Contacts of the helix formed by residues 294 - 310 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A ASP* 3.6 27.9 + - + +
292A GLN 3.4 1.2 - - - -
293A PRO* 1.3 91.6 - - - +
295A GLU* 1.3 62.6 + - - +
296A ARG 3.4 2.5 - - - -
297A GLN* 3.1 31.4 + - + +
298A VAL* 3.0 28.6 + - + +
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Residues in contact with GLU 295 (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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132A TYR* 4.3 11.1 - - + -
135A ARG* 3.1 45.4 + - - +
292A GLN* 3.5 31.4 + - + +
293A PRO 3.3 2.5 - - - +
294A ASN* 1.3 75.4 - - - +
296A ARG* 1.4 61.8 + - - +
298A VAL* 3.4 7.4 + - - +
299A ARG* 3.2 35.1 + - - +
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Residues in contact with ARG 296 (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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293A PRO 5.1 1.0 + - - +
294A ASN 3.4 0.6 - - - -
295A GLU* 1.4 76.0 - - - +
297A GLN* 1.3 96.5 + - - +
299A ARG* 3.4 10.1 + - - +
300A ILE* 3.3 47.1 + - + +
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Residues in contact with GLN 297 (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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293A PRO 4.3 5.3 + - - +
294A ASN* 3.1 41.3 + - + +
296A ARG* 1.3 106.4 - - - +
298A VAL* 1.4 55.1 + - - +
300A ILE* 3.2 11.8 + - - +
301A GLN* 2.9 51.9 + - - +
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Residues in contact with VAL 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ASP* 3.4 51.8 - - + +
129A TRP* 3.6 21.5 - - + -
132A TYR* 3.8 19.5 - - + -
294A ASN* 3.0 21.1 + - + +
295A GLU* 3.6 11.0 - - - +
297A GLN* 1.4 71.2 - - + +
299A ARG* 1.4 56.1 + - - +
301A GLN* 3.2 11.8 + - - +
302A LEU* 2.8 42.7 + - + +
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Residues in contact with ARG 299 (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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80A ARG* 5.0 14.8 - - - +
132A TYR* 3.2 38.6 + - + -
164A ASN* 2.9 30.5 + - - +
165A ALA* 3.8 7.5 + - - +
166A GLU* 3.6 21.4 - - - +
295A GLU* 3.2 22.1 + - - +
296A ARG* 3.6 10.3 - - - +
297A GLN 3.3 0.2 - - - -
298A VAL* 1.4 74.8 - - - +
300A ILE* 1.4 56.4 + - + +
302A LEU* 3.5 9.0 + - - +
303A LYS* 3.0 38.3 + - + +
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Residues in contact with ILE 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ARG* 3.3 59.4 + - + +
297A GLN* 3.2 9.0 + - - +
299A ARG* 1.4 77.7 - - + +
301A GLN* 1.4 51.3 + - + +
303A LYS* 3.3 11.3 + - + +
304A ASP* 2.9 51.0 + - - +
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Residues in contact with GLN 301 (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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126A LYS* 3.2 27.9 + - + +
128A ASP* 4.3 0.9 - - - +
129A TRP* 2.9 39.0 + - + +
297A GLN* 2.9 35.4 + - - +
298A VAL* 3.4 9.6 - - - +
300A ILE* 1.4 68.9 - - + +
302A LEU* 1.4 56.5 + - - +
304A ASP* 3.4 8.8 + - - +
305A HIS* 2.8 32.9 + - - +
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Residues in contact with LEU 302 (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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116A LEU* 3.8 23.6 - - + -
129A TRP* 3.7 35.6 - - + -
132A TYR* 3.6 36.1 - - + -
133A ILE* 4.2 12.1 - - + -
161A LEU* 4.6 11.9 - - + -
165A ALA* 3.6 17.7 - - + +
298A VAL* 2.8 31.4 + - + +
299A ARG* 3.7 0.4 - - - +
301A GLN* 1.4 69.1 - - - +
303A LYS* 1.4 55.3 + - - +
305A HIS* 3.1 3.8 + - - +
306A ILE* 2.9 39.5 + - + +
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Residues in contact with LYS 303 (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 GLU 4.2 4.3 - - - +
164A ASN* 3.4 59.5 - - + +
165A ALA* 3.9 2.4 - - + +
299A ARG* 3.0 24.4 + - + +
300A ILE* 3.4 9.6 - - + +
302A LEU* 1.4 73.6 - - - +
304A ASP* 1.4 58.4 + - - +
306A ILE* 3.1 9.0 + - - +
307A ASP* 2.9 43.6 + - - +
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Residues in contact with ASP 304 (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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300A ILE* 2.9 37.7 + - - +
301A GLN* 3.4 9.9 - - - +
303A LYS* 1.4 76.5 - - - +
305A HIS* 1.4 56.7 + - - +
307A ASP* 3.4 10.2 + - - +
308A ARG* 2.9 32.5 + - - +
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Residues in contact with HIS 305 (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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116A LEU* 3.9 18.4 - - + +
119A ASN* 3.6 14.2 + - + -
120A THR* 3.4 31.2 + - + +
129A TRP* 3.6 31.0 - + + -
301A GLN 2.8 16.5 + - - +
302A LEU 3.1 8.7 + - - +
304A ASP* 1.4 72.3 - - - +
306A ILE* 1.3 55.5 + - - +
308A ARG* 3.1 47.9 + - - +
309A THR* 2.6 44.1 + - - -
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Residues in contact with ILE 306 (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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110A ALA* 3.6 18.4 - - + +
116A LEU* 4.9 7.2 - - + -
161A LEU* 4.3 20.2 - - + -
162A THR 3.5 20.9 - - - +
163A GLU 3.8 13.2 - - - +
165A ALA* 3.9 22.0 - - + +
302A LEU* 2.9 20.2 + - + +
303A LYS* 3.1 6.9 + - - +
305A HIS* 1.3 74.4 - - - +
307A ASP* 1.4 62.3 + - - +
309A THR* 3.4 6.2 + - - -
310A ARG* 3.0 60.0 + - - +
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Residues in contact with ASP 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A GLU* 4.6 5.5 - - - +
303A LYS* 2.9 30.9 + - - +
304A ASP* 3.7 9.6 - - - +
306A ILE* 1.4 83.7 - - - +
308A ARG* 1.4 59.1 + - - +
310A ARG* 3.3 25.7 + - - +
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Residues in contact with ARG 308 (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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119A ASN 3.8 10.5 + - - -
120A THR* 5.0 2.8 - - - +
121A LYS* 5.4 9.9 - - - +
304A ASP 2.9 16.3 + - - +
305A HIS* 3.1 57.9 + - - +
307A ASP* 1.4 74.2 - - - +
309A THR* 1.3 58.5 + - - +
310A ARG 4.9 1.7 - - - +
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Residues in contact with THR 309 (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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119A ASN* 3.6 33.8 + - + +
305A HIS* 2.6 38.9 + - - -
306A ILE* 3.8 6.5 - - - -
308A ARG* 1.3 79.4 + - - +
310A ARG* 1.4 68.5 + - - +
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Residues in contact with ARG 310 (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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109A GLY 3.8 22.9 + - - -
110A ALA* 4.1 5.9 - - - +
163A GLU* 3.9 28.3 - - - +
306A ILE* 3.0 49.9 + - - +
307A ASP* 3.3 19.1 + - - +
308A ARG 4.9 1.0 - - - +
309A THR* 1.4 84.5 - - - +
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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