Contacts of the helix formed by residues 319 - 332 (chain G) in PDB entry 2OX4
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 THR 319 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21G PRO* 3.5 31.6 - - + -
23G LEU* 3.6 13.7 - - + +
37G GLU* 2.5 28.7 + - - +
316G VAL* 5.7 0.2 - - - +
317G ALA 4.6 0.2 - - - +
318G GLY* 1.3 75.8 - - - +
320G GLY* 1.3 59.9 + - - +
321G VAL* 3.0 16.8 + - - +
322G ALA* 3.2 3.5 + - - +
323G GLU* 3.1 24.9 + - - +
345G THR* 6.2 1.6 - - - -
350G TYR* 4.0 7.6 - - + -
353G LEU* 3.7 23.3 - - + -
354G CYS* 3.9 8.7 - - - -
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Residues in contact with GLY 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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319G THR* 1.3 72.7 - - - +
321G VAL* 1.3 57.3 + - - -
323G GLU* 3.8 7.9 - - - -
324G ALA* 2.9 24.9 + - - +
350G TYR 5.3 2.8 + - - -
354G CYS* 3.6 10.8 - - - +
356G HIS 5.1 1.8 - - - -
358G TYR* 5.1 0.6 - - - -
375G GLN* 3.2 29.0 + - - -
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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
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23G LEU* 3.9 11.9 - - + -
35G LEU* 4.1 15.9 - - + +
36G GLY* 3.9 33.7 - - - +
37G GLU* 3.5 6.1 - - + +
98G ILE* 4.9 3.1 - - + -
319G THR* 3.0 14.6 + - - +
320G GLY* 1.3 72.9 - - - +
322G ALA* 1.3 65.3 + - - +
324G ALA* 4.0 1.2 - - - +
325G ALA* 3.0 24.3 + - - +
354G CYS* 3.7 9.1 - - - -
373G ILE* 3.8 17.5 - - + +
375G GLN* 3.8 19.5 - - + -
376G ASP 5.2 0.9 - - - -
377G ILE* 4.5 10.8 - - + -
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Residues in contact with ALA 322 (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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37G GLU* 3.0 33.5 + - + +
98G ILE* 6.1 3.4 - - - -
288G ASP* 5.8 4.9 - - - +
289G LEU* 4.9 3.0 - - - +
290G GLY* 6.6 0.4 - - - -
316G VAL* 4.6 4.4 - - + +
317G ALA 3.4 25.4 - - - +
319G THR 3.2 3.5 + - - +
321G VAL* 1.3 74.9 - - - +
323G GLU* 1.3 62.6 + - - +
325G ALA* 3.5 5.3 + - - +
326G SER* 3.1 24.5 + - - -
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Residues in contact with GLU 323 (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 VAL* 3.8 19.2 - - + +
319G THR 3.1 15.0 + - - +
320G GLY* 3.6 6.7 + - - +
322G ALA* 1.3 74.3 - - - +
324G ALA* 1.3 65.9 + - - +
326G SER* 2.7 21.9 + - - +
327G LEU* 3.4 10.2 + - + +
339G HIS* 2.9 28.9 + - + +
340G GLU 3.5 6.2 - - - +
341G HIS* 3.1 26.4 + - - -
342G HIS* 5.7 1.3 - - - -
345G THR* 3.6 18.2 - - + +
358G TYR* 4.6 5.8 - - + +
365G TYR* 3.3 24.8 + - + +
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Residues in contact with ALA 324 (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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320G GLY 2.9 20.0 + - - +
321G VAL 4.0 1.1 - - - +
323G GLU* 1.3 77.8 - - - +
325G ALA* 1.3 63.1 + - - +
327G LEU* 3.3 19.2 + - - +
328G HIS* 3.2 19.7 - - - -
358G TYR* 4.0 19.6 - - + -
368G PRO* 4.2 3.3 - - + +
373G ILE* 3.6 19.7 - - + +
375G GLN* 3.9 17.0 - - + -
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Residues in contact with ALA 325 (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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98G ILE* 4.0 19.5 - - + -
289G LEU* 3.5 12.1 - - + -
295G PHE* 3.2 41.5 - - + -
321G VAL 3.0 19.2 + - - +
322G ALA* 3.8 5.2 - - - +
324G ALA* 1.3 75.8 - - - +
326G SER* 1.3 62.3 + - - +
328G HIS* 3.2 15.0 + - - +
329G ALA 3.2 1.2 + - - -
373G ILE* 4.4 6.6 - - + +
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Residues in contact with SER 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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289G LEU* 3.6 14.6 - - - +
314G ALA* 4.2 11.4 - - - -
315G HIS 5.6 0.4 - - - -
316G VAL* 3.6 22.2 - - - +
322G ALA 3.1 14.4 + - - -
323G GLU 2.7 19.8 + - - -
325G ALA* 1.3 77.2 - - - +
327G LEU* 1.3 61.9 + - - +
329G ALA* 3.2 2.7 + - - +
330G GLU* 3.0 29.5 + - - +
339G HIS* 3.2 19.7 - - - -
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Residues in contact with LEU 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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124G LEU* 3.7 20.8 - - + +
323G GLU* 3.4 15.9 - - + +
324G ALA* 3.3 8.0 + - - +
325G ALA 3.2 0.4 - - - -
326G SER* 1.3 82.0 + - - +
328G HIS* 1.3 62.2 + - - +
330G GLU* 3.5 1.0 + - - +
331G ILE* 3.1 27.5 + - - +
339G HIS* 3.6 24.7 - - + -
358G TYR* 4.6 7.2 - - + -
365G TYR* 3.6 39.5 - - + -
366G LYS 3.8 18.6 - - - +
367G VAL* 3.8 8.8 - - + +
368G PRO* 3.8 23.6 - - + -
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Residues in contact with HIS 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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111G PRO* 3.8 5.6 - - + -
112G VAL* 3.6 12.1 + - + -
113G TYR* 3.0 33.8 + - - +
116G LEU* 3.8 3.0 - - - +
295G PHE* 4.0 10.5 - - + -
324G ALA 3.2 24.9 - - - -
325G ALA* 3.2 8.1 + - - +
327G LEU* 1.3 75.0 - - - +
329G ALA* 1.3 65.0 + - - +
330G GLU 3.4 0.5 + - - -
331G ILE* 3.6 2.8 - - - +
332G ALA* 3.4 24.9 + - - +
367G VAL* 3.6 11.0 - - + +
368G PRO* 3.4 28.9 + - + +
370G LEU 4.8 0.2 - - - -
372G GLY 3.5 17.3 - - - -
373G ILE* 3.0 35.4 + - + -
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Residues in contact with ALA 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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116G LEU* 4.0 11.7 - - - -
289G LEU* 4.0 20.9 - - + -
295G PHE* 3.9 5.5 - - + -
298G PHE* 3.7 31.1 - - + -
325G ALA 3.2 8.5 + - - +
326G SER* 3.2 9.0 + - - +
328G HIS* 1.3 78.9 - - - +
330G GLU* 1.3 62.6 + - - +
332G ALA* 3.5 8.0 + - - +
333G ILE* 3.7 19.8 + - - +
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Residues in contact with GLU 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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121G ARG* 2.9 19.2 + - - -
124G LEU* 3.5 15.7 - - + +
298G PHE* 4.6 6.3 - - + -
312G VAL 5.5 0.2 - - - +
314G ALA* 2.9 43.6 + - + +
326G SER 3.0 17.3 + - - +
329G ALA* 1.3 74.4 - - - +
331G ILE* 1.3 62.3 + - - +
332G ALA 3.1 2.9 + - - -
333G ILE* 3.3 18.9 - - + +
336G PHE* 3.5 32.1 - - + +
338G ILE 3.8 4.5 - - - +
339G HIS* 2.5 37.6 + - - -
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Residues in contact with ILE 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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113G TYR* 3.6 35.7 - - + -
119G LYS* 3.6 14.3 - - + -
120G ASN* 2.8 35.2 + - - +
121G ARG* 3.3 38.9 + - + +
122G GLU 4.3 11.4 - - - +
123G ASP* 4.7 2.0 - - - +
124G LEU* 4.1 15.2 - - + +
327G LEU 3.1 19.2 + - - +
328G HIS 3.6 0.7 - - - +
330G GLU* 1.3 77.7 - - - +
332G ALA* 1.3 59.5 + - - +
333G ILE 3.4 0.2 - - - -
367G VAL* 3.7 31.9 - - + +
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Residues in contact with ALA 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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69D GLU* 3.6 20.6 - - - +
113G TYR* 4.2 7.0 - - + +
116G LEU* 3.7 32.5 - - + +
118G GLY 3.2 18.2 - - - +
120G ASN* 3.1 13.5 + - - -
299G LYS* 5.2 0.7 + - - -
328G HIS 3.4 15.0 + - - +
329G ALA 3.5 4.0 + - - +
330G GLU 3.1 1.2 - - - -
331G ILE* 1.3 77.8 - - - +
333G ILE* 1.3 61.4 + - + +
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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