Contacts of the helix formed by residues 149 - 168 (chain A) in PDB entry 1JTF
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 SER 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A PRO* 1.4 77.3 - - - +
150A THR* 1.3 53.4 + - - +
151A ALA* 3.1 15.5 + - - +
152A ASP* 2.8 35.3 + - - +
153A LEU* 2.8 30.7 + - - +
183A GLN* 5.1 5.8 - - - +
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Residues in contact with THR 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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148A PRO 3.7 1.0 + - - -
149A SER* 1.3 73.6 - - - +
151A ALA* 1.3 56.5 + - - +
153A LEU* 3.4 10.5 - - - +
154A LEU* 2.8 44.0 + - + +
177A ARG* 5.2 1.4 + - - -
179A PRO* 3.5 27.7 - - + +
180A TRP 4.4 0.7 + - - -
183A GLN* 2.7 44.6 + - - +
184A TRP* 4.8 0.9 - - + -
185A ILE* 3.6 27.6 - - + +
188A PHE* 6.1 0.2 - - + -
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Residues in contact with ALA 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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149A SER* 3.2 12.7 - - - +
150A THR* 1.3 79.8 - - - +
152A ASP* 1.3 66.0 + - - +
154A LEU* 3.9 6.4 - - - +
155A SER* 3.1 22.3 + - - -
185A ILE* 3.9 16.7 - - + +
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Residues in contact with ASP 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A SER* 3.8 24.4 - - - +
148A PRO* 3.3 27.4 - - + +
149A SER* 2.8 29.0 + - - +
151A ALA* 1.3 75.1 - - - +
153A LEU* 1.3 64.7 + - - +
155A SER* 3.0 9.9 + - - -
156A ASN* 3.0 26.3 + - - +
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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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148A PRO* 4.3 21.3 - - + +
149A SER 2.8 16.5 + - - +
150A THR* 3.4 9.6 - - - +
152A ASP* 1.3 76.1 - - - +
154A LEU* 1.3 57.7 + - - +
156A ASN* 2.9 17.1 + - - +
157A TYR* 2.8 48.9 + - + +
177A ARG* 3.2 53.4 - - + +
179A PRO* 3.7 22.4 - - + -
401A M7G 6.1 0.2 - - - +
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Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A THR* 2.8 44.0 + - + +
151A ALA* 3.9 5.4 - - - +
153A LEU* 1.3 71.5 - - + +
155A SER* 1.3 58.2 + - - +
157A TYR* 3.1 6.8 + - + +
158A ALA* 2.7 32.9 + - - +
179A PRO* 5.1 0.4 - - + -
185A ILE* 4.1 20.4 - - + -
186A LYS* 4.1 26.9 - - + +
188A PHE* 3.0 52.7 - - + -
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Residues in contact with SER 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ALA 3.1 11.4 + - - -
152A ASP* 3.0 12.7 + - - -
154A LEU* 1.3 80.4 - - - +
156A ASN* 1.3 63.3 + - - +
158A ALA* 3.4 7.5 - - - +
159A LEU* 3.1 21.5 + - - +
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Residues in contact with ASN 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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139A VAL* 4.5 23.4 - - + +
140A ARG* 4.4 4.3 - - - -
141A SER* 3.9 33.2 + - - +
148A PRO* 5.8 0.9 - - - +
152A ASP* 3.0 19.9 + - - +
153A LEU* 2.9 21.3 + - - +
155A SER* 1.3 80.8 - - - +
157A TYR* 1.3 71.8 + - + +
159A LEU* 2.9 11.9 + - - +
160A GLN* 2.9 28.4 + - + +
175A LYS* 6.1 0.6 - - + -
400A SAH 6.0 1.4 + - - -
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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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153A LEU* 2.8 52.2 + - + +
154A LEU* 3.7 7.6 - - - +
156A ASN* 1.3 77.5 - - + +
158A ALA* 1.3 61.7 + - - +
160A GLN* 3.5 21.1 + - - +
161A ASN* 3.1 29.9 + - - +
175A LYS* 3.4 23.7 - - + -
176A TRP* 3.4 24.9 - + - -
177A ARG* 2.3 42.1 + - - +
179A PRO* 4.6 1.1 - - + -
188A PHE* 3.8 33.0 - + + -
189A TYR 5.4 1.6 - - - +
190A ILE* 5.0 6.3 - - + -
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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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154A LEU 2.7 16.8 + - - +
155A SER* 3.4 10.5 - - - +
157A TYR* 1.3 76.0 - - - +
159A LEU* 1.3 62.6 + - - +
161A ASN* 3.0 20.0 + - - +
162A VAL* 3.0 14.1 + - - +
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Residues in contact with LEU 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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116A VAL* 4.2 11.9 - - + +
117A ASP* 4.8 0.9 - - - -
118A GLU* 4.8 7.2 - - + +
121A LEU* 3.9 24.0 - - + -
139A VAL* 4.8 9.0 - - + -
155A SER 3.1 9.2 + - - +
156A ASN* 2.9 12.8 + - - +
158A ALA* 1.3 77.2 - - - +
160A GLN* 1.3 65.8 + - - +
162A VAL* 3.0 11.9 + - + +
163A MET* 2.9 43.7 + - + +
400A SAH 4.0 24.0 - - + +
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Residues in contact with GLN 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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137A SER* 2.7 26.3 + - - +
139A VAL* 4.2 13.4 - - + +
156A ASN* 2.9 16.7 + - - +
157A TYR* 3.8 22.6 - - - +
159A LEU* 1.3 74.8 - - - +
161A ASN* 1.3 63.7 + - - +
163A MET* 3.2 27.3 + - - +
164A ILE* 3.2 14.5 + - - +
174A LEU* 3.5 33.9 - - + +
175A LYS* 3.4 39.5 + - - +
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Residues in contact with ASN 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 3.1 17.4 + - - +
158A ALA* 3.0 13.4 + - - +
160A GLN* 1.3 79.5 - - - +
162A VAL* 1.3 57.0 + - - +
164A ILE* 3.6 5.6 + - - +
165A SER* 2.8 27.4 + - - -
189A TYR* 3.3 28.5 + - - +
190A ILE* 4.5 1.0 - - - +
191A PRO* 3.3 32.7 - - - +
219A MET* 4.0 9.9 - - + +
221A LEU* 4.6 11.9 - - - +
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Residues in contact with VAL 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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118A GLU* 3.2 47.1 - - + +
121A LEU* 3.6 17.3 - - + -
158A ALA 3.0 10.9 + - - +
159A LEU* 3.0 17.7 + - + +
161A ASN* 1.3 74.3 - - - +
163A MET* 1.3 61.2 + - - +
164A ILE 3.4 0.2 - - - -
165A SER* 3.2 9.0 - - - +
166A ILE* 3.0 39.4 + - + +
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Residues in contact with MET 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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67A ILE* 3.7 45.1 - - + -
116A VAL* 4.3 2.9 - - + -
121A LEU* 4.0 14.1 - - + -
135A LEU* 3.5 16.4 - - + -
137A SER* 3.7 30.5 - - - +
139A VAL* 4.1 9.2 - - + -
159A LEU* 2.9 37.9 + - + +
160A GLN* 3.2 20.8 + - - +
162A VAL* 1.3 78.7 - - - +
164A ILE* 1.3 54.4 + - - +
167A LEU* 2.7 48.0 + - + +
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Residues in contact with ILE 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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135A LEU* 4.3 12.8 - - + -
160A GLN 3.2 13.9 + - - +
161A ASN* 4.0 5.4 - - - +
163A MET* 1.3 77.2 - - - +
165A SER* 1.3 57.4 + - - +
168A ASN* 2.8 30.5 + - - +
169A PRO* 3.6 25.8 - - + -
172A SER* 3.9 4.0 - - - +
174A LEU* 3.7 24.7 - - + -
191A PRO* 3.7 15.5 - - + -
214A TYR* 3.0 39.7 - - + +
219A MET* 4.4 14.4 - - + -
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Residues in contact with SER 165 (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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122A ARG* 5.7 0.2 + - - -
161A ASN 2.8 19.5 + - - -
162A VAL* 3.2 20.8 + - - +
164A ILE* 1.3 76.5 - - - +
166A ILE* 1.3 61.6 + - - +
168A ASN* 4.3 6.6 + - - +
219A MET* 4.6 17.9 - - - +
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Residues in contact with ILE 166 (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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118A GLU* 3.4 47.3 - - + +
121A LEU* 3.7 30.1 - - + +
122A ARG* 3.4 43.7 - - + +
125A LYS* 3.5 20.5 - - + +
162A VAL* 3.0 19.8 + - + +
163A MET 4.3 0.4 - - - +
165A SER* 1.3 80.4 - - - +
167A LEU* 1.3 64.4 + - - +
168A ASN* 3.1 5.3 + - - +
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Residues in contact with LEU 167 (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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65A VAL* 4.7 3.1 - - + -
67A ILE* 4.4 10.3 - - + -
121A LEU* 3.2 55.9 - - + +
124A ILE* 3.9 18.8 - - + -
125A LYS* 3.1 30.3 + - + -
133A ILE* 3.6 26.7 - - + +
135A LEU* 4.5 11.2 - - + -
163A MET* 2.7 32.9 + - + +
166A ILE* 1.3 75.1 - - - +
168A ASN* 1.3 68.1 + - - +
169A PRO* 3.3 5.8 - - + -
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Residues in contact with ASN 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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125A LYS* 4.2 11.7 + - - +
133A ILE* 5.1 2.3 + - - +
164A ILE* 2.8 17.1 + - - +
165A SER 4.5 5.4 - - - +
166A ILE 3.1 6.9 - - - +
167A LEU* 1.3 80.2 - - - +
169A PRO* 1.3 72.6 + - - +
170A VAL* 5.3 2.1 - - - +
214A TYR* 5.7 3.2 - - - +
217A GLU* 6.1 3.0 - - - +
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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