Contacts of the helix formed by residues 295 - 310 (chain A) in PDB entry 4Y5O
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 ALA 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A ALA* 3.3 5.1 - - + +
294A SER* 1.3 79.6 + - - +
296A THR* 1.3 63.3 + - - +
297A GLU 3.2 2.0 - - - -
298A LEU* 3.1 27.6 + - + +
299A LEU* 3.2 12.8 + - - +
356A PHE* 5.5 1.6 - - - -
17B LEU* 6.2 4.7 - - + -
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Residues in contact with THR 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 ALA* 4.0 21.0 + - - +
294A SER 3.3 2.2 - - - -
295A ALA* 1.3 77.2 - - - +
297A GLU* 1.3 62.8 + - - +
299A LEU* 3.3 12.9 + - + +
300A GLN* 3.2 41.9 + - + +
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Residues in contact with GLU 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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294A SER 4.2 8.6 + - - +
295A ALA 3.2 0.2 - - - -
296A THR* 1.3 80.2 - - - +
298A LEU* 1.3 65.8 + - + +
300A GLN* 3.1 18.0 + - - +
301A ASP* 3.0 51.6 + - - +
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Residues in contact with LEU 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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294A SER 4.9 2.9 - - - +
295A ALA* 3.1 25.5 + - + +
297A GLU* 1.3 88.9 - - + +
299A LEU* 1.3 60.4 + - - +
301A ASP* 4.2 14.8 - - + +
302A TYR* 3.5 15.2 + - - +
355A PRO* 6.0 6.3 - - + -
356A PHE* 3.5 17.5 - - + -
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Residues in contact with LEU 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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295A ALA 3.2 10.3 + - - +
296A THR* 3.4 13.9 - - + +
297A GLU 3.2 0.4 - - - -
298A LEU* 1.3 77.1 - - - +
300A GLN* 1.3 62.9 + - + +
302A TYR* 3.2 2.6 + - - +
303A MET* 2.8 49.0 + - + +
356A PHE* 3.6 28.2 - - + -
11B MET* 4.0 35.9 - - + +
14B LEU* 3.9 19.7 - - + -
15B VAL* 4.1 22.0 - - + +
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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
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296A THR* 3.4 30.2 - - + +
297A GLU* 3.1 21.0 + - + +
299A LEU* 1.3 79.1 - - + +
301A ASP* 1.3 61.0 + - - +
303A MET* 3.3 9.7 + - - +
304A LEU* 2.8 30.4 + - - +
11B MET* 5.9 6.7 - - + +
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Residues in contact with ASP 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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297A GLU* 3.0 38.6 + - - +
298A LEU* 4.2 17.3 - - + +
300A GLN* 1.3 78.9 - - - +
302A TYR* 1.3 58.3 + - - +
304A LEU* 3.4 13.5 + - - +
305A THR* 2.9 31.2 + - - -
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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
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298A LEU 3.5 13.4 + - - +
299A LEU 3.2 7.9 + - - +
301A ASP* 1.3 77.2 - - - +
303A MET* 1.3 68.1 + - + +
305A THR* 3.2 13.7 + - + -
306A LEU* 3.0 46.4 + - + +
318A PHE* 3.7 3.4 - + - -
348A PHE 4.6 2.0 - - - -
349A LEU* 2.9 38.7 + - - +
352A GLY* 3.2 36.1 - - - +
353A LEU* 3.4 23.0 - - + +
356A PHE* 4.0 11.4 - + + -
14B LEU* 3.5 33.7 - - + -
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Residues in contact with MET 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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299A LEU* 2.8 38.4 + - + +
300A GLN* 3.6 7.9 - - - +
302A TYR* 1.3 73.9 - - + +
304A LEU* 1.3 58.4 + - - +
306A LEU* 3.4 14.5 + - + +
307A ARG* 2.9 32.5 + - - +
7B LEU* 4.0 21.1 - - + +
10B ILE* 3.6 18.4 - - + +
11B MET* 4.0 28.9 - - + -
14B LEU* 3.5 31.4 - - + -
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Residues in contact with LEU 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 GLN 2.8 17.3 + - - +
301A ASP* 3.4 16.2 - - - +
303A MET* 1.3 78.6 - - - +
305A THR* 1.3 51.2 + - - +
307A ARG* 3.4 17.7 + - - +
308A THR* 2.7 56.1 + - + +
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Residues in contact with THR 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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301A ASP 2.9 14.9 + - - -
302A TYR* 3.4 19.5 - - + -
304A LEU* 1.3 76.0 - - - +
306A LEU* 1.3 63.6 + - + +
308A THR* 3.3 7.4 + - - -
309A LYS* 3.0 46.8 + - + +
348A PHE* 3.8 22.8 - - + +
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Residues in contact with LEU 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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302A TYR* 3.0 29.5 + - + +
303A MET* 3.6 20.6 - - + +
305A THR* 1.3 78.8 - - + +
307A ARG* 1.3 63.0 + - - +
310A LEU* 3.2 47.7 + - + +
315A ILE* 3.9 6.7 - - + +
318A PHE* 4.0 6.7 - - + -
348A PHE* 5.7 1.8 - - + -
349A LEU* 3.7 33.0 - - + -
7B LEU* 4.1 9.9 - - + -
10B ILE* 3.8 40.4 - - + -
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Residues in contact with ARG 307 (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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303A MET* 2.9 19.5 + - - +
304A LEU* 3.7 20.2 - - - +
306A LEU* 1.3 75.7 - - - +
308A THR* 1.3 64.3 + - + +
310A LEU 4.5 5.1 - - - +
315A ILE* 4.5 4.7 - - - -
3B GLU* 4.4 12.0 - - - +
4B GLN* 3.5 32.9 + - - +
7B LEU* 3.6 34.6 - - + +
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Residues in contact with THR 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LEU* 2.7 41.6 + - + +
305A THR* 3.3 10.6 + - - -
306A LEU 3.1 0.2 - - - -
307A ARG* 1.3 87.5 - - + +
309A LYS* 1.3 64.6 + - - +
310A LEU 3.9 0.7 - - - -
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Residues in contact with LYS 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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305A THR* 3.0 36.8 + - + +
308A THR* 1.3 88.1 - - - +
310A LEU* 1.3 61.2 + - - +
311A SER 4.1 0.2 + - - -
346A ARG* 3.5 20.1 + - - +
348A PHE* 3.6 43.5 - - + -
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Residues in contact with LEU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A LEU* 3.2 38.5 + - + +
307A ARG 4.5 5.4 - - - +
308A THR 5.3 0.3 - - - -
309A LYS* 1.3 83.4 - - - +
311A SER* 1.3 62.7 + - - +
314A GLU* 3.9 33.2 - - + +
315A ILE* 3.6 24.8 - - + +
318A PHE* 4.7 5.6 - - + -
342A TYR* 4.9 2.5 - - + +
346A ARG* 4.1 23.1 - - + +
348A PHE* 4.0 24.0 - - + -
349A LEU* 4.6 15.9 - - + -
3B GLU* 4.7 2.3 - - - +
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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