Contacts of the helix formed by residues 414 - 429 (chain C) in PDB entry 5A31
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 MET 414 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409C TYR* 3.3 30.5 + - + +
410C GLU* 5.0 0.2 - - - -
412C LEU* 3.1 17.0 - - + +
413C LYS* 1.3 76.2 - - - +
415C PRO* 1.3 66.9 - - - +
416C PHE 3.2 1.8 - - - -
417C TYR* 3.7 24.7 - - + -
418C CYS* 3.2 25.0 + - - +
300O LEU* 3.2 57.9 - - + +
303O ALA* 6.3 0.7 - - - -
304O ALA* 4.7 2.9 - - - -
326O GLU* 3.8 13.0 - - + -
330O ILE* 3.5 29.2 - - + -
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Residues in contact with PRO 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C GLU* 5.4 3.4 - - + -
413C LYS* 2.7 22.6 - - - +
414C MET* 1.3 74.3 - - - +
416C PHE* 1.3 67.0 + - - +
418C CYS* 3.8 11.2 - - - -
419C LEU* 3.0 24.6 + - - +
442C CYS* 3.9 22.4 - - - +
445C LYS* 4.1 36.1 - - + +
446C LEU* 4.0 11.4 - - + +
326O GLU* 3.2 19.3 - - - +
329O ARG* 5.1 2.7 - - - +
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Residues in contact with PHE 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C MET 3.2 0.8 - - - -
415C PRO* 1.3 84.1 - - - +
417C TYR* 1.3 65.9 + - - +
419C LEU* 3.4 21.4 - - + +
420C TYR* 4.2 2.1 + - - +
446C LEU* 3.5 18.8 - - + +
307O LEU* 3.5 26.4 - - + +
311O HIS* 3.7 19.7 - - - -
319O GLN* 3.6 35.4 - - + -
322O LEU* 3.9 22.0 - - + -
323O ALA* 3.3 33.4 - - + -
326O GLU* 3.6 23.1 - - + +
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Residues in contact with TYR 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C TYR* 3.3 53.3 + + - -
414C MET* 3.4 26.6 + - + +
415C PRO 3.2 0.2 - - - -
416C PHE* 1.3 86.9 - - + +
418C CYS* 1.3 57.7 + - - +
420C TYR* 3.6 17.8 + - - +
421C TYR* 3.9 11.7 + + - -
275O LEU* 3.4 40.9 + - + +
278O PHE* 4.4 2.9 - - - +
279O ASP* 4.3 0.2 + - - -
303O ALA* 3.9 33.1 - - + +
304O ALA* 4.4 14.1 - - + -
307O LEU* 3.5 26.7 - - + +
326O GLU* 4.5 2.9 - - + +
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Residues in contact with CYS 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C GLY* 3.3 22.6 - - - +
409C TYR* 3.2 25.6 - - + -
410C GLU* 3.4 25.8 - - - -
414C MET 3.2 13.8 + - - +
415C PRO* 3.9 2.2 - - - -
417C TYR* 1.3 74.2 - - - +
419C LEU* 1.3 66.7 + - - +
420C TYR 3.1 0.7 - - - -
421C TYR* 3.4 11.5 + - - +
422C TYR* 3.1 28.9 + - - -
442C CYS* 3.8 17.7 - - - -
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Residues in contact with LEU 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A LYS* 4.7 8.3 - - - +
415C PRO 3.0 13.6 + - - +
416C PHE* 3.4 21.8 - - + +
418C CYS* 1.3 77.1 - - - +
420C TYR* 1.3 63.3 + - - +
422C TYR* 3.4 7.1 + - - -
423C ARG* 3.1 31.7 + - - +
439C LEU* 3.4 27.6 - - + -
442C CYS* 4.6 12.1 - - + -
443C TYR* 3.9 29.4 - - + +
446C LEU* 3.7 28.9 - - + -
319O GLN* 5.6 0.2 - - - +
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Residues in contact with TYR 420 (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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37A LEU* 4.7 2.4 - - - +
389C ARG* 4.8 4.9 + - - -
402C TRP* 4.3 9.7 - + - -
416C PHE 4.2 2.1 + - - +
417C TYR 3.6 13.4 + - - +
418C CYS 3.1 0.6 - - - -
419C LEU* 1.3 80.8 - - - +
421C TYR* 1.3 89.7 + + - +
423C ARG* 3.4 27.3 + - - +
424C ARG* 3.1 42.4 + - + +
271O THR* 4.9 12.3 - - + -
272O HIS* 2.6 42.5 + + - -
275O LEU* 3.1 35.7 - - + -
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Residues in contact with TYR 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C ARG* 4.1 7.1 + - - -
402C TRP* 3.5 34.4 - + + +
405C LEU* 3.3 32.1 - - + -
406C GLY* 3.5 19.1 - - - +
409C TYR* 3.3 35.5 - + - -
417C TYR* 3.9 16.5 - + - -
418C CYS* 3.4 12.8 + - - +
420C TYR* 1.3 97.1 - + - +
422C TYR* 1.3 67.4 + - - +
424C ARG* 3.1 2.9 + - - +
425C ALA* 2.9 23.2 + - - +
275O LEU* 4.1 11.1 - - + +
279O ASP* 2.9 28.4 + - - -
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Residues in contact with TYR 422 (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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403C TYR* 3.7 46.7 - + - -
406C GLY* 3.3 8.5 - - - -
407C GLN* 3.0 18.5 - - - -
410C GLU* 3.1 15.4 + - - -
418C CYS* 3.1 31.8 + - - +
419C LEU* 3.9 4.5 - - - +
420C TYR 3.3 0.2 - - - -
421C TYR* 1.3 76.2 - - - +
423C ARG* 1.3 57.3 - - - +
425C ALA* 3.0 6.1 + - + +
426C HIS* 2.8 30.7 + - - +
435C MET* 4.7 4.8 - - + +
438C ALA* 3.9 18.8 - - + -
439C LEU* 4.1 18.6 - - + +
442C CYS* 3.8 20.9 - - - -
52R ARG* 2.4 28.4 + - - -
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Residues in contact with ARG 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A LYS* 6.2 0.2 - - - +
168A ASP* 3.0 61.8 + - - +
169A TYR* 4.3 2.7 - - - +
170A ILE* 4.1 38.5 - - + +
217A LEU* 6.5 0.9 - - + -
419C LEU* 3.1 32.9 + - - +
420C TYR* 3.4 38.4 + - - +
422C TYR* 1.3 75.2 - - - +
424C ARG* 1.3 65.6 + - - +
426C HIS* 3.2 9.3 + - - +
427C GLN* 3.0 23.7 + - - +
439C LEU* 4.2 13.9 - - + +
443C TYR* 4.1 8.7 - - - +
268O PHE* 6.2 0.2 - - - -
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Residues in contact with ARG 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 4.9 8.3 - - - +
120A ASP* 4.4 14.6 + - - -
170A ILE* 4.1 18.5 - - + +
396C LYS* 4.6 16.1 + - - +
402C TRP* 3.7 45.1 - - + +
420C TYR* 3.1 48.5 + - + +
421C TYR 3.1 3.8 + - - +
423C ARG* 1.3 80.7 - - - +
425C ALA* 1.3 59.2 + - - +
427C GLN* 3.6 35.6 + - - +
428C LEU* 3.6 20.7 + - - +
272O HIS* 4.1 14.7 + - - -
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Residues in contact with ALA 425 (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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399C TYR* 4.2 7.7 - - - +
402C TRP* 3.7 22.7 - - + +
403C TYR* 3.8 17.5 - - + +
421C TYR 2.9 12.8 + - - +
422C TYR* 3.3 10.3 - - - +
424C ARG* 1.3 74.1 - - - +
426C HIS* 1.3 66.1 + - - +
428C LEU* 3.1 21.9 + - - +
429C ARG* 3.2 9.4 + - - +
435C MET* 4.0 15.7 - - + +
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Residues in contact with HIS 426 (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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170A ILE 4.7 13.1 + - - -
171A ALA* 6.0 0.4 - - - -
172A SER 5.5 7.4 - - - -
217A LEU* 6.4 1.6 - - + -
422C TYR 2.8 18.1 + - - +
423C ARG* 3.2 6.4 + - - +
425C ALA* 1.3 76.3 - - - +
427C GLN* 1.3 66.0 + - - +
428C LEU 3.1 0.5 + - - -
429C ARG 3.1 27.8 + - - +
430C PRO* 3.5 26.0 + - + +
432C ASP 4.5 0.9 - - - -
435C MET* 3.9 19.9 - - + +
436C LEU* 3.3 37.4 - - + +
439C LEU* 4.0 17.0 - - + +
458C ARG* 3.6 12.7 + - - -
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Residues in contact with GLN 427 (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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155A GLN* 5.4 0.4 + - - -
157A SER* 5.0 5.1 + - - +
158A CYS* 3.2 29.9 - - + -
160A ASN* 4.9 2.2 + - - +
170A ILE* 3.5 36.7 - - + +
171A ALA 4.3 2.0 - - - +
172A SER* 3.4 29.1 + - - +
397C ARG* 4.5 15.2 + - - +
423C ARG 3.0 10.3 + - - +
424C ARG* 3.7 40.7 + - - +
425C ALA 3.3 0.2 - - - -
426C HIS* 1.3 80.5 + - - +
428C LEU* 1.3 64.7 + - - +
430C PRO* 4.5 3.3 - - - +
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Residues in contact with LEU 428 (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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396C LYS 3.4 19.7 - - - +
397C ARG* 3.0 70.9 + - + +
399C TYR* 3.7 16.6 - - + -
402C TRP* 3.6 22.4 - - + +
424C ARG* 3.6 10.6 + - - +
425C ALA 3.1 11.2 + - - +
426C HIS 3.0 0.2 - - - -
427C GLN* 1.3 85.1 - - - +
429C ARG* 1.3 66.2 + - - +
430C PRO* 3.8 5.4 - - - +
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Residues in contact with ARG 429 (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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242C GLN* 5.5 12.3 - - - +
277C ARG* 5.1 7.3 - - - +
399C TYR* 3.7 49.6 - - + +
425C ALA 3.2 5.7 + - - +
426C HIS* 3.1 16.2 + - - +
428C LEU* 1.3 86.7 + - - +
430C PRO* 1.3 68.5 - - + +
431C ASN* 3.5 1.9 + - + +
432C ASP* 3.5 42.7 + - + +
435C MET* 4.9 2.6 - - - +
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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
------------------------------------------------------------
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