Contacts of the helix formed by residues 418 - 431 (chain C) in PDB entry 6N0M
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 GLU 418 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257C ASP* 5.1 10.8 - - - +
264C ARG* 6.1 4.3 - - - +
414C ASN 5.4 0.4 - - - -
416C LEU 3.4 6.4 + - - +
417C LEU* 1.3 77.3 - - - +
419C ARG* 1.3 67.7 + - - +
420C ASN* 3.8 8.8 + - - +
421C LEU* 3.8 21.9 - - + +
422C LYS* 3.3 17.5 + - - +
442C LEU 4.2 2.8 - - - +
443C PHE* 3.4 9.4 - - - -
444C TRP* 3.1 45.6 + - + +
445C ARG 5.0 0.3 + - - -
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Residues in contact with ARG 419 (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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380A MET 5.4 7.6 + - - -
381A HIS* 6.3 2.9 - - - -
382A SER* 5.7 3.2 + - - -
293C GLU* 5.8 3.4 - - - -
294C SER 5.3 0.6 + - - -
295C LEU* 3.7 30.3 - - - +
418C GLU* 1.3 74.7 - - - +
420C ASN* 1.3 72.5 + - - +
422C LYS* 2.8 27.3 + - - +
423C VAL* 2.9 21.4 + - + +
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Residues in contact with ASN 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C GLU* 3.6 8.3 + - - +
419C ARG* 1.3 91.1 + - - +
421C LEU* 1.3 57.7 + - - +
423C VAL* 3.7 10.3 - - + +
424C TYR* 2.9 29.1 + - - +
439C MET* 4.8 3.0 - - - +
442C LEU* 3.5 40.5 + - + +
443C PHE* 3.4 22.6 - - + +
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Residues in contact with LEU 421 (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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393C ILE* 4.1 5.4 - - + -
417C LEU* 3.6 36.6 - - + -
418C GLU* 3.7 19.1 + - + +
419C ARG 3.1 0.8 - - - -
420C ASN* 1.3 72.7 - - - +
422C LYS* 1.3 61.9 + - - +
424C TYR* 3.3 1.2 + - + +
425C ILE* 2.8 56.0 + - + +
443C PHE* 3.3 43.2 - - + +
444C TRP* 3.6 36.3 - - + +
455C VAL* 4.4 7.6 - - + -
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Residues in contact with LYS 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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290C GLU* 2.6 27.9 + - - -
293C GLU* 3.0 29.4 + - - +
295C LEU* 4.1 10.0 - - + +
396C TYR* 3.8 34.4 + - + +
413C VAL* 4.2 5.6 - - - +
414C ASN* 2.8 21.8 + - - +
417C LEU* 3.6 27.6 - - + +
418C GLU 3.3 17.5 + - - +
419C ARG* 2.8 12.4 + - - +
421C LEU* 1.3 78.7 - - - +
423C VAL* 1.3 62.4 + - - +
425C ILE* 4.5 1.8 - - - -
426C LYS* 3.1 26.2 + - - +
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Residues in contact with VAL 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C LEU* 4.0 37.4 - - + +
419C ARG* 2.9 30.9 + - + +
420C ASN* 3.7 14.4 - - + +
422C LYS* 1.3 74.2 - - - +
424C TYR* 1.3 63.9 + - - +
426C LYS* 3.3 2.1 + - - +
427C THR* 2.8 33.8 + - - +
439C MET* 4.0 29.2 - - + -
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Residues in contact with TYR 424 (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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213C GLY 2.7 19.2 + - - -
420C ASN 2.9 18.3 + - - +
421C LEU 3.8 2.2 - - - +
423C VAL* 1.3 76.7 - - - +
425C ILE* 1.3 60.0 + - + +
427C THR* 3.2 1.4 + - - -
428C VAL* 2.8 58.9 + - + +
435C THR* 3.9 18.2 - - + -
439C MET* 4.2 15.9 - - + -
440C TYR* 3.5 34.6 - + - -
443C PHE* 3.1 39.0 - + + -
452C LYS 4.8 1.6 - - - -
455C VAL* 4.7 13.0 - - + -
456C ASN* 2.6 33.6 + - - -
459C LEU* 5.3 0.9 - - + -
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Residues in contact with ILE 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C ILE* 4.0 23.8 - - + -
396C TYR* 4.0 21.1 - - + -
397C ILE* 3.4 34.3 - - + -
417C LEU* 4.9 2.0 - - + -
421C LEU* 2.8 52.5 + - + +
422C LYS* 3.9 4.3 - - - +
424C TYR* 1.3 73.7 - - + +
426C LYS* 1.3 53.4 + - - +
428C VAL 3.2 1.6 + - - -
429C ALA* 2.7 33.8 + - - +
455C VAL* 4.1 19.3 - - + -
459C LEU* 3.6 13.0 - - + +
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Residues in contact with LYS 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C GLU 5.9 0.4 + - - -
291C LYS 4.9 6.3 + - - -
292C SER 5.3 0.2 + - - -
293C GLU 3.4 22.0 + - - -
294C SER* 5.1 0.6 - - - +
295C LEU* 4.1 33.9 - - + +
323C TYR* 3.9 32.2 + - - -
332C GLN 5.0 3.6 + - - -
396C TYR* 4.1 15.0 - - + +
397C ILE* 6.0 0.2 - - - -
400C VAL* 3.9 22.0 - - + -
422C LYS 3.1 16.9 + - - +
423C VAL* 3.9 3.1 - - - +
425C ILE* 1.3 81.9 - - - +
427C THR* 1.3 55.5 + - - +
429C ALA* 3.2 3.5 + - - -
430C CYS* 2.7 51.0 + - + +
431C TYR* 6.3 0.2 - - - -
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Residues in contact with THR 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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295C LEU 5.2 7.2 + - - -
423C VAL* 2.8 26.9 + - - +
424C TYR 3.4 4.0 - - - -
426C LYS* 1.3 77.5 - - - +
428C VAL* 1.3 57.1 + - - +
430C CYS* 5.3 0.2 - - - -
431C TYR* 2.8 60.3 + - + +
432C PRO 3.0 0.5 - - - -
434C LYS* 3.8 14.8 - - + +
435C THR* 3.9 7.4 - - - +
439C MET* 3.7 35.0 - - + +
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Residues in contact with VAL 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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209C SER* 2.9 46.3 + - - +
213C GLY* 3.8 6.1 - - - +
424C TYR* 2.8 51.6 + - + +
425C ILE 3.7 3.1 - - - +
427C THR* 1.3 71.7 - - - +
429C ALA* 1.3 56.0 + - - +
432C PRO* 3.4 13.7 - - - +
435C THR* 3.4 23.1 - - + +
456C ASN* 3.4 23.3 - - - +
459C LEU* 3.8 13.2 - - + -
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Residues in contact with ALA 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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167C ALA 5.0 0.2 - - - +
209C SER* 4.3 2.2 - - - -
397C ILE* 4.6 14.8 - - + -
400C VAL* 5.5 1.3 - - + -
401C PHE* 3.8 18.3 - - + -
425C ILE 2.7 21.1 + - - +
426C LYS* 3.7 6.1 - - - +
428C VAL* 1.3 75.9 - - - +
430C CYS* 1.3 65.4 + - - +
432C PRO* 4.8 0.2 - - - -
459C LEU* 4.0 16.6 - - + +
463C ARG* 3.3 33.5 + - - +
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Residues in contact with CYS 430 (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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123C HIS* 4.5 2.1 - - - -
168C HIS* 4.2 15.1 + - - -
323C TYR* 3.8 33.1 - - + +
400C VAL* 3.6 31.0 - - - -
401C PHE* 4.1 5.8 - - - -
426C LYS* 2.7 30.6 + - + +
429C ALA* 1.3 79.3 - - - +
431C TYR* 1.3 82.0 + - + +
432C PRO* 3.6 8.4 - - - +
433C GLU* 4.1 3.6 - - - +
463C ARG* 5.6 0.7 - - - +
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Residues in contact with TYR 431 (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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168C HIS* 5.8 1.6 - + - -
322C GLY* 3.2 21.6 - - - -
323C TYR* 3.7 13.5 - + + -
324C GLU* 2.9 51.1 + - + +
326C PHE* 4.7 8.0 - + - -
427C THR* 2.8 32.0 + - + +
430C CYS* 1.3 86.0 - - + +
432C PRO* 1.4 67.5 - - - +
433C GLU* 3.2 18.6 - - - +
434C LYS* 3.0 27.4 + - + -
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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