Contacts of the helix formed by residues 325 - 338 (chain G) in PDB entry 5O9Z
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 LEU 325 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1404A THR* 6.2 1.8 - - - -
1405A LEU* 5.5 5.8 - - + +
1406A GLU* 4.5 26.5 - - + +
320G GLU* 6.1 0.9 - - - +
323G GLY 3.4 3.5 + - - +
324G LYS* 1.3 74.0 - - - +
326G GLN* 1.3 61.8 + - - +
328G ALA* 3.7 2.7 - - - +
329G ARG* 2.9 25.9 + - - +
353G GLN* 5.7 9.0 - - + -
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Residues in contact with GLN 326 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325G LEU* 1.3 78.6 - - - +
327G VAL* 1.3 57.6 + - - +
329G ARG* 3.4 9.1 - - + +
330G ASN* 2.9 30.3 + - - +
175P LYS* 4.7 7.1 - - + +
176P GLU* 6.1 0.2 - - - -
179P LEU* 3.6 30.1 + - + -
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Residues in contact with VAL 327 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319G GLU* 5.8 1.1 - - + -
324G LYS* 3.6 25.5 - - + -
325G LEU 3.1 1.0 - - - +
326G GLN* 1.3 78.9 - - - +
328G ALA* 1.3 58.4 + - - +
330G ASN* 3.5 4.9 + - - +
331G LEU* 2.9 27.9 + - - +
175P LYS* 5.0 17.8 + - + +
178P ARG* 6.2 1.1 - - - -
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Residues in contact with ALA 328 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316G ALA* 4.4 7.6 - - + +
319G GLU* 4.1 9.4 - - + -
320G GLU* 3.7 36.1 - - + +
324G LYS* 2.9 21.1 + - - +
325G LEU* 3.9 2.5 - - - +
327G VAL* 1.3 73.6 - - - +
329G ARG* 1.3 59.5 + - - +
331G LEU* 3.7 9.0 - - - +
332G ILE* 2.9 26.7 + - - +
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Residues in contact with ARG 329 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325G LEU 2.9 13.7 + - - +
326G GLN* 3.4 13.5 - - - +
327G VAL 3.2 0.2 - - - -
328G ALA* 1.3 76.0 - - - +
330G ASN* 1.3 60.8 + - - +
332G ILE* 3.0 8.5 + - - +
333G MET* 2.9 26.3 + - - +
357G THR* 6.5 1.6 - - - -
179P LEU* 6.4 0.4 - - - -
182P GLN* 4.8 7.1 - - + +
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Residues in contact with ASN 330 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326G GLN 2.9 16.0 + - - +
327G VAL* 4.0 4.3 - - - +
329G ARG* 1.3 75.9 - - - +
331G LEU* 1.3 57.4 + - - +
333G MET* 3.4 2.6 + - - +
334G LYS* 2.9 27.4 + - - +
178P ARG* 3.6 40.4 - - + +
182P GLN* 4.0 13.1 - - + +
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Residues in contact with LEU 331 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312G TRP* 5.0 5.7 - - - +
315G SER 5.9 0.4 - - - +
316G ALA* 5.3 11.5 - - + +
319G GLU* 5.4 6.3 - - + -
327G VAL 2.9 19.2 + - - +
328G ALA* 3.9 10.1 - - + +
330G ASN* 1.3 74.5 - - - +
332G ILE* 1.3 60.5 + - - +
334G LYS* 3.8 7.3 - - - +
335G GLY* 2.9 23.7 + - - -
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Residues in contact with ILE 332 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316G ALA* 5.5 7.2 - - + -
328G ALA 2.9 20.6 + - - +
329G ARG* 3.0 8.9 + - - +
331G LEU* 1.3 78.4 - - - +
333G MET* 1.3 57.5 + - - +
335G GLY* 3.4 2.0 + - - +
336G THR* 2.9 27.7 + - - -
349G ALA* 3.9 32.5 - - + +
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Residues in contact with MET 333 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329G ARG 2.9 13.3 + - - +
330G ASN* 3.4 8.9 + - - +
332G ILE* 1.3 77.1 - - - +
334G LYS* 1.3 59.8 + - - +
336G THR* 3.3 7.2 + - - +
337G GLU* 2.9 29.6 + - - +
182P GLN* 4.5 16.6 - - + +
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Residues in contact with LYS 334 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330G ASN 2.9 18.0 + - - +
331G LEU* 3.8 8.1 - - - +
332G ILE 3.4 0.2 - - - -
333G MET* 1.3 76.6 - - - +
335G GLY* 1.3 58.2 + - - +
337G GLU* 4.1 5.2 - - - +
338G MET* 2.9 30.8 + - - +
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Residues in contact with GLY 335 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308G HIS* 4.4 4.5 - - - +
312G TRP* 4.4 20.9 - - - -
331G LEU 2.9 16.3 + - - -
332G ILE* 3.4 3.1 + - - -
333G MET 3.2 0.2 - - - -
334G LYS* 1.3 77.2 - - - +
336G THR* 1.3 58.9 + - - +
338G MET* 4.3 4.5 - - - -
339G CYS* 2.9 33.6 + - - +
345G VAL* 5.5 4.3 - - - +
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Residues in contact with THR 336 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332G ILE 2.9 17.2 + - - -
333G MET* 3.3 8.3 + - - -
335G GLY* 1.3 76.5 - - - +
337G GLU* 1.3 59.0 + - - +
339G CYS 4.6 3.4 - - - -
340G PRO* 3.2 30.2 - - - +
346G TRP* 6.5 1.1 - - - -
349G ALA* 5.7 5.8 - - - +
364G GLN 6.5 0.2 - - - -
365G ALA* 5.7 10.3 - - - -
368G HIS* 4.9 5.3 - - - +
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Residues in contact with GLU 337 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333G MET 2.9 16.4 + - - +
334G LYS* 4.1 6.3 - - - +
336G THR* 1.3 76.8 - - - +
338G MET* 1.3 64.7 + - - +
340G PRO* 3.6 9.0 - - - +
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Residues in contact with MET 338 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306G PRO* 3.9 27.4 - - - +
307G HIS* 6.1 0.2 - - + -
308G HIS* 4.4 6.5 - - + -
334G LYS 2.9 21.0 + - - +
335G GLY* 4.1 4.7 - - - +
337G GLU* 1.3 79.4 - - - +
339G CYS* 1.3 59.8 + - - +
340G PRO* 3.6 3.8 - - - +
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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