Contacts of the helix formed by residues 400 - 414 (chain C) in PDB entry 2O2C
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 ARG 400 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B TRP* 4.5 9.2 - - - -
400B ARG* 4.4 12.5 - - - +
435B GLU* 3.6 30.3 + - - -
210C LEU* 4.5 12.7 - - + +
213C VAL* 3.9 24.2 - - + +
214C MET* 3.8 25.5 - - + +
217C GLU* 4.4 3.8 - - + -
397C TYR 4.7 1.0 + - - -
398C LEU 3.1 1.0 - - - -
399C TRP* 1.3 135.1 + - + +
401C LEU* 1.3 62.4 + - - +
402C PRO 3.5 1.8 - - - -
403C ALA* 3.5 31.8 + - - +
404C TYR* 3.2 21.3 + - - +
435C GLU* 5.5 2.0 + - - -
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Residues in contact with LEU 401 (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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214C MET* 3.9 19.1 - - + +
391C ILE* 4.5 2.7 - - + -
393C PRO* 4.3 6.5 - - + -
398C LEU* 3.0 46.2 + - + +
400C ARG* 1.3 76.2 - - - +
402C PRO* 1.4 67.9 - - + +
404C TYR* 3.1 3.3 + - + +
405C LEU* 2.9 41.7 + - + +
460C ILE* 3.9 28.5 - - + -
539C LEU* 5.1 0.2 - - + -
542C ILE* 4.6 9.0 - - + -
543C ILE* 3.5 31.4 - - + -
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Residues in contact with PRO 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C ILE* 3.6 34.8 - - + +
393C PRO* 3.9 13.2 - - + -
398C LEU 3.7 5.4 - - - +
399C TRP 3.6 15.0 - - - +
400C ARG 3.7 0.7 - - - -
401C LEU* 1.4 90.7 - - + +
403C ALA* 1.3 54.9 + - - +
405C LEU* 3.5 2.4 + - + +
406C GLN* 3.0 31.7 + - - +
432C ILE* 4.2 4.7 - - - +
433C PHE* 4.7 2.2 - - - -
434C GLY* 3.3 34.8 - - - +
435C GLU* 4.2 4.0 - - - +
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Residues in contact with ALA 403 (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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435B GLU* 4.0 13.5 - - + +
443B ALA* 5.5 0.9 - - - +
210C LEU* 3.7 21.3 - - + +
400C ARG* 3.5 44.6 + - - +
401C LEU 3.2 0.4 - - - -
402C PRO* 1.3 79.0 - - - +
404C TYR* 1.3 61.5 + - - +
406C GLN* 3.2 25.2 + - - +
407C GLN 3.4 5.0 + - - -
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Residues in contact with TYR 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C LEU* 3.7 16.3 - - + +
211C GLY* 3.4 39.5 - - - -
214C MET* 3.9 22.7 - - + -
326C ARG* 3.5 24.3 + - - -
327C TYR* 4.8 0.3 - - - -
329C MET* 3.5 26.2 + - + +
400C ARG 3.2 10.8 + - - +
401C LEU* 3.1 8.6 + - + +
403C ALA* 1.3 79.4 - - - +
405C LEU* 1.3 68.8 + - + +
406C GLN 3.1 0.2 - - - -
407C GLN* 3.2 8.8 + - + +
408C LEU* 3.1 36.3 + - + +
543C ILE* 3.6 29.8 - - + +
547C GLU* 4.3 4.2 + - - -
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Residues in contact with LEU 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C ILE* 3.8 39.5 - - + -
401C LEU* 2.9 31.6 + - + +
402C PRO 4.1 3.4 - - - +
404C TYR* 1.3 82.7 - - + +
406C GLN* 1.3 59.8 + - - +
407C GLN 3.3 0.2 - - - -
408C LEU* 3.7 27.3 - - + +
409C ASP* 2.9 34.1 + - + +
432C ILE* 4.2 5.3 - - + +
543C ILE* 4.8 3.4 - - + -
546C TYR* 3.7 45.1 - - + -
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Residues in contact with GLN 406 (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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433B PHE* 4.0 19.4 - - - +
434B GLY 4.8 4.6 + - - +
435B GLU* 3.8 14.4 + - - +
443B ALA* 4.1 2.0 - - + +
444B PHE* 3.6 30.8 - - + -
402C PRO 3.0 14.2 + - - +
403C ALA* 3.2 17.9 - - - +
405C LEU* 1.3 77.9 - - - +
407C GLN* 1.3 56.2 + - - +
410C MET* 3.0 49.9 + - - +
432C ILE* 2.7 38.6 + - + +
433C PHE* 4.2 7.1 - - - +
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Residues in contact with GLN 407 (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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442B HIS 2.9 10.8 + - - -
443B ALA* 3.3 22.8 - - + +
206C GLY 3.3 12.0 - - - +
207C GLY* 3.3 13.7 + - - +
210C LEU* 3.2 32.6 - - + +
326C ARG* 3.7 14.0 - - + +
403C ALA 3.4 1.4 + - - -
404C TYR* 3.2 10.0 + - + +
406C GLN* 1.3 77.3 - - - +
408C LEU* 1.3 66.0 + - - +
411C GLU* 2.9 42.1 + - - +
5003C G6Q 2.9 36.2 + - - -
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Residues in contact with LEU 408 (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 ARG* 3.9 20.6 - - + +
327C TYR* 3.4 39.0 - - + +
404C TYR* 3.1 28.3 + - + +
405C LEU* 3.7 27.6 - - + +
407C GLN* 1.3 75.9 - - - +
409C ASP* 1.3 58.3 + - + +
412C SER* 2.7 31.5 + - - -
543C ILE* 4.5 1.6 - - + +
546C TYR* 4.0 5.6 - - + -
547C GLU* 3.9 32.1 - - + +
550C VAL* 4.0 10.0 - - + +
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Residues in contact with ASP 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C LEU* 2.9 18.1 + - + +
408C LEU* 1.3 75.8 - - - +
410C MET* 1.3 60.5 + - - +
412C SER* 3.3 0.9 + - - -
413C ASN* 2.8 41.1 + - - +
414C GLY 4.2 0.2 + - - -
429C GLY* 4.6 0.7 - - - -
430C PRO* 3.8 21.5 - - - +
432C ILE* 3.7 29.2 - - + +
546C TYR* 6.0 0.5 - - - -
549C LYS* 4.2 15.9 + - - +
550C VAL* 4.0 21.2 - - + +
553C GLN* 4.4 7.5 - - - +
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Residues in contact with MET 410 (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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433B PHE* 4.0 18.8 - - + -
443B ALA 4.7 0.2 - - - -
444B PHE* 3.7 26.2 - - + +
446B GLN* 4.2 0.5 - - - +
447B LEU* 3.7 45.6 + - + +
448B ILE* 5.5 0.4 - - + -
455B ILE* 5.2 0.4 - - + -
406C GLN* 3.0 38.9 + - - +
409C ASP* 1.3 75.1 - - - +
411C GLU* 1.3 56.2 + - - +
414C GLY* 3.0 27.2 + - - -
430C PRO 3.5 16.6 - - - +
431C ILE* 3.9 13.7 - - + -
432C ILE* 3.5 25.1 - - + +
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Residues in contact with GLU 411 (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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441B GLN 4.4 0.3 - - - +
442B HIS* 3.6 16.2 - - - +
443B ALA 3.3 13.9 + - - +
446B GLN* 3.5 32.6 + - + +
326C ARG* 3.1 20.3 + - - +
407C GLN* 2.9 29.4 + - - +
410C MET* 1.3 77.1 - - - +
412C SER* 1.3 61.5 + - - +
415C LYS* 3.5 9.7 + - - -
563C ASP 3.7 0.7 - - - +
564C GLN* 4.1 7.9 - - + -
567C VAL* 4.0 14.2 - - - +
5003C G6Q 3.0 47.6 + - - +
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Residues in contact with SER 412 (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 ARG* 2.7 19.6 + - - +
327C TYR* 2.9 14.7 + - - -
408C LEU 2.7 25.2 + - - -
409C ASP 3.3 0.6 + - - -
410C MET 3.3 0.4 - - - -
411C GLU* 1.3 79.9 - - - +
413C ASN* 1.3 61.8 + - - +
414C GLY 3.6 0.2 - - - -
415C LYS* 2.8 26.3 + - - +
550C VAL* 3.5 17.7 - - - -
559C ILE* 4.5 0.2 - - - +
561C SER* 3.2 26.1 + - - -
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Residues in contact with ASN 413 (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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409C ASP* 2.8 21.8 + - - +
412C SER* 1.3 74.4 - - - +
414C GLY* 1.3 55.5 + - - +
415C LYS 2.9 11.2 + - - -
428C THR* 3.3 6.2 + - - -
429C GLY* 2.9 26.4 + - - -
550C VAL* 3.1 35.1 + - - +
553C GLN* 3.8 14.6 + - - +
554C GLY* 3.7 9.1 - - - +
557C TRP* 3.9 14.1 - - + -
559C ILE* 3.7 14.1 - - + +
561C SER* 2.6 28.7 + - - -
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Residues in contact with GLY 414 (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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446B GLN* 3.1 31.9 + - - +
447B LEU* 3.8 24.0 - - - +
450B GLN 3.4 9.7 - - - +
451B GLY* 3.9 6.1 - - - -
410C MET 3.0 20.7 + - - -
411C GLU 4.6 0.2 - - - -
412C SER 3.6 1.8 - - - -
413C ASN* 1.3 72.8 - - - +
415C LYS* 1.3 58.4 + - - -
428C THR* 4.6 1.1 - - - -
429C GLY 4.8 0.7 - - - -
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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