Contacts of the helix formed by residues 320 - 336 (chain C) in PDB entry 2O1S
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 320 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318C LEU 3.8 0.6 + - - -
319C PRO* 1.3 77.3 - - - +
321C TYR* 1.3 65.3 + - - +
322C SER* 3.5 12.4 + - - -
323C LYS* 2.9 30.9 + - - +
324C ILE* 3.0 13.6 + - - +
420C ARG* 6.2 0.4 - - - -
479C GLY* 3.0 23.1 - - - -
480C ASN* 3.9 7.8 - - - +
481C ALA* 5.4 0.2 - - - -
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Residues in contact with TYR 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C SER* 1.3 71.6 - - - +
322C SER* 1.3 52.3 + - - +
324C ILE* 3.1 8.8 + - + +
325C PHE* 2.8 35.0 + - - +
451C PRO* 5.4 2.5 - - + -
452C SER 4.0 0.9 + - - -
453C ASP* 3.6 38.9 - - - -
454C GLU* 3.7 9.9 - - + -
457C CYS* 4.1 17.3 - - + -
476C TYR* 3.3 37.4 - - + -
477C PRO* 3.7 24.2 - - + +
479C GLY 3.1 16.4 + - - +
480C ASN 3.5 19.8 + - - -
481C ALA* 3.8 13.3 - - + +
482C VAL* 4.3 5.4 - - - +
513C THR* 3.3 32.4 - - + +
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Residues in contact with SER 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C SER* 3.1 10.3 + - - -
321C TYR* 1.3 80.4 - - - +
323C LYS* 1.3 56.6 + - - +
325C PHE* 3.4 5.8 + - - +
326C GLY* 2.9 24.6 + - - -
348C GLU 5.4 0.2 - - - -
349C GLY 3.2 11.8 + - - -
350C SER 3.6 17.1 - - - +
351C GLY* 3.8 7.6 - - - -
419C ASP* 2.5 30.0 + - - -
420C ARG* 2.9 18.1 + - - -
476C TYR* 4.3 0.9 - - - -
477C PRO 5.6 0.2 + - - -
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Residues in contact with LYS 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C PRO* 4.3 14.5 - - + +
320C SER* 2.9 24.8 + - - +
322C SER* 1.3 75.9 - - - +
324C ILE* 1.3 67.7 + - + +
326C GLY* 3.2 2.0 + - - +
327C ASP* 2.8 59.0 + - - +
351C GLY* 5.0 4.5 - - - +
354C GLU* 5.4 6.7 + - - -
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Residues in contact with ILE 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C PRO* 4.1 22.0 - - + -
320C SER 3.0 15.2 + - - +
321C TYR* 3.1 13.2 + - + +
323C LYS* 1.3 77.0 - - - +
325C PHE* 1.3 64.1 + - - +
327C ASP* 3.2 9.0 + - - +
328C TRP* 2.9 22.1 + - + +
454C GLU* 3.7 36.8 - - + +
457C CYS* 4.3 14.4 - - - -
458C ARG* 3.5 38.7 + - + +
461C LEU* 5.1 1.3 - - + -
481C ALA* 5.0 0.7 - - + -
486C LEU* 5.1 7.9 - - + -
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Residues in contact with PHE 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C TYR 2.8 17.3 + - - +
322C SER* 3.6 4.5 - - - +
324C ILE* 1.3 74.3 - - - +
326C GLY* 1.3 56.6 + - - +
328C TRP* 3.2 6.6 + + - +
329C LEU* 2.8 68.8 + - + +
341C ALA* 5.6 0.2 - - + -
350C SER* 3.4 22.4 - - - -
352C MSE 4.2 2.0 - - + -
388C ILE* 3.9 13.5 - - + -
390C ALA* 4.0 22.4 - - + -
417C ALA* 3.4 23.8 - - + -
457C CYS* 5.4 0.4 - - - -
461C LEU* 3.7 35.0 - - + +
476C TYR* 3.3 25.8 - - + +
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Residues in contact with GLY 326 (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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322C SER 2.9 11.5 + - - -
323C LYS* 3.6 3.4 - - - -
325C PHE* 1.3 76.7 - - - +
327C ASP* 1.3 66.6 + - - +
329C LEU* 3.3 10.3 + - - +
330C CYS* 3.1 29.6 + - - -
351C GLY 3.3 24.7 - - - -
352C MSE 5.3 0.7 - - - -
354C GLU* 6.4 0.9 - - - -
355C PHE* 4.7 2.3 - - - +
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Residues in contact with ASP 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C PRO* 6.0 0.2 - - - +
323C LYS* 2.8 59.7 + - - +
324C ILE* 3.7 8.6 - - - +
326C GLY* 1.3 72.4 - - - +
328C TRP* 1.3 64.1 + - - +
330C CYS* 3.2 7.6 + - - +
331C GLU* 3.0 32.9 + - - +
354C GLU* 4.6 13.3 - - - +
458C ARG* 5.9 2.9 - - - +
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Residues in contact with TRP 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C ILE 2.9 13.7 + - - +
325C PHE* 3.4 17.0 - + - +
327C ASP* 1.3 77.9 - - - +
329C LEU* 1.3 81.7 + - + +
331C GLU* 3.5 8.9 - - - +
332C THR* 2.8 47.9 + - + -
339C LEU* 4.8 1.8 - - + -
388C ILE* 3.6 30.3 - - + -
415C LEU* 4.0 5.4 - - + -
458C ARG* 4.4 25.9 - - + +
461C LEU* 3.5 49.4 - - + -
462C TYR* 3.9 13.6 - + - +
465C TYR* 3.7 30.5 - + + -
489C LEU* 4.0 25.6 - - + +
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Residues in contact with LEU 329 (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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325C PHE* 2.8 49.8 + - + +
326C GLY* 3.6 9.0 - - - +
328C TRP* 1.3 84.0 - - + +
330C CYS* 1.3 59.0 + - - +
332C THR* 3.8 2.6 - - - -
333C ALA* 2.9 32.1 + - - +
339C LEU* 4.1 8.6 - - + +
341C ALA* 3.9 14.1 - - + -
352C MSE 3.9 30.1 - - + -
355C PHE* 3.8 18.9 - - + -
388C ILE* 3.4 32.8 - - + -
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Residues in contact with CYS 330 (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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326C GLY 3.1 16.0 + - - +
327C ASP* 3.6 8.3 - - - +
328C TRP 3.2 0.2 - - - -
329C LEU* 1.3 80.8 - - - +
331C GLU* 1.3 63.8 + - - +
332C THR 3.2 0.2 + - - -
333C ALA 3.3 0.2 + - - -
334C ALA* 3.1 22.4 + - - +
354C GLU* 3.8 28.5 - - - +
355C PHE* 3.6 35.9 - - - -
358C LYS* 4.5 12.1 - - + +
359C PHE* 3.5 18.7 - - + -
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Residues in contact with GLU 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C ASP* 3.0 20.8 + - - +
328C TRP* 3.5 12.1 - - + +
330C CYS* 1.3 77.1 - - - +
332C THR* 1.3 66.3 + - - +
334C ALA* 3.8 7.3 + - - +
335C LYS* 3.1 37.2 + - - +
458C ARG* 2.6 34.7 + - - -
489C LEU* 4.0 13.7 - - - +
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Residues in contact with THR 332 (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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328C TRP* 2.8 46.3 + - + -
329C LEU 3.8 2.2 - - - -
331C GLU* 1.3 79.0 - - - +
333C ALA* 1.3 55.0 + - - +
334C ALA 3.2 0.2 - - - -
335C LYS* 3.0 16.2 + - + +
336C ASP* 2.7 35.8 + - + +
339C LEU* 3.6 22.0 - - + -
462C TYR* 5.9 1.8 - - + -
465C TYR* 3.9 28.7 - - + +
466C HIS* 5.8 1.1 - - - +
489C LEU* 5.4 1.6 - - - +
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Residues in contact with ALA 333 (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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329C LEU 2.9 19.4 + - - +
332C THR* 1.3 76.6 - - - +
334C ALA* 1.3 62.5 + - - +
336C ASP 3.2 12.8 + - - +
339C LEU* 4.1 14.1 - - + +
355C PHE* 3.9 10.8 - - + -
359C PHE* 3.8 27.5 - - + -
362C ARG* 2.4 36.6 + - - +
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Residues in contact with ALA 334 (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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330C CYS 3.1 17.3 + - - +
331C GLU* 3.8 10.1 - - - +
332C THR 3.2 0.2 - - - -
333C ALA* 1.3 78.2 - - - +
335C LYS* 1.3 62.3 + - + +
359C PHE* 3.5 16.3 - - + -
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Residues in contact with LYS 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C GLU* 3.1 31.8 + - + +
332C THR* 3.0 16.0 + - - +
334C ALA* 1.3 84.0 - - + +
336C ASP* 1.3 58.6 + - + +
337C ASN 4.0 1.4 + - - -
462C TYR* 5.5 6.5 - - - -
489C LEU* 5.0 10.3 - - - +
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Residues in contact with ASP 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C THR* 2.7 23.8 + - + +
333C ALA* 3.2 7.0 - - - +
335C LYS* 1.3 74.4 - - + +
337C ASN* 1.3 62.5 + - - +
338C LYS* 2.7 55.8 + - - +
339C LEU* 3.4 6.8 + - - +
362C ARG* 2.8 17.1 + - - -
386C LYS* 3.8 1.6 - - - +
465C TYR* 3.0 34.9 + - + +
466C HIS* 4.9 4.3 - - - -
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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
------------------------------------------------------------
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