Contacts of the strand formed by residues 156 - 163 (chain D) in PDB entry 1OP8
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 156 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D ILE* 3.5 14.2 + - + +
19D GLY* 2.8 27.0 + - - +
20D ASN* 2.9 28.5 - - - +
21D GLU* 4.0 9.6 - - + +
22D VAL* 4.3 1.3 - - - +
139D ALA* 3.0 3.1 - - - -
140D GLY 2.7 36.4 + - - +
144D THR* 3.5 25.9 - - - +
152D SER* 3.4 16.6 - - - +
154D THR* 3.2 16.0 + - - +
155D LEU* 1.3 79.1 - - - +
157D GLU* 1.3 59.0 + - - +
1015D SO4 2.7 37.4 + - - -
1022D SO4 3.5 13.1 + - - -
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Residues in contact with GLU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ILE* 3.8 4.0 - - - -
19D GLY* 3.1 0.7 - - - -
20D ASN* 2.8 31.5 + - - +
22D VAL* 3.5 15.3 - - + -
27D ARG* 2.6 45.3 + - - -
29D TYR* 4.6 3.5 + - - -
137D GLN* 2.3 42.6 + - - +
138D VAL 3.1 20.8 - - - +
139D ALA* 3.8 10.0 + - + +
156D ARG* 1.3 74.9 - - - +
158D VAL* 1.3 64.3 + - - +
159D ASN* 5.2 1.6 + - - +
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Residues in contact with VAL 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ILE* 3.4 22.9 - - + -
17D ILE 3.7 6.7 - - - +
18D GLY 3.4 22.4 - - - +
19D GLY* 3.8 3.1 - - - -
137D GLN* 3.3 5.2 - - - -
138D VAL* 2.9 41.7 + - + +
157D GLU* 1.3 78.0 - - - +
159D ASN* 1.3 67.8 + - - +
160D ILE* 3.8 7.4 + - + +
188D ARG* 3.6 27.4 - - + +
189D ASP* 4.0 19.3 - - - +
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Residues in contact with ASN 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D MET* 6.4 2.2 - - + -
136D CYS 3.6 3.9 - - - +
137D GLN* 2.7 41.7 + - - +
157D GLU* 5.2 1.0 + - - +
158D VAL* 1.3 74.8 - - - +
160D ILE* 1.3 60.8 + - - +
188D ARG* 2.9 42.8 + - - +
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Residues in contact with ILE 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D MET* 3.6 7.3 - - - +
136D CYS* 2.7 58.8 + - + +
138D VAL* 4.1 24.0 - - + -
158D VAL* 4.1 9.0 - - + +
159D ASN* 1.3 80.2 - - - +
161D THR* 1.3 57.0 - - - +
183D ALA* 3.4 28.9 - - + +
184D GLY* 3.5 15.5 - - - +
188D ARG* 3.2 46.9 - - + +
189D ASP* 4.1 2.7 - - - +
199D LEU* 4.2 0.9 - - + -
228D TYR* 4.8 2.5 - - - +
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Residues in contact with THR 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D GLY* 3.3 24.9 + - - -
134D THR 3.2 8.1 - - - -
135D MET* 4.0 15.0 - - - -
160D ILE* 1.3 76.7 - - - +
162D ILE* 1.3 67.4 + - - +
163D ILE* 3.4 7.6 + - + +
183D ALA* 4.0 3.6 - - - -
184D GLY 3.0 30.5 + - - +
185D SER* 5.0 3.8 - - - -
188D ARG* 3.6 15.3 - - + -
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Residues in contact with ILE 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D VAL* 3.1 39.3 - - + +
131D LYS 3.1 17.7 - - - +
132D PRO* 3.2 22.0 - - + +
133D GLY 3.1 16.3 + - - +
134D THR 3.0 7.6 + - - +
136D CYS* 3.3 30.5 - - - -
161D THR* 1.3 73.5 + - - +
163D ILE* 1.3 71.6 + - - +
164D ASP* 3.9 1.0 + - - -
165D ARG 5.3 0.9 - - - +
181D VAL* 5.1 12.8 - - + -
182D CYS 2.9 13.7 - - - +
183D ALA* 3.7 6.3 - - + +
199D LEU* 5.3 2.9 - - + -
201D CYS* 4.3 1.3 - - - -
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Residues in contact with ILE 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D THR* 3.7 18.4 - - + +
162D ILE* 1.3 81.5 - - - +
164D ASP* 1.3 72.0 + - - +
165D ARG* 3.2 2.9 + - - -
167D VAL* 3.7 30.7 - - + -
168D CYS* 4.3 7.6 - - + +
171D HIS* 4.8 4.0 - - + +
181D VAL* 5.6 0.3 - - - -
182D CYS* 2.6 39.0 + - + +
184D GLY 4.2 8.3 - - - +
185D SER* 4.3 17.3 - - - +
186D LEU* 4.1 29.4 - - + +
225D PRO* 4.2 12.8 - - + -
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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