Contacts of the helix formed by residues 309 - 321 (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 PRO 309 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279G SER* 6.3 3.6 - - - -
306G PRO* 5.1 2.9 - - + -
307G HIS 4.1 3.4 - - - +
308G HIS* 1.3 88.8 - - - +
310G PRO* 1.4 63.4 - - + +
313G ILE* 2.6 41.2 + - - +
339G CYS* 3.8 10.1 - - + -
342G SER* 3.6 22.9 - - - -
344G ASP* 6.2 2.9 - - + -
345G VAL* 4.3 10.1 - - + +
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Residues in contact with PRO 310 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279G SER* 5.4 16.4 - - - +
280G MET 6.0 2.9 - - - +
281G ILE* 4.7 7.0 - - + +
307G HIS* 3.8 8.7 - - - +
309G PRO* 1.4 100.7 - - + +
311G ALA* 1.3 60.5 + - + +
313G ILE* 3.4 4.3 + - + +
314G ALA* 2.9 30.8 + - - +
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Residues in contact with ALA 311 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298G LEU 5.0 1.1 - - - +
301G VAL* 3.4 39.0 - - + +
302G ARG* 4.3 8.8 - - + +
307G HIS 3.1 20.0 + - - +
308G HIS* 5.3 0.2 - - + -
310G PRO* 1.3 76.8 - - + +
312G TRP* 1.3 54.7 + - - +
314G ALA* 4.5 2.0 - - - +
315G SER* 2.5 41.1 + - - +
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Residues in contact with TRP 312 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308G HIS* 3.5 36.1 - - + +
311G ALA* 1.3 74.9 - - - +
313G ILE* 1.3 60.1 + - - +
315G SER* 4.5 0.9 - - - -
316G ALA* 2.4 41.3 + - + +
331G LEU 5.0 4.5 - - - +
332G ILE* 6.4 0.2 - - - -
335G GLY* 4.4 15.3 - - - -
345G VAL* 5.3 5.6 - - + -
348G GLU* 6.1 0.5 - - - +
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Residues in contact with ILE 313 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281G ILE* 4.6 12.1 - - + -
309G PRO 2.6 26.2 + - - +
310G PRO* 3.5 6.1 - - + +
311G ALA 3.3 0.2 - - - -
312G TRP* 1.3 77.1 - - - +
314G ALA* 1.3 58.6 + - - +
316G ALA* 4.5 0.2 - - - +
317G ARG* 2.9 31.9 + - - +
344G ASP* 6.3 2.5 - - + -
345G VAL* 5.5 6.2 - - + +
348G GLU* 5.8 8.7 - - + -
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Residues in contact with ALA 314 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1874A VAL 5.3 3.1 - - - +
281G ILE* 4.4 4.5 - - + +
282G PRO* 3.5 35.6 - - + +
310G PRO 2.9 15.9 + - - +
311G ALA* 4.8 1.8 - - - +
313G ILE* 1.3 76.3 - - - +
315G SER* 1.3 60.4 + - - +
317G ARG* 4.1 3.5 - - - +
318G LEU* 2.9 31.7 + - - +
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Residues in contact with SER 315 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298G LEU* 4.0 31.0 - - - -
301G VAL* 6.4 0.2 - - - -
302G ARG* 6.3 0.9 - - - -
311G ALA* 2.5 24.2 + - - +
312G TRP* 4.5 1.6 - - - -
314G ALA* 1.3 77.4 - - - +
316G ALA* 1.3 51.7 + - - +
318G LEU* 4.5 3.3 - - - +
319G GLU* 2.7 37.4 + - - +
331G LEU* 5.9 0.6 - - - +
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Residues in contact with ALA 316 (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* 2.4 37.0 + - + +
315G SER* 1.3 77.8 - - - +
317G ARG* 1.3 59.5 + - - +
319G GLU* 3.8 4.7 - - - +
320G GLU* 2.9 31.7 + - - +
328G ALA* 4.4 8.3 - - + +
331G LEU* 5.3 15.7 - - + +
332G ILE* 5.5 5.6 - - + +
348G GLU* 6.4 1.3 - - + -
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Residues in contact with ARG 317 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282G PRO* 5.9 4.3 - - + +
313G ILE 2.9 23.3 + - - +
314G ALA* 4.1 4.0 - - - +
316G ALA* 1.3 78.2 - - - +
318G LEU* 1.3 57.5 + - - +
320G GLU* 3.7 3.0 - - - +
321G VAL* 2.9 27.6 + - - +
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Residues in contact with LEU 318 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282G PRO* 6.6 0.4 - - + -
288G ILE* 6.4 2.0 - - + -
314G ALA 2.9 20.3 + - - +
315G SER* 4.5 3.6 - - - +
317G ARG* 1.3 74.1 - - - +
319G GLU* 1.3 65.9 + - - +
321G VAL* 3.3 20.4 + - - +
322G THR* 3.6 7.3 + - - +
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Residues in contact with GLU 319 (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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315G SER 2.7 24.1 + - - +
316G ALA* 3.8 6.7 - - - +
318G LEU* 1.3 77.4 - - - +
320G GLU* 1.3 57.6 + - - +
321G VAL 3.1 0.2 - - - -
322G THR 3.4 7.4 - - - +
323G GLY 3.2 16.1 - - - +
324G LYS* 3.2 16.9 - - + +
327G VAL 5.8 0.7 - - - -
328G ALA* 4.1 16.2 - - + -
331G LEU* 5.4 4.7 - - + -
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Residues in contact with GLU 320 (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 2.9 18.1 + - - +
317G ARG* 3.7 3.1 - - - +
319G GLU* 1.3 75.4 - - - +
321G VAL* 1.3 64.6 + - - +
323G GLY 4.0 9.5 + - - +
324G LYS 4.4 0.4 - - - -
325G LEU* 6.1 0.7 - - - +
328G ALA* 3.7 17.4 - - + +
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Residues in contact with VAL 321 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195G GLU* 5.6 7.1 + - - -
285G GLY 5.2 4.7 - - - +
286G GLY* 5.0 17.5 - - - +
317G ARG 2.9 19.1 + - - +
318G LEU* 3.3 14.4 - - - +
319G GLU 3.1 0.4 - - - -
320G GLU* 1.3 81.0 - - - +
322G THR* 1.3 60.4 + - - +
323G GLY 4.0 1.4 + - - -
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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