Contacts of the helix formed by residues 319 - 338 (chain A) in PDB entry 3ORY
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 SER 319 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A VAL* 4.3 0.4 - - - -
317A ASP 3.8 0.8 + - - -
318A PHE* 1.3 73.7 - - - +
320A ILE* 1.3 59.0 + - - +
321A ASP* 3.3 9.0 + - - +
322A ARG* 3.1 57.6 + - - +
323A VAL* 2.9 32.4 + - - +
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Residues in contact with ILE 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LYS* 3.8 33.2 - - + -
313A VAL* 3.9 22.1 - - + +
318A PHE 3.4 4.0 + - - -
319A SER* 1.3 72.0 + - - +
321A ASP* 1.3 70.2 + - - +
323A VAL* 5.4 0.7 - - + -
324A SER* 2.7 57.5 + - - +
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Residues in contact with ASP 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A SER* 3.3 7.5 + - - +
320A ILE* 1.3 89.7 - - - +
322A ARG* 1.3 59.6 + - + +
324A SER* 3.9 2.9 - - - -
325A THR* 2.9 37.8 + - - +
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Residues in contact with ARG 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TYR* 3.6 22.2 + - + +
319A SER* 3.1 34.7 + - - +
321A ASP* 1.3 81.3 - - + +
323A VAL* 1.3 63.3 + - + +
325A THR* 3.7 4.4 + - - -
326A ALA* 3.1 24.9 + - - +
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Residues in contact with VAL 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 4.3 13.0 - - + -
67A TYR* 4.2 11.9 - - - +
308A VAL* 4.5 4.0 - - + -
309A LYS* 4.6 7.0 - - + -
312A LEU* 4.1 20.4 - - + -
313A VAL* 3.9 18.8 - - + -
318A PHE* 3.7 25.4 - - + -
319A SER 2.9 21.4 + - - +
320A ILE* 4.2 0.9 - - + +
322A ARG* 1.3 76.4 - - + +
324A SER* 1.3 58.4 + - - +
326A ALA* 3.3 2.4 + - - +
327A LEU* 2.9 47.3 + - + +
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Residues in contact with SER 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ILE* 2.7 43.2 + - - +
321A ASP* 3.9 3.4 - - - -
323A VAL* 1.3 76.5 - - - +
325A THR* 1.3 56.4 + - - +
327A LEU* 3.3 11.7 + - - +
328A GLU* 2.9 39.7 + - - +
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Residues in contact with THR 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ASP* 2.9 20.4 + - - +
322A ARG* 4.0 5.2 - - - -
324A SER* 1.3 76.1 - - - +
326A ALA* 1.3 62.1 + - - +
328A GLU* 3.3 20.9 + - - +
329A ARG* 3.2 58.8 + - - +
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Residues in contact with ALA 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 3.8 21.8 - - + -
67A TYR* 3.8 13.5 - - + -
70A ILE* 3.8 13.6 - - + +
322A ARG 3.1 18.9 + - - +
323A VAL 3.7 3.4 - - - +
325A THR* 1.3 76.0 - - - +
327A LEU* 1.3 52.8 + - - +
329A ARG* 3.2 10.8 + - - +
330A TYR* 2.7 36.9 + - - +
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Residues in contact with LEU 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 4.1 13.9 - - + -
303A PRO* 5.8 1.1 - - + -
305A PRO* 3.7 42.4 - - + +
308A VAL* 3.9 29.4 - - + -
309A LYS* 4.6 4.5 - - + +
323A VAL* 2.9 36.2 + - + +
324A SER* 3.3 8.5 + - - +
326A ALA* 1.3 72.6 - - - +
328A GLU* 1.3 64.8 + - - +
330A TYR* 4.1 18.8 - - + -
331A VAL* 2.8 32.7 + - + +
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Residues in contact with GLU 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A SER* 2.9 25.7 + - - +
325A THR* 3.3 21.6 + - - +
327A LEU* 1.3 77.0 - - - +
329A ARG* 1.3 63.6 + - + +
331A VAL* 3.3 18.3 - - - +
332A LYS* 3.4 16.1 + - - +
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Residues in contact with ARG 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLU* 3.6 19.7 - - - +
325A THR* 3.2 39.9 + - - +
326A ALA* 3.7 9.3 - - - +
328A GLU* 1.3 79.4 + - + +
330A TYR* 1.3 65.5 + - - +
332A LYS* 3.4 7.0 + - - +
333A ALA* 3.0 24.1 + - - +
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Residues in contact with TYR 330 (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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70A ILE* 3.8 39.3 - - + -
73A VAL* 4.0 32.1 - - + -
74A GLU* 4.4 0.4 + - - -
146A MET* 2.5 55.0 + - + -
148A ILE* 3.3 21.0 - - + +
303A PRO* 3.5 19.7 - - + -
326A ALA 2.7 21.5 + - - +
327A LEU* 3.7 19.1 - - + +
329A ARG* 1.3 73.2 - - - +
331A VAL* 1.3 59.5 + - + +
333A ALA* 3.3 4.4 + - + -
334A PHE* 2.8 41.3 + + - +
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Residues in contact with VAL 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A PRO* 4.2 21.5 - - + +
305A PRO* 4.1 25.8 - - + -
327A LEU* 2.8 23.1 + - + +
328A GLU* 3.3 17.5 - - - +
330A TYR* 1.3 75.0 - - + +
332A LYS* 1.3 82.0 + - - +
334A PHE* 3.4 7.5 + - - +
335A LYS* 3.1 25.3 + - - +
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Residues in contact with LYS 332 (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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328A GLU 3.4 13.2 + - - +
329A ARG* 3.4 8.7 + - - +
330A TYR 3.3 0.6 - - - -
331A VAL* 1.3 99.9 - - - +
333A ALA* 1.3 63.5 + - - +
335A LYS* 3.3 23.7 + - - +
336A GLU* 3.1 38.6 + - - +
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Residues in contact with ALA 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A VAL* 4.2 6.5 - - + -
74A GLU* 3.7 36.8 - - + -
329A ARG 3.0 16.8 + - - +
330A TYR* 3.9 3.8 - - - +
332A LYS* 1.3 75.8 - - - +
334A PHE* 1.3 57.6 + - - +
336A GLU* 4.0 9.9 - - - +
337A ASN* 2.8 40.2 + - - +
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Residues in contact with PHE 334 (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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73A VAL* 4.1 7.1 - - - +
146A MET 4.1 1.8 - - - -
147A GLY 4.1 9.0 - - - -
148A ILE* 4.4 2.7 - - + -
300A TRP* 3.9 20.2 - - + -
301A HIS 3.0 33.7 - - - -
302A THR* 4.3 2.9 - - - -
303A PRO* 3.6 24.2 - - + -
330A TYR* 2.8 47.6 + + + +
331A VAL 3.6 5.4 - - - +
333A ALA* 1.3 76.1 - - - +
335A LYS* 1.3 60.3 - - - +
338A ILE* 2.9 55.7 + - + +
339A ARG 3.2 17.4 + - - -
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Residues in contact with LYS 335 (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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331A VAL 3.1 16.6 + - - +
332A LYS* 3.3 22.2 + - - +
334A PHE* 1.3 78.1 - - - +
336A GLU* 1.3 64.3 + - + +
339A ARG* 3.2 34.0 - - - +
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Residues in contact with GLU 336 (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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332A LYS* 3.1 32.9 + - - +
333A ALA* 3.9 7.4 + - - +
335A LYS* 1.3 83.8 - - + +
337A ASN* 1.3 70.0 + - - +
338A ILE 3.6 0.2 - - - -
339A ARG* 4.9 1.7 + - - -
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Residues in contact with ASN 337 (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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21A ARG* 5.4 4.7 + - - +
25A GLY* 5.9 0.3 - - - -
73A VAL* 2.8 29.8 + - + +
74A GLU* 3.5 13.9 + - - +
75A ALA 4.3 0.2 - - - -
76A GLY* 3.4 27.9 - - - +
78A LYS* 3.6 18.9 - - - +
333A ALA* 2.8 24.7 + - - +
336A GLU* 1.3 85.8 - - - +
338A ILE* 1.3 63.2 + - + +
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Residues in contact with ILE 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A VAL* 3.8 31.2 - - + -
77A ILE 4.7 2.5 - - - +
78A LYS* 4.3 28.6 + - + +
79A PRO* 4.7 3.6 - - + -
148A ILE* 4.8 0.4 - - + -
300A TRP* 3.5 47.8 - - + +
334A PHE* 2.9 46.5 + - + +
337A ASN* 1.3 84.4 - - + +
339A ARG* 1.3 71.8 + - + +
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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
------------------------------------------------------------
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