Contacts of the helix formed by residues 155 - 167 (chain A) in PDB entry 2OKC
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 PRO 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A GLN* 4.7 11.0 - - - +
153A PHE* 4.4 9.4 - - + -
154A THR* 1.4 91.3 - - + +
156A ARG* 1.3 66.1 + - - +
157A PRO* 4.2 9.6 - - + -
158A LEU* 3.1 24.2 + - + +
159A ILE* 3.3 10.8 + - - +
340A ILE* 3.5 32.3 - - + +
341A PHE* 3.9 22.7 - - + -
380A LEU* 4.9 7.4 - - + -
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Residues in contact with ARG 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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135A GLU* 3.0 41.6 + - - +
138A LEU* 5.1 0.4 - - - +
139A GLU* 6.0 0.7 - - - -
153A PHE* 3.3 28.5 - - - -
154A THR 2.8 27.6 + - - -
155A PRO* 1.3 71.4 - - - +
157A PRO* 1.3 72.8 - - + +
158A LEU 3.1 0.2 + - - -
159A ILE* 3.2 12.5 + - + +
160A GLN* 2.9 42.2 + - - +
181A THR* 3.0 21.0 + - - -
183A GLY* 3.4 22.2 - - - +
186A LEU* 5.9 0.2 - - - +
187A THR* 5.6 5.2 - - - +
226A ASN* 4.3 0.6 - - - +
500A SAM 3.0 21.7 + - - -
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Residues in contact with PRO 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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155A PRO* 3.4 9.0 - - + -
156A ARG* 1.3 93.4 - - + +
158A LEU* 1.3 58.1 + - - +
160A GLN* 3.5 11.3 + - - +
161A ALA* 3.2 18.9 + - - +
379A LYS* 6.2 1.6 - - - -
380A LEU* 3.6 32.8 - - + +
381A GLU* 3.7 21.8 - - - +
382A ARG* 3.5 32.2 - - + +
385A LEU* 3.9 3.3 - - + +
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Residues in contact with LEU 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 THR* 4.2 14.6 - - + -
155A PRO* 3.1 16.6 + - + +
157A PRO* 1.3 75.9 - - - +
159A ILE* 1.3 67.8 + - - +
161A ALA* 3.3 2.2 + - + +
162A MSE 3.1 37.6 + - + +
305A VAL* 4.4 9.6 - - + -
334A LEU* 4.7 4.3 - - + -
336A LEU* 3.8 32.3 - - + -
340A ILE* 4.5 5.2 - - + -
341A PHE* 3.9 27.6 - - + -
350A VAL* 4.1 14.6 - - + -
380A LEU* 4.6 8.3 - - + +
385A LEU* 4.1 16.4 - - + -
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Residues in contact with ILE 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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154A THR* 3.7 21.5 - - + +
155A PRO 3.3 10.2 + - - +
156A ARG* 3.2 35.6 + - + +
158A LEU* 1.3 79.7 - - - +
160A GLN* 1.3 57.0 + - - +
162A MSE 3.5 1.2 - - - +
163A VAL* 2.9 30.2 + - + +
183A GLY* 3.6 25.1 - - - +
184A PHE* 3.6 34.8 - - + +
187A THR* 3.4 29.2 - - - +
500A SAM 3.8 7.0 - - - +
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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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156A ARG* 2.9 33.5 + - + +
157A PRO* 3.6 8.3 - - - +
159A ILE* 1.3 76.9 - - + +
161A ALA* 1.3 56.5 + - - +
163A VAL* 3.4 1.2 + - - +
164A ASP* 2.9 39.7 + - - +
187A THR* 4.0 24.9 + - + +
382A ARG* 3.7 29.3 - - + +
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Residues in contact with ALA 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 PRO 3.2 5.7 + - - +
158A LEU* 3.8 3.8 - - + +
160A GLN* 1.3 78.4 - - - +
162A MSE 1.3 59.0 + - + +
164A ASP* 3.3 3.3 + - - +
165A CYS* 2.9 36.4 + - - -
382A ARG* 3.7 16.7 - - - +
385A LEU* 3.6 40.6 - - + -
388A PHE* 5.1 7.2 - - + -
389A VAL* 4.1 9.4 - - + +
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Residues in contact with MSE 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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158A LEU* 3.1 29.5 + - + +
159A ILE 3.5 8.1 - - - +
161A ALA* 1.3 77.1 - - + +
163A VAL* 1.3 62.3 + - - +
165A CYS* 3.3 2.9 + - - +
166A ILE* 3.0 27.9 + - - +
184A PHE* 3.6 33.9 - - + -
257A LEU* 4.5 4.3 - - + -
258A ALA 3.9 1.6 - - - +
303A ALA* 3.3 41.5 - - + +
304A VAL 3.7 3.8 - - - +
305A VAL* 3.7 25.1 - - + -
334A LEU* 6.2 0.4 - - + -
350A VAL* 3.7 23.8 - - + -
352A PHE* 4.3 13.2 - - + -
388A PHE* 5.8 0.4 - - + -
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Residues in contact with VAL 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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159A ILE* 2.9 32.1 + - + +
160A GLN 3.8 2.9 - - - +
162A MSE 1.3 72.5 - - - +
164A ASP* 1.3 54.0 + - - +
166A ILE* 4.5 4.9 - - - -
167A ASN* 2.7 32.1 + - - -
168A PRO* 3.2 15.3 - - + +
184A PHE* 4.3 5.2 - - + +
187A THR* 4.1 23.1 - - + +
188A ALA* 4.0 12.3 - - - +
191A TYR* 3.9 32.9 - - + -
257A LEU* 3.8 26.9 - - + -
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Residues in contact with ASP 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 GLN* 2.9 27.3 + - - +
161A ALA 3.6 5.2 - - - +
163A VAL* 1.3 78.2 - - - +
165A CYS* 1.3 62.3 + - - +
167A ASN* 3.4 14.0 + - - +
191A TYR* 3.3 32.4 + - + -
382A ARG* 3.0 33.8 + - - +
389A VAL* 4.7 10.1 - - + -
393A ASN* 5.3 2.3 - - - +
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Residues in contact with CYS 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 ALA 2.9 20.3 + - - +
162A MSE 3.7 3.4 - - - +
164A ASP* 1.3 75.7 - - - +
166A ILE* 1.3 65.1 + - - +
167A ASN* 3.4 5.2 + - - +
352A PHE* 3.9 7.2 - - + -
388A PHE* 3.7 18.6 - - - -
389A VAL* 4.0 16.2 - - - -
392A TYR* 3.4 67.4 - - + -
393A ASN* 5.2 5.1 - - - +
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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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162A MSE 3.0 19.5 + - - +
163A VAL 3.9 2.2 - - - +
165A CYS* 1.3 72.5 - - - +
167A ASN* 1.3 68.8 + - - +
168A PRO* 4.0 9.9 - - + -
255A VAL* 3.6 26.5 - - + -
256A ILE 4.9 0.4 - - - +
257A LEU* 4.1 10.1 - - + -
301A ARG* 2.8 54.6 + - + +
302A ALA* 3.8 28.9 - - - +
303A ALA* 3.6 18.8 - - + +
352A PHE* 4.3 9.9 - - + -
392A TYR* 4.7 5.4 - - - +
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Residues in contact with ASN 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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163A VAL 2.7 17.0 + - - -
164A ASP 3.6 11.2 - - - +
165A CYS 3.2 5.3 - - - +
166A ILE* 1.3 75.8 - - - +
168A PRO* 1.4 69.3 - - - +
169A GLN* 3.1 32.5 + - - +
191A TYR* 2.5 27.3 + - - -
301A ARG* 3.3 6.4 + - - -
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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