Contacts of the helix formed by residues 310 - 322 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B LEU* 5.5 0.2 - - - +
72B LEU* 3.8 22.0 - - - +
73B ASN* 4.9 4.1 + - - +
249B GLU* 3.7 14.6 + - - -
250B VAL* 4.7 8.1 - - - +
253B MET* 4.2 2.8 - - - -
306B TYR* 2.8 33.4 + - + +
308B MET 3.6 2.0 - - - +
309B MET* 1.3 80.6 + - - +
311B LYS* 1.3 56.4 + - - +
312B GLN* 3.8 12.0 + - - +
313B PHE* 2.9 33.0 + - + +
314B ARG* 2.8 38.8 + - - +
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Residues in contact with LYS 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B GLU* 4.1 17.0 + - - +
309B MET 4.1 0.6 - - - -
310B ASN* 1.3 71.5 - - - +
312B GLN* 1.3 56.0 + - - +
314B ARG* 3.6 21.6 - - - +
315B ASN* 2.9 54.4 + - - +
330B ASP* 4.1 6.4 - - - +
332B GLU* 3.1 21.0 + - - +
333B ALA* 3.1 31.9 - - + +
1509B HTG 3.0 42.5 + - - +
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Residues in contact with GLN 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LYS* 3.8 18.3 + - - +
68B LEU* 4.0 22.6 - - + +
70B THR* 5.0 6.8 - - - +
73B ASN* 4.6 8.7 + - - +
249B GLU* 5.4 0.4 + - - -
310B ASN* 3.2 10.1 + - - +
311B LYS* 1.3 79.7 - - - +
313B PHE* 1.3 58.0 + - - +
315B ASN* 3.7 1.9 - - - +
316B CYS* 2.9 29.6 + - - +
332B GLU* 3.3 21.3 + - + +
335B THR* 2.7 42.5 + - - +
337B VAL* 3.9 5.5 - - + +
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Residues in contact with PHE 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 5.1 1.8 - - + -
58B THR* 3.9 30.7 - - + -
61B VAL* 3.8 26.2 - - + -
62B THR* 4.1 5.2 - - - -
68B LEU* 4.2 20.4 - - + +
306B TYR* 3.4 58.3 - + + +
307B ILE* 3.8 31.2 - - + -
310B ASN* 2.9 26.3 + - + +
312B GLN* 1.3 72.6 - - - +
314B ARG* 1.3 58.9 + - - +
316B CYS* 3.3 4.9 + - - +
317B MET* 2.9 36.4 + - + +
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Residues in contact with ARG 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B ILE* 3.0 32.7 + - + +
308B MET 3.4 22.0 + - - -
309B MET 4.4 1.0 - - - -
310B ASN 2.8 17.9 + - - +
311B LYS* 3.6 37.1 - - - +
313B PHE* 1.3 80.9 - - - +
315B ASN* 1.3 56.0 + - - +
317B MET* 3.1 10.4 + - + +
318B VAL* 2.8 27.5 + - - +
1401B HTO 3.7 31.3 + - - -
1509B HTG 3.1 61.7 + - + -
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Residues in contact with ASN 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B LYS* 2.9 43.6 + - - +
312B GLN 3.7 2.9 - - - +
314B ARG* 1.3 74.8 - - - +
316B CYS* 1.3 63.1 + - - +
318B VAL* 2.7 27.9 - - + +
319B THR* 2.8 14.8 + - - -
327B PRO* 6.5 0.7 - - + -
331B ASP* 3.8 17.0 + - - +
332B GLU* 3.4 19.8 + - + -
336B THR* 4.6 2.0 - - + -
1509B HTG 2.8 39.0 + - - -
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Residues in contact with CYS 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B VAL* 3.9 2.2 - - + -
65B HIS* 3.0 19.3 - - - +
68B LEU* 4.0 19.1 - - + -
312B GLN* 2.9 18.3 + - - +
313B PHE 3.7 4.5 - - - +
315B ASN* 1.3 76.3 - - - +
317B MET* 1.3 57.5 + - - +
319B THR* 3.3 1.1 + - - -
320B THR* 2.9 31.7 + - - -
336B THR* 4.1 1.8 - - - -
337B VAL* 2.9 64.2 - - - -
341B GLU* 5.1 0.2 - - - -
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Residues in contact with MET 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 4.2 16.4 - - + -
57B LEU* 3.4 34.5 - - + -
61B VAL* 3.8 17.5 - - + +
307B ILE* 3.4 46.4 - - + -
313B PHE* 2.9 18.6 + - + +
314B ARG* 3.1 16.4 + - + +
316B CYS* 1.3 73.8 - - - +
318B VAL* 1.3 67.6 + - - +
320B THR* 3.0 3.6 + - - -
321B LEU* 2.9 31.7 + - + +
1509B HTG 4.0 25.1 - - + -
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Residues in contact with VAL 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B ARG 2.8 11.0 + - - +
315B ASN* 2.7 44.6 - - + +
317B MET* 1.3 75.3 - - - +
319B THR* 1.3 64.8 + - - +
321B LEU* 3.2 6.5 + - - +
322B CYS* 3.0 33.0 + - - -
326B ASN 5.1 5.4 - - - +
327B PRO* 5.3 13.2 - - + +
1509B HTG 4.1 44.2 - - + -
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Residues in contact with THR 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B GLN* 6.0 0.4 - - - +
65B HIS* 4.7 0.2 - - + -
315B ASN* 2.8 16.2 + - - +
316B CYS 3.5 7.4 - - - -
318B VAL* 1.3 82.9 - - - +
320B THR* 1.3 63.1 + - - +
322B CYS 3.2 12.1 + - - -
323B CYS 3.5 12.5 - - - +
324B GLY 4.4 3.4 - - - +
325B LYS* 3.6 32.0 + - + +
327B PRO* 4.3 8.0 - - - +
336B THR* 4.8 1.0 - - - +
338B SER* 2.9 31.4 - - - +
341B GLU* 3.2 24.0 + - - +
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Residues in contact with THR 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 5.3 1.3 - - + -
60B TYR* 3.9 21.3 - - + -
61B VAL* 3.8 18.6 - - + +
64B GLN* 3.0 25.9 + - - +
65B HIS* 2.7 31.2 + - - -
316B CYS 2.9 10.0 + - - -
317B MET 3.0 8.2 + - - -
319B THR* 1.3 77.4 - - - +
321B LEU* 1.3 66.2 + - + +
323B CYS* 3.4 15.4 + - - -
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Residues in contact with LEU 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PHE* 4.6 5.4 - - + -
57B LEU* 3.6 28.3 - - + -
317B MET* 2.9 33.2 + - + +
318B VAL* 3.2 4.7 + - - +
320B THR* 1.3 74.3 - - + +
322B CYS* 1.3 59.3 + - - +
323B CYS* 3.0 11.0 + - - -
1322B PLM 4.0 58.5 - - + +
1323B PLM 3.7 16.5 - - - +
1509B HTG 4.2 20.4 - - + -
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Residues in contact with CYS 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B VAL* 3.0 32.3 + - - +
319B THR 3.2 2.4 + - - -
321B LEU* 1.3 74.8 - - - +
323B CYS* 1.3 55.7 + - - +
324B GLY* 2.5 22.5 + - - -
325B LYS 3.5 17.0 + - - +
326B ASN* 4.0 23.7 + - + +
1322B PLM 1.9 54.0 - - - +
1323B PLM 3.2 5.6 - - - +
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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