Contacts of the helix formed by residues 311 - 323 (chain C) in PDB entry 3OS8
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 311 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309C SER 4.7 4.0 - - - +
310C LEU* 1.3 76.0 - - - +
312C ALA* 1.3 65.0 + - - +
313C ASP* 3.5 8.7 + - - +
314C GLN* 2.8 41.0 + - - +
315C MET* 2.9 22.6 + - - +
481C LYS* 4.8 2.7 - - - +
485C THR* 5.1 0.2 - - - -
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Residues in contact with ALA 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311C THR* 1.3 72.7 - - - +
313C ASP* 1.3 61.9 + - - +
315C MET 3.4 0.2 + - - -
316C VAL* 3.2 30.4 + - + +
481C LYS* 5.2 3.0 - - - +
484C ASP* 4.7 2.0 - - + +
485C THR* 3.5 28.3 - - + +
488C HIS* 3.3 44.9 - - + +
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Residues in contact with ASP 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311C THR* 3.2 8.1 + - - +
312C ALA* 1.3 74.9 - - - +
314C GLN* 1.3 60.7 + - + +
316C VAL* 3.3 7.1 + - - +
317C SER* 2.9 30.6 + - - -
488C HIS* 3.1 28.1 + - - -
489C LEU* 5.7 1.9 - - - +
492C LYS* 3.5 20.9 + - - -
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Residues in contact with GLN 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309C SER 4.1 2.4 - - - +
310C LEU* 3.3 28.7 - - + +
311C THR* 2.8 45.3 + - - +
313C ASP* 1.3 78.6 - - + +
315C MET* 1.3 57.1 + - - +
317C SER* 3.6 6.5 - - - -
318C ALA* 2.9 31.8 + - - +
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Residues in contact with MET 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307C ALA 4.2 11.2 - - - +
310C LEU* 4.3 15.4 - - + +
311C THR 2.9 16.1 + - - +
312C ALA 3.7 2.2 - - - +
313C ASP 3.3 0.2 - - - -
314C GLN* 1.3 76.0 - - - +
316C VAL* 1.3 64.0 + - - +
318C ALA* 3.4 2.9 + - - +
319C LEU* 3.0 42.4 + - + +
364C VAL* 6.3 0.2 - - - -
365C PRO* 3.6 31.9 - - + +
447C CYS* 5.4 0.7 - - - -
478C VAL* 5.1 6.3 - - + +
481C LYS* 3.6 34.3 - - + -
482C ILE* 4.5 20.0 - - + -
485C THR* 3.6 26.2 - - + +
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Residues in contact with VAL 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312C ALA 3.2 16.2 + - - +
313C ASP* 3.6 8.5 - - - +
315C MET* 1.3 74.4 - - - +
317C SER* 1.3 56.8 + - - +
319C LEU* 3.1 7.4 + - - +
320C LEU* 2.8 48.1 + - + +
443C GLU* 3.6 32.1 - - + +
446C VAL* 5.2 1.6 - - + -
447C CYS* 4.8 3.4 - - - -
485C THR* 3.5 19.5 - - + -
489C LEU* 3.9 25.4 - - + -
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Residues in contact with SER 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313C ASP 2.9 17.5 + - - -
314C GLN* 3.6 7.6 - - - -
316C VAL* 1.3 78.6 - - - +
318C ALA* 1.3 63.2 + - - +
320C LEU* 3.4 7.6 + - - +
321C ASP* 2.9 41.2 + - - +
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Residues in contact with ALA 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C LEU* 5.0 3.8 - - + -
314C GLN 2.9 19.1 + - - +
315C MET 3.6 4.3 - - - +
317C SER* 1.3 76.6 + - - +
319C LEU* 1.3 63.6 + - - +
321C ASP* 3.3 8.6 + - - +
322C ALA* 3.1 23.4 + - - +
363C ARG* 4.9 6.6 + - - +
365C PRO* 4.1 22.7 - - + -
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Residues in contact with LEU 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C MET* 3.0 38.3 + - + +
316C VAL* 3.1 4.4 + - - +
318C ALA* 1.3 74.4 - - - +
320C LEU* 1.3 65.9 + - - +
322C ALA* 3.1 13.8 + - + +
323C GLU* 3.3 15.8 + - - +
360C TRP* 4.9 6.8 + - - +
363C ARG 5.1 0.4 - - - +
364C VAL* 4.4 11.4 - - + -
365C PRO* 3.7 26.5 - - + -
446C VAL* 3.7 36.3 - - + +
447C CYS* 4.1 13.2 - - - +
450C SER* 3.3 30.7 - - - +
482C ILE* 5.6 1.6 - - + -
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Residues in contact with LEU 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316C VAL* 2.8 42.3 + - + +
317C SER* 3.8 7.6 - - - +
319C LEU* 1.3 71.8 - - - +
321C ASP* 1.3 66.8 + - - +
322C ALA 3.3 0.7 + - - -
323C GLU* 3.3 23.1 + - + +
442C GLY* 4.5 13.5 - - - +
443C GLU* 4.3 14.4 - - + +
446C VAL* 4.0 23.8 - - + -
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Residues in contact with ASP 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317C SER* 2.9 34.3 + - - +
318C ALA* 3.5 8.2 - - - +
320C LEU* 1.3 81.0 - - - +
322C ALA* 1.3 59.1 + - - +
323C GLU 3.3 3.5 + - - +
363C ARG* 3.4 29.5 + - - +
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Residues in contact with ALA 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318C ALA 3.1 15.7 + - - +
319C LEU* 3.1 9.3 + - + +
321C ASP* 1.3 75.3 - - - +
323C GLU* 1.3 68.1 + - - +
324C PRO* 3.2 2.6 - - - +
360C TRP* 3.3 32.6 - - + +
363C ARG* 3.6 45.1 + - + +
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Residues in contact with GLU 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C LEU 3.3 4.3 + - - +
320C LEU* 3.3 21.8 + - + +
321C ASP 3.3 3.5 - - - +
322C ALA* 1.3 80.0 - - - +
324C PRO* 1.3 75.4 - - + +
325C PRO* 4.5 0.9 - - - +
360C TRP* 4.2 5.4 + - - -
393C TRP* 5.4 2.1 + - - -
445C PHE* 3.6 14.3 - - - -
446C VAL* 3.7 27.6 - - + +
449C LYS* 2.6 37.8 + - - -
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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
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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