Contacts of the helix formed by residues 152 - 160 (chain A) in PDB entry 1OPL
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 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A VAL* 1.3 78.3 - - - +
153A ARG* 1.3 60.2 + - - +
154A ASN* 3.7 2.4 + - - +
155A ALA* 3.1 22.9 + - - +
156A ALA* 2.8 27.7 + - - +
171A ARG* 4.2 2.5 - - - +
174A GLU* 3.6 14.8 + - - -
364A THR* 5.8 0.2 - - - +
513A GLU* 3.0 42.3 + - - -
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Residues in contact with ARG 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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152A SER* 1.3 73.7 - - - +
154A ASN* 1.3 69.0 + - - +
156A ALA* 3.3 4.3 + - - +
157A GLU* 3.1 34.2 + - - +
171A ARG* 3.7 29.1 - - - +
192A HIS* 3.4 53.0 + - + +
513A GLU 5.3 8.7 + - - +
516A PHE 3.1 22.0 + - - -
517A GLN* 3.5 35.6 + - - +
518A GLU* 5.1 0.6 - - - +
519A SER 4.5 10.7 + - - +
520A SER 5.4 0.2 - - - +
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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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152A SER* 3.2 6.9 + - - +
153A ARG* 1.3 82.6 - - - +
155A ALA* 1.3 66.0 + - - +
157A GLU* 3.3 15.7 + - - +
158A TYR* 3.1 17.3 + - - +
357A VAL* 4.0 8.7 - - + +
360A LEU* 3.1 40.1 - - + +
361A TYR* 5.2 5.4 - - - +
364A THR* 5.2 2.6 + - - +
512A PHE 3.1 28.5 + - - -
513A GLU* 4.3 13.7 + - - +
516A PHE* 4.3 19.5 + - - +
521A ILE* 5.7 1.2 + - - +
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Residues in contact with ALA 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 VAL* 3.6 20.9 - - + -
152A SER* 3.1 22.1 + - - +
154A ASN* 1.3 76.3 - - - +
156A ALA* 1.3 57.6 + - - +
158A TYR* 3.0 4.7 + - - +
159A LEU* 2.9 33.2 + - + +
361A TYR* 4.2 28.5 - - + -
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Residues in contact with ALA 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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151A VAL* 3.5 6.7 - - + +
152A SER 2.8 16.4 + - - +
153A ARG 3.4 5.4 - - - +
155A ALA* 1.3 77.6 - - - +
157A GLU* 1.3 61.7 + - - +
159A LEU* 3.2 2.4 + - - +
160A LEU* 3.0 29.9 + - - +
169A LEU* 4.1 14.4 - - + -
171A ARG* 3.8 13.5 - - - +
183A SER* 3.7 28.7 - - - +
192A HIS* 4.4 0.9 - - + -
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Residues in contact with GLU 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 ARG* 3.1 26.4 + - - +
154A ASN* 3.6 15.9 - - - +
155A ALA 3.2 0.4 - - - -
156A ALA* 1.3 75.5 - - - +
158A TYR* 1.3 60.6 + - - +
160A LEU* 3.5 1.7 + - - +
161A SER* 3.1 22.9 + - - -
190A VAL* 4.1 26.7 - - + +
192A HIS* 2.9 31.4 + - + +
357A VAL* 3.8 26.3 - - + +
516A PHE 5.4 0.2 - - - +
520A SER* 3.9 28.5 - - - -
521A ILE* 4.8 2.6 + - - +
522A SER* 4.9 0.5 + - - -
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Residues in contact with TYR 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 3.1 9.9 + - - +
155A ALA 3.0 9.6 + - - +
157A GLU* 1.3 75.4 - - - +
159A LEU* 1.3 85.6 + - + +
161A SER* 2.7 33.5 + - - -
162A SER* 4.1 2.7 + - - -
239A ARG* 5.9 3.4 - - - -
357A VAL* 3.7 11.8 - - + +
358A VAL* 4.0 21.1 - - + -
361A TYR* 3.9 37.9 - + + -
393A ASN* 3.4 35.1 + - + +
394A HIS* 3.0 38.0 + + + -
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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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148A HIS* 3.7 26.2 - - + +
151A VAL* 4.3 20.4 - - + -
155A ALA* 2.9 18.5 + - + +
156A ALA 3.2 5.6 + - - +
158A TYR* 1.3 95.2 - - + +
160A LEU* 1.3 60.3 + - - +
162A SER* 3.2 22.7 + - - -
163A GLY* 4.6 0.7 + - - -
169A LEU* 3.7 19.7 - - + -
236A ALA* 4.5 9.1 - - + +
237A PRO* 4.5 15.1 - - - +
239A ARG* 4.6 13.8 + - + +
240A ASN* 5.8 3.4 - - - +
361A TYR* 5.4 4.5 - - + +
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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 ALA 3.0 15.5 + - - +
157A GLU 3.8 1.3 - - - +
159A LEU* 1.3 73.2 - - - +
161A SER* 1.3 61.5 + - - +
162A SER 3.1 2.5 - - - -
163A GLY* 3.2 9.4 + - - +
167A SER* 3.7 14.1 - - - +
168A PHE* 3.6 29.2 - - - +
169A LEU* 4.4 5.2 - - + -
183A SER* 3.5 37.7 - - - +
184A LEU* 3.9 6.5 - - - +
185A ARG* 2.9 27.3 + - + -
190A VAL* 3.7 32.5 - - + -
236A ALA* 3.8 19.7 - - + -
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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