Contacts of the helix formed by residues 151 - 161 (chain A) in PDB entry 1JPW
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 ARG 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A ALA* 1.3 67.2 + - - +
153A ILE* 3.1 10.5 - - - +
154A PRO* 2.9 30.7 - - + +
155A GLU* 4.0 26.3 + - - +
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Residues in contact with ALA 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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151A ARG* 1.3 81.8 - - - +
153A ILE* 1.3 68.5 + - + +
155A GLU* 2.9 20.8 + - - +
156A LEU* 3.1 29.4 + - + +
178A LEU* 4.6 11.4 - - + -
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Residues in contact with ILE 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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151A ARG 3.1 6.3 - - - +
152A ALA* 1.3 79.3 - - + +
154A PRO* 1.3 73.5 - - + +
155A GLU 2.9 0.3 + - - -
156A LEU* 3.3 5.4 + - + +
157A THR* 2.8 29.1 + - - +
178A LEU* 4.5 17.7 - - + -
184A SER* 4.8 2.0 - - - +
187A ALA* 4.0 24.0 - - + +
188A ILE* 3.6 29.8 - - + -
191A SER* 4.1 17.7 - - - +
194A MET* 4.0 31.1 - - + +
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Residues in contact with PRO 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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151A ARG* 2.9 30.7 - - + +
153A ILE* 1.3 90.2 - - + +
155A GLU* 1.3 49.7 + - - +
157A THR* 3.7 9.0 - - - +
158A LYS* 2.6 46.5 + - - +
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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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151A ARG* 4.2 25.9 + - - +
152A ALA* 2.9 16.2 + - + +
154A PRO* 1.3 73.5 - - + +
156A LEU* 1.3 56.1 + - + +
157A THR 3.1 1.1 - - - -
158A LYS* 2.7 58.0 + - - +
159A LEU* 2.7 28.9 + - + +
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Residues in contact with LEU 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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152A ALA* 3.1 24.0 + - + +
153A ILE* 4.0 7.2 - - + +
155A GLU* 1.3 73.4 - - + +
157A THR* 1.3 58.4 + - - +
159A LEU* 2.9 21.6 + - + +
160A LEU* 2.6 39.7 + - + +
171A ALA* 4.4 12.6 - - + -
174A MET* 4.4 25.1 - - + -
175A VAL* 3.6 31.2 - - + +
178A LEU* 3.8 27.4 - - + -
194A MET* 5.0 2.9 - - - -
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Residues in contact with THR 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 ILE* 2.8 27.7 + - - +
154A PRO* 3.7 9.0 - - - +
156A LEU* 1.3 78.0 - - - +
158A LYS* 1.3 64.1 + - + +
160A LEU* 3.3 4.1 + - - +
161A ASN* 2.9 36.5 + - - +
191A SER* 5.0 0.7 + - - -
193A GLN* 3.4 38.0 - - + +
194A MET* 3.8 30.9 + - - +
197A ALA* 4.4 1.1 - - + +
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Residues in contact with LYS 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 PRO* 2.6 54.0 + - - +
155A GLU* 2.7 48.7 + - - +
157A THR* 1.3 73.8 - - + +
159A LEU* 1.3 63.8 + - + +
161A ASN* 3.0 25.9 + - - +
162A ASP* 3.6 1.9 + - - +
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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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155A GLU* 2.7 27.2 + - + +
156A LEU* 3.5 26.2 - - + +
158A LYS* 1.3 77.6 - - + +
160A LEU* 1.3 61.4 + - - +
162A ASP* 3.0 28.4 - - - +
167A VAL* 3.9 24.9 - - + +
168A VAL* 3.9 6.4 - - - +
171A ALA* 4.0 14.4 - - + -
174A MET* 5.7 6.1 - - + -
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Residues in contact with LEU 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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156A LEU 2.6 20.5 + - - +
157A THR 3.7 4.0 - - - +
159A LEU* 1.3 73.3 - - - +
161A ASN* 1.3 60.1 + - - +
162A ASP 3.1 3.9 + - - +
168A VAL* 3.5 31.8 - - + +
171A ALA* 4.0 6.5 - - + -
172A ALA* 3.9 33.9 - - + +
175A VAL* 4.1 10.8 - - + -
194A MET* 3.2 34.3 - - + -
197A ALA* 4.0 12.6 - - + -
198A ILE* 4.2 10.3 - - + +
201A THR* 3.9 26.0 + - + +
214A THR* 5.5 2.0 - - + -
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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 THR* 2.9 32.2 + - - +
158A LYS* 3.0 14.9 + - - +
160A LEU* 1.3 77.2 - - - +
162A ASP* 1.3 62.2 + - - +
193A GLN 5.3 0.4 + - - -
197A ALA* 4.5 16.1 - - - +
200A ARG* 5.8 2.6 - - - +
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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