +
121B GLU* 4.1 5.9 - - - +
150B PHE* 2.9 38.5 + + - +
153B LYS* 1.3 123.8 + - + +
155B MET* 1.3 65.1 + - - +
156B PRO* 3.5 8.3 - - - +
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Residues in contact with MET 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ILE* 5.1 5.2 - - + -
63B MET* 3.8 35.2 - - + +
83B ILE* 5.3 3.4 - - + -
117B LEU* 3.8 25.4 - - + +
120B ALA* 3.9 13.5 - - + -
121B GLU* 3.3 53.4 - - + +
124B PHE* 4.6 2.9 - - - -
151B LEU* 2.6 37.7 + - + +
154B TYR* 1.3 78.8 - - + +
156B PRO* 1.3 64.6 - - - +
158B PHE* 3.4 10.2 + - + +
159B MET* 3.3 17.2 + - - +
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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