Contacts of the helix formed by residues 147 - 164 (chain A) in PDB entry 3J8B
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 THR 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A LEU* 1.3 75.8 - - - +
148A PRO* 1.3 64.5 - - - +
150A VAL* 3.0 9.6 + - - +
151A LYS* 2.8 22.8 + - - +
255C HIS* 5.7 9.6 - - - -
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Residues in contact with PRO 148 (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 LEU 3.3 4.9 - - - +
147A THR* 1.3 79.0 - - - +
149A TRP* 1.3 53.4 + - - +
151A LYS* 3.2 7.8 + - + +
152A PHE* 2.6 37.5 + - - +
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Residues in contact with TRP 149 (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* 5.9 2.9 - - + +
101A THR* 5.8 8.4 - - - -
104A ALA* 4.6 17.9 - - + -
146A LEU* 3.3 18.4 + - - +
147A THR 3.0 0.6 - - - -
148A PRO* 1.3 78.3 - - - +
150A VAL* 1.3 59.2 + - - +
152A PHE* 3.4 7.7 + - - +
153A LEU* 3.0 27.5 + - - +
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Residues in contact with VAL 150 (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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101A THR* 6.5 0.4 - - - -
146A LEU 3.2 10.7 + - - +
147A THR* 3.0 12.4 + - - +
149A TRP* 1.3 74.3 - - - +
151A LYS* 1.3 60.3 + - - +
153A LEU* 3.1 8.7 + - - +
154A TRP* 2.9 27.9 + - - +
188A TYR* 6.1 5.2 - - + -
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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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147A THR 2.8 16.0 + - - +
148A PRO* 3.6 10.3 - - + +
150A VAL* 1.3 73.1 - - - +
152A PHE* 1.3 56.6 + - - +
154A TRP* 3.7 6.8 - - - +
155A GLU* 2.9 32.3 + - - +
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Residues in contact with PHE 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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62A ARG* 5.4 12.8 - - + -
64A SER* 5.7 8.1 - - - -
97A ALA* 5.9 1.1 - - - -
148A PRO 2.6 21.5 + - - +
149A TRP* 3.5 9.9 - - - +
150A VAL 3.2 0.2 - - - -
151A LYS* 1.3 73.1 - - - +
153A LEU* 1.3 57.2 + - - +
155A GLU* 3.4 6.6 + - - +
156A SER* 3.0 28.6 + - - -
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Residues in contact with LEU 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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97A ALA* 4.9 19.7 - - + +
98A GLU* 6.3 0.2 - - - -
101A THR* 5.3 9.2 - - - -
149A TRP 3.0 13.6 + - - +
150A VAL* 3.1 12.3 + - - +
152A PHE* 1.3 73.8 - - - +
154A TRP* 1.3 66.4 + - - +
156A SER* 3.1 7.7 + - - -
157A TYR* 2.9 23.4 + - - +
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Residues in contact with TRP 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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150A VAL 2.9 13.0 + - - +
151A LYS* 3.7 10.5 - - - +
153A LEU* 1.3 75.3 - - - +
155A GLU* 1.3 58.4 + - - +
156A SER 3.1 0.3 + - - -
157A TYR* 3.2 8.7 + - - +
158A ARG* 2.9 29.8 + - - +
193A GLU* 5.2 14.4 - - + -
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Residues in contact with GLU 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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64A SER* 5.3 12.3 - - - -
151A LYS 2.9 18.6 + - - +
152A PHE* 3.7 7.2 - - - +
154A TRP* 1.3 76.7 - - - +
156A SER* 1.3 56.3 - - - +
158A ARG* 3.5 8.4 + - - +
159A GLN* 3.0 28.8 + - - +
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Residues in contact with SER 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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64A SER* 6.2 0.6 - - - -
93A TYR 6.0 1.6 - - - -
94A LEU* 6.2 2.5 - - - -
97A ALA* 4.4 17.7 - - - -
152A PHE 3.0 13.9 + - - -
153A LEU* 3.3 12.1 - - - -
154A TRP 3.1 0.2 - - - -
155A GLU* 1.3 74.3 - - - +
157A TYR* 1.3 67.5 + - - +
159A GLN* 3.2 6.5 + - - +
160A CYS* 3.0 25.3 + - - +
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Residues in contact with TYR 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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94A LEU* 6.5 1.6 - - - -
153A LEU 2.9 12.2 + - - +
154A TRP* 3.5 10.8 - - - +
156A SER* 1.3 73.6 - - - +
158A ARG* 1.3 65.0 + - - +
160A CYS* 3.3 5.0 + - - +
161A LEU* 2.9 24.7 + - - +
177A ILE* 5.6 5.7 - - - +
181A ALA* 4.3 26.5 - - + -
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Residues in contact with ARG 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 TRP 2.9 16.0 + - - +
155A GLU* 3.5 9.4 - - - +
157A TYR* 1.3 76.4 - - - +
159A GLN* 1.3 56.8 + - - +
161A LEU* 3.2 8.7 + - - +
162A ASP* 3.0 28.8 + - - +
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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
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68A LYS* 4.6 22.2 - - + -
155A GLU 3.0 18.1 + - - +
156A SER* 3.2 6.5 + - - +
158A ARG* 1.3 76.2 - - - +
160A CYS* 1.3 57.7 + - - +
162A ASP* 3.4 7.2 + - - +
163A LEU* 2.9 28.9 + - - +
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Residues in contact with CYS 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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90A VAL* 5.2 21.0 - - + +
93A TYR* 6.1 3.1 - - + -
94A LEU* 5.7 7.2 - - + +
156A SER 3.0 17.0 + - - +
157A TYR* 3.7 5.4 - - - +
159A GLN* 1.3 77.3 - - - +
161A LEU* 1.3 57.9 + - - +
163A LEU* 3.1 7.2 + - - +
164A LEU* 2.9 32.4 + - - +
177A ILE* 5.2 12.3 - - + -
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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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157A TYR 2.9 13.2 + - - +
158A ARG* 3.5 10.8 - - - +
160A CYS* 1.3 77.0 - - - +
162A ASP* 1.3 56.7 + - - +
163A LEU 3.1 0.2 - - - -
164A LEU* 3.5 3.4 + - - -
165A ARG* 3.1 29.8 + - - +
174A TYR* 5.8 2.9 - - - +
177A ILE* 5.5 7.9 - - + +
178A ALA* 6.3 2.7 - - - +
200A ASN* 6.5 0.9 - - + -
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Residues in contact with ASP 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 ARG 3.0 16.6 + - - +
159A GLN* 3.7 6.7 - - - +
161A LEU* 1.3 75.5 - - - +
163A LEU* 1.3 60.7 + - - +
165A ARG* 4.1 13.3 - - - +
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Residues in contact with LEU 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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71A LEU* 5.8 8.7 - - + -
72A TYR* 6.1 6.3 - - + +
90A VAL* 6.4 2.0 - - + -
159A GLN 2.9 16.5 + - - +
160A CYS* 3.4 9.0 - - - +
161A LEU 3.1 0.2 - - - -
162A ASP* 1.3 83.0 - - - +
164A LEU* 1.3 59.6 + - + +
165A ARG 3.3 4.5 + - - +
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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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90A VAL* 5.8 7.6 - - + -
160A CYS 2.9 16.0 + - - +
161A LEU* 3.9 2.2 - - - +
163A LEU* 1.3 75.7 - - + +
165A ARG* 1.3 66.8 + - - +
166A ASN 3.4 1.6 + - - -
167A ASN* 3.8 10.3 + - - +
170A VAL* 4.0 24.2 - - + +
171A GLU* 5.7 0.2 - - - -
173A LEU* 5.4 2.2 - - + -
174A TYR* 3.7 34.6 - - + +
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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