Contacts of the helix formed by residues 297 - 308 (chain A) in PDB entry 4WB7
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 GLN 297 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A ALA* 4.1 1.2 - - - +
296A ASP* 1.3 90.5 + - + +
298A PRO* 1.3 80.5 - - + +
299A ILE* 4.2 7.4 - - + +
300A GLN* 2.9 36.1 + - - +
301A ILE* 3.1 14.5 + - - +
253B LEU* 3.8 22.6 - - + +
267B SER* 4.6 11.9 - - - +
24J ASP* 3.6 20.7 + - - +
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Residues in contact with PRO 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A PRO* 4.3 11.7 - - + -
296A ASP 4.0 5.2 - - - +
297A GLN* 1.3 94.8 - - - +
299A ILE* 1.3 63.0 + - + +
301A ILE* 3.0 12.3 + - + +
302A TYR* 2.9 54.9 + - + +
15I ARG* 4.1 22.2 - - - +
24J ASP* 5.8 4.3 - - - +
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Residues in contact with ILE 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A GLN* 3.1 4.1 - - + +
298A PRO* 1.3 77.2 - - + +
300A GLN* 1.3 76.7 + - - +
302A TYR* 3.2 12.1 + - + +
303A GLU* 3.1 42.0 + - + +
253B LEU* 4.2 31.2 - - + -
265B ILE* 4.0 24.7 - - + +
299B ILE* 5.2 7.2 - - + -
302B TYR* 3.7 38.6 - - + -
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Residues in contact with GLN 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ALA* 3.7 17.5 - - + -
297A GLN* 2.9 27.7 + - + +
299A ILE* 1.3 82.2 - - - +
301A ILE* 1.3 65.3 + - - +
303A GLU* 3.1 31.4 + - - +
304A LYS* 3.2 28.7 + - - +
265B ILE 3.0 25.4 + - - +
266B LEU* 3.7 14.4 + - - +
267B SER* 3.8 19.9 - - - -
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Residues in contact with ILE 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A PRO* 4.0 15.7 - - + +
258A GLU* 3.6 31.6 - - + +
293A PHE* 3.8 16.2 - - + +
294A PHE 4.0 1.8 - - - -
295A ALA* 3.5 36.5 - - - +
297A GLN 3.1 7.6 + - - +
298A PRO* 3.0 19.9 + - + +
300A GLN* 1.3 76.2 - - - +
302A TYR* 1.3 58.7 + - + +
304A LYS* 3.1 9.6 + - - +
305A ILE* 3.0 45.6 + - + +
15I ARG* 3.8 9.2 - - - +
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Residues in contact with TYR 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LEU* 6.3 0.2 - - + -
257A PRO* 3.4 32.3 - - + +
260A LEU* 3.7 20.6 - - + -
265A ILE* 3.7 36.3 - - + -
298A PRO* 2.9 38.8 + - + +
299A ILE* 3.2 9.2 + - + +
301A ILE* 1.3 77.3 - - + +
303A GLU* 1.3 62.3 + - + +
305A ILE* 3.3 4.5 + - + +
306A VAL* 3.1 30.5 + - - +
299B ILE* 3.8 36.6 - - + -
22I ILE* 3.3 24.8 - - - +
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Residues in contact with GLU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ILE* 3.1 27.8 + - + +
300A GLN* 3.1 36.7 + - - +
302A TYR* 1.3 79.1 - - + +
304A LYS* 1.3 60.5 + - + +
306A VAL* 3.5 8.5 - - - +
307A SER* 3.3 22.2 + - - -
265B ILE* 4.1 6.9 - - - +
266B LEU* 3.9 19.4 - - - +
302B TYR* 5.7 1.6 - - - +
303B GLU* 6.2 0.5 - - - -
306B VAL* 4.6 6.7 - - - +
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Residues in contact with LYS 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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293A PHE* 3.7 20.9 - - + -
294A PHE 3.3 36.3 - - - +
295A ALA* 4.0 13.7 - - - -
300A GLN* 3.2 14.2 + - - +
301A ILE* 3.1 9.2 + - - +
303A GLU* 1.3 75.2 - - + +
305A ILE* 1.3 61.5 + - - +
307A SER* 2.9 9.9 + - - -
308A GLY* 2.8 27.0 + - - -
309A LYS 4.3 1.0 + - - +
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Residues in contact with ILE 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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257A PRO 3.5 24.7 - - - +
258A GLU 4.3 6.5 - - - +
260A LEU 3.5 26.2 - - - +
262A PRO* 3.9 12.0 - - + +
265A ILE* 3.6 21.1 - - + -
277A TRP* 3.8 17.2 - - + -
293A PHE* 3.6 28.7 - - + -
301A ILE* 3.0 28.4 + - + +
302A TYR* 3.3 7.8 + - + +
304A LYS* 1.3 76.1 - - - +
306A VAL* 1.3 58.5 + - - +
308A GLY* 2.9 19.9 + - - -
330A VAL* 3.9 8.1 - - - +
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Residues in contact with VAL 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A PRO* 4.2 17.3 - - + -
265A ILE* 3.7 34.1 - - + -
266A LEU* 4.2 18.4 - - + -
302A TYR 3.1 18.1 + - - +
303A GLU* 3.5 11.9 - - - +
305A ILE* 1.3 74.3 - - - +
307A SER* 1.3 68.1 + - - +
308A GLY* 4.3 0.2 - - - -
330A VAL* 4.1 13.7 - - - +
303B GLU* 4.2 15.3 - - - +
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Residues in contact with SER 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A GLU 3.3 15.5 + - - -
304A LYS* 2.9 13.7 + - - -
306A VAL* 1.3 79.9 - - - +
308A GLY* 1.3 62.2 + - - +
309A LYS* 3.0 38.9 + - - +
330A VAL* 4.2 5.5 - - - +
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Residues in contact with GLY 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A TRP* 5.0 0.2 - - - -
293A PHE* 4.0 9.9 - - - -
304A LYS 2.8 9.0 + - - -
305A ILE 2.9 15.9 + - - -
307A SER* 1.3 81.1 + - - +
309A LYS* 1.3 63.5 + - - -
310A VAL* 3.1 15.0 + - - +
328A LEU 4.8 3.8 - - - +
330A VAL* 3.7 16.5 - - - +
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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