Contacts of the helix formed by residues 294 - 311 (chain B) in PDB entry 4OBP
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 ASN 294 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ASP* 3.6 28.2 + - + +
292B GLN 3.4 0.6 - - - -
293B PRO* 1.3 92.5 - - - +
295B GLU* 1.4 62.4 + - - +
296B ARG* 3.4 2.9 - - - -
297B GLN* 3.3 13.8 + - + +
298B VAL* 3.0 27.9 + - + +
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Residues in contact with GLU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B TYR* 4.4 12.6 - - + -
135B ARG* 3.1 43.9 + - - +
139B ARG* 5.6 0.2 + - - -
292B GLN* 3.5 31.0 + - + +
293B PRO 3.3 3.0 + - - +
294B ASN* 1.4 73.5 - - - +
296B ARG* 1.4 62.8 + - - +
298B VAL* 3.3 8.7 + - - +
299B ARG* 3.1 23.8 + - - +
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Residues in contact with ARG 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B PRO 5.1 1.1 + - - +
294B ASN 3.4 0.8 - - - -
295B GLU* 1.4 78.6 - - - +
297B GLN* 1.3 61.4 + - - +
299B ARG* 3.5 6.1 + - - +
300B ILE* 3.2 38.0 + - + +
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Residues in contact with GLN 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ASN* 3.3 16.5 + - + +
296B ARG* 1.3 75.4 - - - +
298B VAL* 1.4 54.7 + - + +
300B ILE* 3.2 23.0 + - - +
301B GLN* 2.7 71.4 + - - +
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Residues in contact with VAL 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ASP* 3.4 43.3 - - + +
129B TRP* 3.6 19.9 + - + -
132B TYR* 3.8 28.0 - - + -
294B ASN* 3.0 22.3 + - + +
295B GLU* 3.3 10.1 + - - +
297B GLN* 1.4 73.9 - - + +
299B ARG* 1.4 55.6 + - - +
301B GLN* 3.1 13.1 + - - +
302B LEU* 2.9 38.4 + - + +
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Residues in contact with ARG 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ARG* 3.7 24.4 - - - +
132B TYR* 3.4 33.3 + - + +
164B ASN* 2.7 35.3 + - - +
165B ALA* 3.9 8.2 + - - +
166B GLU* 3.4 23.4 - - - +
295B GLU 3.1 12.5 + - - +
296B ARG* 3.6 10.1 - - - +
298B VAL* 1.4 74.4 - - - +
300B ILE* 1.4 59.1 + - + +
302B LEU* 3.3 12.3 + - - +
303B LYS* 3.0 28.0 + - + +
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Residues in contact with ILE 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ARG* 3.2 30.9 + - + +
297B GLN* 3.2 25.9 + - - +
299B ARG* 1.4 76.3 - - + +
301B GLN* 1.4 58.6 + - + +
303B LYS* 3.2 7.0 + - - +
304B ASP* 2.9 51.2 + - - +
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Residues in contact with GLN 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LYS* 3.6 24.5 + - - +
129B TRP* 2.9 36.8 + - + +
297B GLN* 2.7 52.9 + - - +
298B VAL* 3.4 12.7 - - - +
300B ILE* 1.4 71.3 - - - +
302B LEU* 1.4 56.0 + - - +
304B ASP* 3.6 8.7 + - - +
305B HIS* 3.0 27.7 + - - +
308B ARG* 4.9 1.0 + - - -
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Residues in contact with LEU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LEU* 3.9 22.0 - - + -
129B TRP* 3.7 35.2 - - + -
132B TYR* 3.7 36.3 - - + -
133B ILE* 4.4 10.3 - - + -
161B LEU* 4.8 10.3 - - + -
165B ALA* 3.9 15.3 - - + +
298B VAL* 2.9 28.8 + - + +
299B ARG* 3.6 7.0 - - - +
301B GLN* 1.4 72.4 - - - +
303B LYS* 1.4 60.4 + - - +
305B HIS* 3.4 5.5 + - - +
306B ILE* 3.1 34.0 + - + +
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Residues in contact with LYS 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B GLU* 3.3 25.3 + - - +
164B ASN* 3.9 24.0 - - - +
165B ALA* 3.7 7.6 - - + +
299B ARG* 3.0 15.4 + - + +
300B ILE* 3.5 12.1 - - - +
302B LEU* 1.4 73.0 - - - +
304B ASP* 1.4 66.8 + - - +
306B ILE* 3.4 5.5 + - - +
307B ASP* 3.1 59.8 + - - +
310B ARG* 4.5 3.4 - - - +
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Residues in contact with ASP 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B ILE* 2.9 41.0 + - - +
301B GLN* 3.7 8.0 - - - +
303B LYS* 1.4 81.5 - - - +
305B HIS* 1.4 55.4 + - - +
307B ASP* 3.6 8.7 + - - +
308B ARG* 3.0 52.6 + - - +
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Residues in contact with HIS 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LEU* 3.5 29.9 - - + +
119B ASN* 3.4 22.1 + - + -
120B THR* 3.3 22.1 + - + +
129B TRP* 3.9 25.1 - + + -
301B GLN 3.0 18.7 + - - +
302B LEU* 3.6 6.5 - - - +
303B LYS 3.3 0.4 - - - -
304B ASP* 1.4 72.9 - - - +
306B ILE* 1.4 57.5 + - - +
308B ARG* 3.4 13.4 + - + +
309B THR* 2.7 53.0 + - - -
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Residues in contact with ILE 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ALA* 3.7 30.5 - - + +
116B LEU* 5.2 6.1 - - + -
161B LEU* 4.3 20.2 - - + -
162B THR 3.4 21.1 - - - +
163B GLU* 4.1 11.0 - - - +
165B ALA* 3.7 21.3 - - + +
302B LEU* 3.1 23.0 + - + +
303B LYS* 3.4 4.7 + - - +
305B HIS* 1.4 74.5 - - - +
307B ASP* 1.4 58.9 + - - +
309B THR* 3.4 7.2 + - - -
310B ARG* 3.0 46.6 + - - +
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Residues in contact with ASP 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B LYS* 3.1 45.3 + - - +
304B ASP* 3.8 8.7 - - - +
305B HIS 3.3 0.2 - - - -
306B ILE* 1.4 74.4 - - - +
308B ARG* 1.4 63.5 + - - +
310B ARG* 3.1 48.0 + - - +
311B LYS* 3.4 30.1 + - - +
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Residues in contact with ARG 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B GLN 4.9 0.8 + - - -
304B ASP* 3.0 53.7 + - - +
305B HIS* 3.4 15.0 + - + +
307B ASP* 1.4 76.5 - - - +
309B THR* 1.4 60.4 + - - +
310B ARG 3.8 0.2 + - - -
311B LYS* 4.0 15.4 + - - +
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Residues in contact with THR 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ASN* 3.6 33.7 + - + +
305B HIS* 2.7 39.9 + - + -
306B ILE* 3.8 7.0 - - - -
307B ASP 3.3 0.2 - - - -
308B ARG* 1.4 74.1 - - - +
310B ARG* 1.4 64.4 + - - +
311B LYS 3.5 5.2 + - - +
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Residues in contact with ARG 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B GLU* 4.0 20.2 - - - +
303B LYS* 4.5 4.2 - - - +
306B ILE* 3.0 28.9 + - + +
307B ASP* 3.1 48.4 + - - +
309B THR* 1.4 77.6 - - - +
311B LYS* 1.3 75.6 + - + +
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Residues in contact with LYS 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B ASP* 3.4 27.8 + - - +
308B ARG* 4.0 12.5 + - - +
309B THR 3.5 5.0 - - - +
310B ARG* 1.3 93.6 - - + +
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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