Contacts of the helix formed by residues 297 - 304 (chain A) in PDB entry 4OWT
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 SER 297 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A MSE 5.2 3.7 + - - -
250A ILE 4.0 3.4 + - - -
295A ARG 3.7 3.2 + - - -
296A THR* 1.3 85.7 - - - +
298A ARG* 1.3 65.7 + - - +
299A LYS* 3.0 20.8 + - - +
300A PHE* 3.1 32.4 + - - -
301A LEU* 3.5 3.7 + - - +
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Residues in contact with ARG 298 (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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296A THR 3.5 2.5 + - - +
297A SER* 1.3 71.2 + - - +
299A LYS* 1.3 65.2 + - - +
301A LEU* 3.8 9.9 - - + +
302A ALA* 3.0 28.4 + - + +
355A GLY 3.1 24.8 + - - +
356A VAL* 4.0 30.8 + - + +
358A HIS* 3.0 38.7 + - - +
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Residues in contact with LYS 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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165A MSE 4.4 11.0 - - - -
203A ILE* 3.8 37.2 - - + -
207A MSE 4.0 23.5 - - + +
297A SER* 3.0 15.4 + - - +
298A ARG* 1.3 79.0 - - - +
300A PHE* 1.3 63.9 + - + +
302A ALA* 4.2 3.4 - - - +
303A CYS* 3.3 22.0 + - - +
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Residues in contact with PHE 300 (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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203A ILE* 3.8 16.4 - - + -
206A ALA* 3.7 37.9 - - + -
207A MSE 3.5 26.9 - - + -
210A TYR* 3.3 48.4 - + + -
249A MSE 4.0 11.4 - - + -
250A ILE* 3.8 27.4 - - + -
296A THR* 3.9 6.3 - - + -
297A SER* 3.1 30.7 + - - +
299A LYS* 1.3 78.9 - - + +
301A LEU* 1.3 64.9 + - - +
303A CYS* 3.2 23.5 - - - -
304A ARG 3.9 1.0 + - - -
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Residues in contact with LEU 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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210A TYR* 3.8 18.8 - - - +
253A ASP* 3.9 24.5 - - - +
256A ARG* 4.9 0.2 - - - +
296A THR* 4.1 18.8 - - + +
297A SER 3.9 9.4 - - - +
298A ARG* 3.3 5.3 + - + +
300A PHE* 1.3 77.4 - - - +
302A ALA* 1.3 61.7 + - - +
303A CYS 3.6 0.2 + - - -
304A ARG* 3.7 11.7 + - - +
305A LEU* 4.4 5.9 + - - +
348A ASP* 4.9 2.9 - - - +
351A ARG* 4.0 41.2 - - + +
352A TYR* 4.1 13.9 - - - +
355A GLY* 4.1 19.1 - - - +
356A VAL* 3.7 17.5 - - + -
411A ASN* 5.9 0.7 - - - +
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Residues in contact with ALA 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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169A LYS* 2.8 22.7 + - - +
298A ARG* 3.0 17.7 + - + +
299A LYS* 4.3 3.8 - - - +
301A LEU* 1.3 73.6 - - - +
303A CYS* 1.3 64.8 + - - +
304A ARG 3.1 3.4 - - - -
305A LEU* 3.1 11.8 + - - +
310A GLU* 4.2 10.7 - - - +
352A TYR* 4.0 24.6 - - + -
356A VAL* 4.8 5.6 - - + -
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Residues in contact with CYS 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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165A MSE 6.0 0.2 - - - +
169A LYS* 3.8 27.6 - - + +
207A MSE 3.7 26.7 - - + -
210A TYR* 3.8 21.3 - - - -
211A THR* 4.1 16.2 - - - +
299A LYS 3.3 13.9 + - - +
300A PHE* 3.2 24.4 + - - -
302A ALA* 1.3 76.4 - - - +
304A ARG* 1.3 79.0 + - - +
305A LEU 3.3 2.6 + - - +
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Residues in contact with ARG 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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168A MSE 2.9 29.1 + - - -
169A LYS* 4.2 2.4 + - - +
171A ILE* 3.0 24.6 + - - +
173A GLY* 3.7 21.4 + - - +
210A TYR* 3.6 31.2 - - + +
211A THR* 3.7 31.7 + - - +
214A ARG* 3.5 30.5 - - + +
215A LEU* 3.9 13.0 - - - +
301A LEU 3.7 7.3 + - - +
302A ALA 3.1 1.4 - - - -
303A CYS* 1.3 95.8 + - - +
305A LEU* 1.3 68.5 + - - +
306A THR 4.4 0.2 + - - -
309A MSE 4.7 0.7 - - - +
345A LEU* 4.3 8.8 - - - +
348A ASP* 3.9 27.1 - - + +
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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