Contacts of the helix formed by residues 310 - 322 (chain A) in PDB entry 3OAX
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 ASN 310 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A LEU* 5.9 0.2 - - - +
72A LEU* 3.8 25.9 - - - +
73A ASN* 5.3 3.7 + - - +
249A GLU* 3.5 15.3 + - - -
250A VAL* 4.6 5.5 - - - +
253A MET* 4.4 3.2 - - - -
306A TYR* 2.9 29.8 + - + +
307A ILE 4.2 0.4 + - - -
308A MET 3.7 1.6 - - - -
309A MET* 1.3 78.5 + - - +
311A LYS* 1.3 66.7 + - - +
312A GLN* 3.4 12.8 + - - +
313A PHE* 2.7 36.0 + - + +
314A ARG* 3.0 24.5 + - - +
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Residues in contact with LYS 311 (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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249A GLU* 3.0 17.5 + - - +
309A MET 4.0 0.4 - - - -
310A ASN* 1.3 70.6 - - - +
312A GLN* 1.3 62.8 + - - +
314A ARG* 3.3 32.8 + - - +
315A ASN* 2.9 47.4 + - - +
330A ASP* 2.7 20.5 + - - -
332A GLU* 3.1 30.3 - - - +
333A ALA* 5.5 1.1 - - - -
959A ZN 1.9 41.9 - - - -
100B HIS* 3.8 2.0 - - - -
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Residues in contact with GLN 312 (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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67A LYS* 5.3 3.4 + - - +
68A LEU* 3.6 24.9 - - + +
70A THR* 5.3 4.7 - - - +
73A ASN* 4.5 7.6 + - - +
249A GLU* 5.4 0.6 + - - -
310A ASN* 3.2 10.2 + - - +
311A LYS* 1.3 77.9 - - - +
313A PHE* 1.3 65.1 + - - +
315A ASN* 3.0 5.9 + - - +
316A CYS* 3.0 22.4 + - - +
332A GLU* 3.7 22.3 + - + +
335A THR* 3.4 38.9 + - - +
336A THR* 4.0 10.2 + - - -
337A VAL* 4.2 9.3 - - + +
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Residues in contact with PHE 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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58A THR* 3.8 30.1 - - + -
61A VAL* 3.8 23.3 - - + -
62A THR* 3.5 20.0 - - - -
68A LEU* 3.8 20.6 - - + +
73A ASN* 5.2 0.2 - - - +
306A TYR* 3.4 52.3 - + + +
307A ILE* 3.9 26.9 - - + -
310A ASN* 2.7 25.8 + - + +
312A GLN* 1.3 73.6 + - - +
314A ARG* 1.3 59.0 + - - +
316A CYS* 3.1 6.6 + - - +
317A MET* 2.9 32.5 + - + +
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Residues in contact with ARG 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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307A ILE* 3.0 48.9 + - + +
308A MET* 3.1 22.4 + - - -
310A ASN 3.0 14.5 + - - +
311A LYS* 3.5 46.1 - - - +
313A PHE* 1.3 77.7 - - - +
315A ASN* 1.3 64.7 + - - +
317A MET* 3.3 11.1 + - + +
318A VAL* 3.0 35.6 + - + +
1508A HTG 6.0 0.4 - - - -
99B LEU* 3.6 50.1 + - - +
100B HIS* 5.9 1.6 + - - -
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Residues in contact with ASN 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A LYS* 2.9 45.4 + - - +
312A GLN 3.5 6.5 - - - +
314A ARG* 1.3 78.7 - - - +
316A CYS* 1.3 56.2 + - - +
318A VAL* 3.4 8.8 + - - +
319A THR* 3.0 31.9 + - - -
327A PRO* 4.4 9.7 - - + +
330A ASP* 4.8 0.3 - - - +
331A ASP* 2.9 40.5 + - - +
332A GLU* 3.1 25.9 - - + +
336A THR* 5.0 2.9 - - + -
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Residues in contact with CYS 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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61A VAL* 3.8 9.6 - - + -
65A HIS* 3.0 29.1 - - + +
68A LEU* 4.4 6.3 - - + -
312A GLN* 3.0 17.7 + - - +
313A PHE* 3.5 10.3 - - - +
315A ASN* 1.3 76.0 - - - +
317A MET* 1.3 58.8 + - - +
319A THR* 3.3 2.8 + - - -
320A THR* 2.9 25.5 + - - -
336A THR* 5.1 4.5 - - - -
337A VAL* 3.0 53.6 - - - -
341A GLU* 5.5 0.9 - - - -
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Residues in contact with MET 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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57A LEU* 3.6 37.5 - - + -
58A THR* 6.5 0.2 - - - -
61A VAL* 3.7 14.5 - - + +
307A ILE* 3.6 49.6 - - + -
313A PHE* 2.9 18.2 + - + +
314A ARG* 3.5 16.2 - - + +
316A CYS* 1.3 74.9 - - - +
318A VAL* 1.3 66.4 + - + +
320A THR* 3.2 2.8 + - - -
321A LEU* 2.8 41.2 + - + +
45B PHE* 4.4 13.2 - - + -
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Residues in contact with VAL 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 ARG* 3.0 25.6 + - + +
315A ASN* 3.6 11.4 - - - +
316A CYS 3.3 0.2 - - - -
317A MET* 1.3 81.5 - - + +
319A THR* 1.3 57.9 + - - +
321A LEU* 3.2 7.1 + - - +
322A CYS* 2.7 53.2 + - - -
326A ASN 4.4 9.2 - - - +
327A PRO* 4.5 11.9 - - + +
328A LEU* 4.7 6.1 - - + -
1322A PLM 5.1 4.3 - - + -
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Residues in contact with THR 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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64A GLN* 5.6 1.6 - - - +
65A HIS* 4.5 2.9 - - + +
315A ASN 3.0 16.6 + - - -
316A CYS* 3.5 12.2 - - - +
318A VAL* 1.3 78.3 - - - +
320A THR* 1.3 57.4 + - - +
322A CYS 3.7 0.9 + - - -
323A CYS 2.6 29.1 - - - +
324A GLY 4.3 4.0 - - - +
325A LYS* 3.7 38.0 - - + +
326A ASN 5.3 0.7 - - - -
327A PRO* 3.8 17.7 - - - +
338A SER* 4.1 9.2 - - - +
341A GLU* 3.8 22.3 + - + +
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Residues in contact with THR 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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57A LEU* 5.3 1.3 - - + -
60A TYR* 3.9 28.7 - - + -
61A VAL* 3.7 15.2 - - + +
64A GLN* 2.7 32.6 + - - +
65A HIS* 2.8 17.2 + - - -
316A CYS 2.9 10.4 + - - -
317A MET 3.5 7.6 - - - -
318A VAL 3.1 0.2 - - - -
319A THR* 1.3 75.2 - - - +
321A LEU* 1.3 71.6 + - + +
323A CYS* 3.2 15.5 + - - +
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Residues in contact with LEU 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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57A LEU* 4.1 24.7 - - + -
317A MET* 2.8 37.0 + - + +
318A VAL* 3.9 5.6 - - + +
320A THR* 1.3 72.1 - - + +
322A CYS* 1.3 58.1 + - - +
323A CYS* 2.8 13.6 + - - -
1322A PLM 3.8 68.6 - - + -
1323A PLM 3.5 27.4 - - + +
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Residues in contact with CYS 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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318A VAL* 2.7 38.2 + - - +
320A THR 3.3 0.2 - - - -
321A LEU* 1.3 68.6 - - - +
323A CYS* 1.3 67.7 + - - +
324A GLY 3.4 0.9 + - - -
325A LYS 3.0 25.2 + - - +
326A ASN* 4.1 10.2 - - + +
328A LEU* 4.8 3.4 - - - -
1322A PLM 1.9 57.9 - - - +
1323A PLM 3.0 11.1 - - - +
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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