Contacts of the helix formed by residues 312 - 328 (chain A) in PDB entry 2O7R
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 ASP 312 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305A TYR* 5.4 0.9 - - - +
308A VAL* 2.7 28.7 + - + +
309A LYS 3.8 4.0 - - - +
311A GLU* 1.3 77.8 - - + +
313A PRO* 1.4 62.4 - - - +
314A GLU* 3.0 20.8 + - - +
315A LYS* 3.3 34.0 + - + +
316A ALA* 3.0 26.0 + - - +
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Residues in contact with PRO 313 (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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311A GLU 3.4 10.3 - - - +
312A ASP* 1.4 86.1 - - - +
314A GLU* 1.3 54.3 + - - +
316A ALA* 3.7 8.1 - - + +
317A LYS* 2.8 48.8 + - - +
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Residues in contact with GLU 314 (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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312A ASP* 3.0 11.5 + - - +
313A PRO* 1.3 76.9 - - - +
315A LYS* 1.3 64.9 + - + +
317A LYS* 3.4 22.4 + - - +
318A GLN* 3.1 50.9 + - - +
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Residues in contact with LYS 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ASP* 6.1 1.3 - - - +
302A VAL 4.9 4.6 + - - -
304A GLY* 3.8 29.5 - - - +
308A VAL* 3.8 23.4 - - + +
309A LYS* 4.0 17.8 - - + +
312A ASP* 3.3 31.8 + - + +
314A GLU* 1.3 75.2 - - + +
316A ALA* 1.3 66.1 + - - +
318A GLN* 3.3 17.4 + - - +
319A PHE* 3.0 23.4 + - - +
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Residues in contact with ALA 316 (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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107A PHE* 4.3 9.0 - - + -
110A GLU* 6.0 1.3 - - + -
309A LYS* 3.5 32.4 - - - +
312A ASP 3.0 9.8 + - - +
313A PRO* 3.7 10.8 - - + +
315A LYS* 1.3 76.4 - - - +
317A LYS* 1.3 62.7 + - - +
319A PHE* 3.1 4.9 + - - +
320A PHE* 2.9 44.9 + - + -
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Residues in contact with LYS 317 (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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110A GLU* 4.8 11.7 + - - -
114A HIS* 5.2 15.1 + - + +
313A PRO* 2.8 36.4 + - - +
314A GLU* 3.4 24.9 - - - +
315A LYS 3.3 0.2 - - - -
316A ALA* 1.3 71.2 - - - +
318A GLN* 1.3 62.5 + - + +
320A PHE* 3.2 13.4 + - + +
321A VAL* 3.2 26.0 + - - +
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Residues in contact with GLN 318 (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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314A GLU* 3.1 37.7 + - - +
315A LYS* 3.7 21.8 - - - +
316A ALA 3.2 0.2 - - - -
317A LYS* 1.3 72.5 - - + +
319A PHE* 1.3 66.3 + - - +
321A VAL* 3.1 23.3 + - - +
322A ILE* 3.4 17.6 + - + +
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Residues in contact with PHE 319 (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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107A PHE* 4.1 7.4 - + - -
166A MET* 3.8 31.4 - - + -
198A VAL* 4.3 8.5 - - + -
200A ASP* 5.1 2.0 - - - -
269A MET* 3.9 22.9 - - - -
271A VAL* 4.1 24.9 - - + -
309A LYS* 3.4 39.0 - - + -
315A LYS 3.0 6.5 + - - +
316A ALA 3.4 4.9 - - - +
318A GLN* 1.3 77.3 - - - +
320A PHE* 1.3 77.3 + + - +
322A ILE* 3.0 14.2 + - + -
323A LEU* 2.8 47.5 + - + +
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Residues in contact with PHE 320 (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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107A PHE* 3.6 39.5 - + - -
110A GLU* 3.6 22.0 - - + -
111A MET* 3.4 40.8 - - + -
114A HIS* 3.9 39.4 - + + +
115A ALA* 4.4 1.9 - - + +
316A ALA* 2.9 35.1 + - + -
317A LYS* 3.2 10.7 + - + +
319A PHE* 1.3 88.7 - + - +
321A VAL* 1.3 58.3 + - - +
323A LEU* 3.9 7.1 - - + +
324A LYS* 2.8 32.2 + - - +
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Residues in contact with VAL 321 (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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114A HIS 5.6 0.2 - - - -
317A LYS 3.2 16.6 + - - +
318A GLN* 3.1 11.8 + - - +
319A PHE 3.1 0.6 - - - -
320A PHE* 1.3 78.4 - - - +
322A ILE* 1.3 63.6 + - + +
324A LYS* 3.5 7.3 + - - +
325A LYS* 3.2 37.4 + - + +
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Residues in contact with ILE 322 (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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269A MET* 3.8 19.5 - - + -
271A VAL* 6.0 1.1 - - + -
297A VAL* 4.7 11.4 - - + -
299A GLN* 4.5 31.6 - - + +
318A GLN* 3.4 22.0 + - + +
319A PHE* 3.0 13.1 + - + +
321A VAL* 1.3 78.2 - - + +
323A LEU* 1.3 58.8 + - - +
325A LYS* 3.3 33.0 - - + +
326A PHE* 3.1 24.8 + - - +
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Residues in contact with LEU 323 (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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86A VAL* 5.8 3.1 - - + -
111A MET* 3.5 33.4 - - + -
115A ALA* 3.9 18.4 - - + -
117A VAL* 5.8 1.1 - - + -
166A MET* 4.4 4.3 - - - -
198A VAL* 4.0 35.7 - - + -
269A MET* 4.2 10.9 - - + +
319A PHE* 2.8 35.8 + - + +
320A PHE* 3.9 6.5 - - + +
322A ILE* 1.3 75.4 - - - +
324A LYS* 1.3 64.9 + - - +
326A PHE* 3.5 4.2 - - + +
327A VAL* 2.9 38.1 + - + +
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Residues in contact with LYS 324 (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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114A HIS 3.6 18.4 - - - +
115A ALA* 3.9 25.2 - - - +
116A GLY* 5.6 2.2 - - - +
320A PHE 2.8 18.5 + - - +
321A VAL* 3.6 7.4 - - - +
323A LEU* 1.3 76.4 - - - +
325A LYS* 1.3 63.2 + - - +
327A VAL* 3.3 3.2 + - - +
328A VAL* 3.1 25.2 + - + +
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Residues in contact with LYS 325 (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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267A ARG* 5.4 0.7 + - - -
321A VAL* 3.2 25.7 + - + +
322A ILE* 3.3 45.4 - - + +
324A LYS* 1.3 79.9 - - - +
326A PHE* 1.3 61.7 + - - +
328A VAL* 3.2 30.5 + - + +
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Residues in contact with PHE 326 (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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164A PHE* 3.9 26.4 - + - -
197A LEU 3.9 1.3 - - - -
198A VAL* 3.8 29.2 - - + -
267A ARG* 3.4 72.0 + - + +
268A VAL 4.1 0.7 - - - -
269A MET* 3.3 53.6 - - + -
297A VAL* 3.8 17.0 - - + -
322A ILE 3.1 8.0 + - - +
323A LEU* 3.2 8.3 + - + +
325A LYS* 1.3 77.5 - - - +
327A VAL* 1.3 64.2 + - + +
328A VAL 3.3 4.5 + - - -
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Residues in contact with VAL 327 (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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84A PRO* 3.4 38.5 - - + +
86A VAL* 5.0 4.3 - - + -
115A ALA 4.8 4.7 - - - +
116A GLY 5.2 0.2 - - - +
117A VAL* 4.1 19.1 - - + -
162A ASN* 5.5 4.2 + - - -
164A PHE* 3.8 40.2 - - + -
198A VAL* 5.6 0.4 - - + -
323A LEU* 2.9 36.5 + - + +
324A LYS* 3.9 5.4 - - - +
326A PHE* 1.3 79.4 - - + +
328A VAL* 1.3 58.9 + - + +
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Residues in contact with VAL 328 (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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324A LYS* 3.1 14.9 + - + +
325A LYS* 3.2 28.0 - - + +
326A PHE 3.1 4.2 - - - -
327A VAL* 1.3 81.5 - - + +
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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