Contacts of the helix formed by residues 149 - 167 (chain A) in PDB entry 1JD7
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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115A ASP* 4.7 5.7 + - - -
146A ASP* 2.8 32.8 + - - -
148A ALA* 1.3 79.3 - - - +
150A ASN* 1.3 63.1 + - - +
151A TYR* 3.1 20.6 + - - +
152A VAL* 3.2 16.2 + - - +
153A GLN* 3.0 26.3 + - - +
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Residues in contact with ASN 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 ALA 3.5 3.8 + - - -
149A SER* 1.3 72.5 + - - +
151A TYR* 1.3 57.6 + - - +
153A GLN* 3.5 7.9 + - - +
154A ASN* 2.9 52.3 + - - +
190A LYS* 2.8 29.2 + - - +
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Residues in contact with TYR 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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110A ILE* 2.7 36.6 + - - +
111A TYR* 3.9 10.3 - + - -
115A ASP* 3.6 28.3 - - - +
149A SER* 3.1 8.6 + - - +
150A ASN* 1.3 77.5 - - - +
152A VAL* 1.3 69.1 + - + +
154A ASN* 3.2 10.8 + - + +
155A THR* 2.8 48.8 + - - +
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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* 4.2 16.4 - - + +
115A ASP* 3.7 31.2 - - + +
145A LEU* 4.3 13.0 - - + -
146A ASP 3.3 27.1 - - - +
147A THR* 4.3 10.8 - - - -
149A SER* 3.2 12.5 + - - +
151A TYR* 1.3 79.5 - - + +
153A GLN* 1.3 66.1 + - - +
155A THR* 3.1 3.3 + - - -
156A ILE* 2.9 44.0 + - + +
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Residues in contact with GLN 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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147A THR* 2.9 28.0 + - - +
148A ALA* 3.4 20.7 + - - +
149A SER 3.0 13.3 + - - +
150A ASN* 3.7 7.4 - - - +
152A VAL* 1.3 80.1 - - + +
154A ASN* 1.3 56.6 + - - +
156A ILE* 3.5 2.4 + - - -
157A ALA* 2.8 32.4 + - - +
183A ASP* 4.3 4.3 + - - +
186A SER* 3.2 35.0 + - - -
187A LEU* 3.5 22.2 - - + +
190A LYS* 3.5 26.6 - - + -
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Residues in contact with ASN 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 ASN* 2.9 43.1 + - - +
151A TYR* 3.6 9.1 - - + +
153A GLN* 1.3 75.8 - - - +
155A THR* 1.3 59.2 + - - +
157A ALA* 3.7 5.2 - - - +
158A ALA* 2.8 32.7 + - - +
190A LYS* 2.9 25.9 + - - +
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Residues in contact with THR 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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55A TYR* 3.6 24.4 - - + -
110A ILE* 3.9 20.4 - - + -
111A TYR* 3.7 14.1 - - + +
151A TYR* 2.8 42.3 + - - +
152A VAL 3.5 4.5 - - - -
154A ASN* 1.3 78.9 - - - +
156A ILE* 1.3 62.6 + - - +
158A ALA* 3.4 5.9 + - - +
159A TYR* 3.1 20.6 + - - +
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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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55A TYR* 3.7 10.1 - - + +
85A THR* 4.8 5.8 - - + -
86A LEU 5.1 0.9 - - - +
87A ILE* 3.7 42.2 - - + +
111A TYR* 3.6 15.3 - - - +
145A LEU* 4.3 5.6 - - + -
147A THR* 4.8 3.8 - - + -
152A VAL* 2.9 36.7 + - + +
153A GLN* 4.0 3.6 - - - +
155A THR* 1.3 74.2 - - - +
157A ALA* 1.3 64.8 + - - +
159A TYR* 3.1 11.3 + - + +
160A ILE* 3.0 33.4 + - + +
187A LEU* 4.0 23.1 - - + -
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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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153A GLN 2.8 21.0 + - - +
154A ASN* 3.7 4.7 - - - +
156A ILE* 1.3 73.6 - - - +
158A ALA* 1.3 61.8 + - - +
160A ILE* 3.0 8.3 + - - +
161A ASN* 2.8 36.6 + - - +
187A LEU* 3.9 11.2 - - + +
190A LYS* 3.6 36.8 - - + +
191A VAL* 4.9 2.5 - - + -
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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 ASN 2.8 22.9 + - - +
155A THR* 3.7 6.7 - - - +
157A ALA* 1.3 72.8 - - - +
159A TYR* 1.3 56.8 + - - +
161A ASN* 4.0 7.6 - - - +
162A ASP* 3.0 31.4 + - - +
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Residues in contact with TYR 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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37A PRO* 3.8 20.8 - - - +
38A ASN* 3.5 26.0 + - + +
55A TYR* 3.6 58.6 - + + -
57A LEU* 4.3 8.9 - - + +
83A VAL* 4.1 4.6 - - + +
84A ASP 5.1 0.3 + - - -
85A THR* 3.9 31.9 - - + -
86A LEU 5.5 0.9 - - - -
155A THR 3.1 12.4 + - - +
156A ILE* 3.1 13.4 + - + +
157A ALA 3.0 0.4 - - - -
158A ALA* 1.3 78.6 - - - +
160A ILE* 1.3 63.1 + - + +
162A ASP* 3.3 5.5 + - + +
163A LEU* 3.1 46.0 + - + +
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Residues in contact with ILE 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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85A THR* 4.4 17.5 - - + -
156A ILE* 3.0 29.7 + - + +
157A ALA* 3.6 6.7 - - - +
159A TYR* 1.3 77.7 - - + +
161A ASN* 1.3 62.2 + - - +
163A LEU* 3.2 2.4 + - - -
164A GLN* 3.0 31.0 + - - +
171A PHE* 3.4 40.2 - - + -
173A PHE* 3.9 32.1 - - + -
187A LEU* 4.5 4.0 - - + -
191A VAL* 4.1 24.7 - - + -
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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 ALA* 2.8 25.2 + - - +
158A ALA* 4.0 6.5 - - - +
160A ILE* 1.3 70.5 - - - +
162A ASP* 1.3 65.6 + - - +
164A GLN* 3.3 16.5 + - - +
165A ALA* 3.1 21.0 + - - +
190A LYS 3.0 25.0 + - - -
191A VAL* 3.6 4.7 - - - +
192A ASN* 2.7 52.1 + - - +
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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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57A LEU* 5.4 0.7 - - - +
64A ARG* 3.6 30.7 + - - -
158A ALA 3.0 19.5 + - - +
159A TYR* 3.6 7.4 - - + +
160A ILE 3.2 0.2 - - - -
161A ASN* 1.3 76.6 - - - +
163A LEU* 1.3 65.0 + - + +
165A ALA* 3.1 19.4 + - - +
166A ILE* 3.1 17.5 + - - +
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Residues in contact with LEU 163 (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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37A PRO* 5.3 0.2 - - + -
57A LEU* 4.1 24.0 - - + -
67A PHE* 3.8 29.6 - - + -
83A VAL* 3.8 18.4 - - + -
159A TYR* 3.1 50.2 + - + +
160A ILE 3.2 7.2 + - - +
162A ASP* 1.3 78.4 - - - +
164A GLN* 1.3 59.7 + - - +
166A ILE* 3.1 8.5 + - + +
167A GLY 3.1 5.9 + - - -
168A VAL* 2.9 31.4 + - + +
171A PHE* 3.6 24.9 - - + -
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Residues in contact with GLN 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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160A ILE* 3.0 19.1 + - - +
161A ASN* 3.3 27.7 + - - +
162A ASP 3.2 0.2 - - - -
163A LEU* 1.3 76.0 - - - +
165A ALA* 1.3 63.2 + - - +
167A GLY* 2.9 14.7 + - - -
168A VAL 3.5 14.3 - - - +
171A PHE* 3.5 15.5 - - + -
191A VAL* 3.4 13.7 - - - +
192A ASN* 3.0 30.1 + - + +
193A GLY* 5.3 0.3 - - - -
194A SER 5.0 0.3 + - - -
195A PRO* 3.3 28.5 - - - +
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Residues in contact with ALA 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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161A ASN 3.1 13.0 + - - +
162A ASP* 3.1 14.1 + - - +
164A GLN* 1.3 76.3 - - - +
166A ILE* 1.3 63.1 + - + +
167A GLY* 3.4 0.5 + - - -
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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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57A LEU* 3.8 28.9 - - + -
64A ARG* 3.8 23.1 - - - +
67A PHE* 4.7 3.4 - - + -
68A ILE* 3.8 39.9 - - + +
71A VAL* 3.8 21.0 - - + +
72A ASN* 4.3 9.9 - - - +
162A ASP* 3.1 18.5 + - - +
163A LEU* 3.4 16.6 - - + +
164A GLN 3.1 0.8 - - - -
165A ALA* 1.3 78.7 - - + +
167A GLY* 1.3 57.0 + - - +
168A VAL* 5.1 1.1 - - + +
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Residues in contact with GLY 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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71A VAL* 3.7 17.1 - - - +
75A SER* 6.1 0.3 - - - -
81A ILE 5.5 1.0 + - - -
164A GLN 2.9 11.0 + - - -
165A ALA 3.2 0.6 - - - -
166A ILE* 1.3 81.1 - - - +
168A VAL* 1.3 67.6 + - - +
169A LYS* 3.1 31.5 + - - +
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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