Contacts of the helix formed by residues 167 - 185 (chain A) in PDB entry 1JT6
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 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A GLU 3.8 1.0 + - - -
166A GLN* 1.3 72.9 - - - +
168A ILE* 1.3 84.6 + - - +
169A ASN* 3.0 27.9 + - - +
170A GLU* 2.9 42.4 + - + +
171A ARG 3.1 8.8 + - - -
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Residues in contact with ILE 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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87A LEU* 4.6 8.3 - - + -
88A THR* 5.2 4.5 - - + -
91A TYR* 3.1 52.2 + - + +
166A GLN 3.6 2.6 + - - -
167A ASN* 1.3 80.5 - - - +
169A ASN* 1.3 73.0 + - - +
171A ARG* 3.4 5.2 + - - +
172A ILE* 3.1 41.1 + - + +
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Residues in contact with ASN 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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167A ASN* 3.0 21.6 + - - +
168A ILE* 1.3 84.7 - - - +
170A GLU* 1.3 62.2 + - - +
172A ILE* 3.4 9.6 + - - +
173A LYS* 2.9 28.7 + - - +
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Residues in contact with GLU 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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166A GLN* 3.6 21.8 - - + +
167A ASN* 2.9 24.5 + - + +
169A ASN* 1.3 79.8 - - - +
171A ARG* 1.3 56.3 + - - +
173A LYS* 3.0 14.7 + - - +
174A LEU* 2.8 58.2 + - - +
147B ALA* 5.7 0.9 - - - +
150B LYS* 4.4 13.7 + - - +
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Residues in contact with ARG 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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87A LEU* 3.9 33.2 + - + +
90A GLU* 4.7 2.0 + - - +
91A TYR* 3.0 43.0 + - - -
159A ILE* 3.5 15.1 + - - +
160A VAL 3.0 24.4 + - - -
163A THR* 3.1 43.2 + - + -
164A HIS* 3.5 28.1 + - - +
166A GLN* 3.9 16.6 - - + +
167A ASN 3.1 14.1 + - - +
168A ILE* 3.8 6.3 - - - +
169A ASN 3.3 0.2 - - - -
170A GLU* 1.3 74.4 - - - +
172A ILE* 1.3 59.4 + - - +
174A LEU* 3.4 5.0 + - - +
175A MET* 2.9 28.6 + - - +
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Residues in contact with ILE 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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84A GLU* 3.8 21.8 - - + +
87A LEU* 3.7 18.4 - - + -
88A THR* 3.7 24.2 - - + -
168A ILE* 3.1 33.4 + - + +
169A ASN* 3.9 8.7 - - - +
171A ARG* 1.3 72.4 - - - +
173A LYS* 1.3 67.4 + - - +
175A MET* 3.5 6.7 + - - +
176A ASN* 3.2 36.4 + - - +
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Residues in contact with LYS 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 ASN 2.9 15.2 + - - +
170A GLU* 3.3 21.1 - - - +
172A ILE* 1.3 78.0 - - - +
174A LEU* 1.3 67.6 + - + +
176A ASN* 3.1 12.5 + - - +
177A LYS* 3.0 39.6 + - + +
147B ALA* 6.5 0.7 - - + -
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Residues in contact with LEU 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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159A ILE* 5.3 7.9 - - + -
163A THR* 5.2 3.8 - - + -
166A GLN* 3.4 26.2 - - - +
170A GLU* 2.8 38.7 + - - +
171A ARG* 3.8 4.7 - - - +
173A LYS* 1.3 82.2 - - + +
175A MET* 1.3 56.5 + - - +
177A LYS* 4.3 4.0 - - + -
178A PHE* 2.9 29.5 + - - +
147B ALA* 3.9 37.9 - - + +
150B LYS* 4.1 22.2 - - + -
151B ILE* 3.4 17.2 - - + +
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Residues in contact with MET 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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80A TYR 5.6 0.2 - - - +
83A ASN* 3.5 46.4 - - + +
84A GLU* 4.3 9.2 - - + +
87A LEU* 4.0 12.3 - - + -
156A VAL* 3.7 24.0 - - + +
159A ILE* 3.7 27.0 - - + +
160A VAL* 3.7 16.4 - - + -
171A ARG 2.9 17.7 + - - +
172A ILE* 3.9 6.7 - - - +
173A LYS 3.3 0.2 - - - -
174A LEU* 1.3 75.7 - - - +
176A ASN* 1.3 60.2 + - - +
178A PHE* 3.3 19.8 + - - +
179A SER* 2.9 30.5 + - - +
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Residues in contact with ASN 176 (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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80A TYR* 3.5 33.0 - - + +
84A GLU* 3.1 34.5 + - - +
172A ILE* 3.2 24.1 + - - +
173A LYS* 3.1 15.3 + - - +
175A MET* 1.3 76.2 - - - +
177A LYS* 1.3 60.1 - - - +
179A SER* 3.2 3.8 + - - +
180A GLN* 2.9 29.1 + - - +
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Residues in contact with LYS 177 (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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173A LYS* 3.0 31.3 + - + +
174A LEU* 3.7 4.5 - - + +
176A ASN* 1.3 75.7 - - - +
178A PHE* 1.3 57.8 + - - +
180A GLN* 3.1 32.5 + - - +
181A ILE* 2.9 51.0 + - + +
143B ASN* 4.9 8.7 + - - +
144B ASP* 3.4 31.9 + - - +
147B ALA* 5.2 5.6 - - + -
148B VAL* 4.9 3.6 - - + -
151B ILE* 3.6 21.8 - - + -
186B LEU* 6.3 0.2 - - - -
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Residues in contact with PHE 178 (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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79A PHE* 4.6 5.6 - + - -
83A ASN* 4.4 5.8 - - - -
152A ALA* 4.8 2.0 - - - -
155A ALA* 3.6 30.7 - - + -
156A VAL* 3.6 22.4 - - + -
159A ILE* 3.5 19.1 - - + -
174A LEU 2.9 14.7 + - - +
175A MET* 3.4 17.3 - - - +
177A LYS* 1.3 77.9 - - - +
179A SER* 1.3 69.3 + - - +
181A ILE* 4.5 3.4 - - - +
182A PHE* 3.0 55.8 + + + +
151B ILE* 3.5 32.7 - - + +
155B ALA* 4.3 6.3 - - + -
178B PHE* 4.3 6.3 - + - -
182B PHE* 4.4 7.9 - + - -
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Residues in contact with SER 179 (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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79A PHE* 4.0 13.2 - - - -
80A TYR* 3.6 30.3 + - - -
83A ASN* 2.9 30.7 + - - +
175A MET* 2.9 15.9 + - - +
176A ASN* 3.2 7.9 + - - -
178A PHE* 1.3 80.5 - - - +
180A GLN* 1.3 57.7 + - - +
182A PHE* 4.0 0.7 - - - +
183A LEU* 3.0 32.7 + - - +
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Residues in contact with GLN 180 (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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76A ARG* 4.5 7.8 + - - +
80A TYR* 3.2 25.2 + - + +
176A ASN 2.9 11.0 + - - +
177A LYS* 3.3 43.4 - - - +
179A SER* 1.3 75.1 - - - +
181A ILE* 1.3 65.8 + - - +
183A LEU* 4.0 2.2 - - - +
184A ASN* 3.0 26.3 + - + +
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Residues in contact with ILE 181 (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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177A LYS* 2.9 49.7 + - + +
178A PHE* 3.9 3.6 - - - +
180A GLN* 1.3 70.7 - - - +
182A PHE* 1.3 59.7 + - - +
184A ASN* 3.0 8.5 + - - +
185A GLY* 2.8 25.1 + - - -
148B VAL* 4.3 9.4 - - + -
151B ILE* 4.2 10.3 - - + -
182B PHE* 3.7 58.6 - - + +
185B GLY* 3.4 14.6 - - - +
186B LEU* 4.1 19.5 - - + -
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Residues in contact with PHE 182 (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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79A PHE* 3.7 18.8 - + + -
131A PHE* 4.0 13.0 - + - -
148A VAL* 3.9 30.1 - - + -
151A ILE* 3.7 28.7 - - + -
152A ALA* 4.1 9.6 - - + -
178A PHE* 3.0 44.8 + + + +
179A SER 4.0 2.2 - - - +
181A ILE* 1.3 82.6 - - - +
183A LEU* 1.3 64.1 + - + +
185A GLY 3.2 8.7 + - - -
186A LEU* 3.5 12.7 + - + +
178B PHE* 4.4 9.4 - + - -
181B ILE* 3.4 37.6 - - + +
182B PHE* 5.5 3.6 - + + -
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Residues in contact with LEU 183 (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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76A ARG* 3.4 66.4 + - + +
79A PHE* 3.7 34.1 - - + -
80A TYR* 4.1 8.3 - - + -
131A PHE* 4.5 3.6 - - + -
140A TRP* 3.8 28.2 - - + +
179A SER 3.0 13.8 + - - +
182A PHE* 1.3 74.5 - - + +
184A ASN* 1.3 63.5 + - - +
186A LEU* 3.4 31.6 + - + +
187A SER* 4.0 7.3 + - - -
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Residues in contact with ASN 184 (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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76A ARG* 4.3 7.6 - - - +
180A GLN* 3.0 20.0 + - + +
181A ILE* 3.0 6.1 + - - +
183A LEU* 1.3 75.5 - - - +
185A GLY* 1.3 60.5 + - - +
186A LEU 3.1 5.9 + - - -
187A SER* 3.2 27.9 + - - -
184B ASN* 4.1 3.8 - - - +
185B GLY* 3.2 21.6 - - - +
187B SER 3.6 14.0 - - - +
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Residues in contact with GLY 185 (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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181A ILE 2.8 10.3 + - - -
182A PHE 3.2 5.5 + - - -
184A ASN* 1.3 76.8 - - - +
186A LEU* 1.3 57.6 + - - +
187A SER 3.3 0.7 - - - -
180B GLN* 5.1 0.5 - - - +
181B ILE* 3.1 37.1 - - - +
184B ASN* 3.0 25.2 + - - +
185B GLY* 3.4 11.6 - - - -
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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