Contacts of the helix formed by residues 418 - 431 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B ASP* 5.6 1.6 - - - +
416B LEU 3.7 4.4 + - - -
417B LEU* 1.3 76.8 - - - +
419B ARG* 1.3 64.3 + - - +
420B ASN* 4.0 9.7 + - + +
421B LEU* 3.5 23.9 + - + +
422B LYS* 3.1 19.8 + - - +
442B LEU 4.0 4.9 - - - +
443B PHE* 3.5 7.3 - - - -
444B TRP* 2.9 45.7 + - + +
445B ARG 4.6 1.0 + - - -
447B PHE* 5.6 0.3 - - - -
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Residues in contact with ARG 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B SER 4.5 4.4 + - - -
295B LEU* 3.6 31.4 - - + +
418B GLU* 1.3 74.4 - - - +
420B ASN* 1.3 73.6 + - - +
422B LYS* 3.1 10.6 + - + +
423B VAL* 3.0 30.7 + - + +
380D MET 5.4 8.9 + - - -
381D HIS* 6.0 6.8 - - - +
382D SER* 4.8 9.7 + - - +
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Residues in contact with ASN 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B GLU* 3.5 9.4 + - - +
419B ARG* 1.3 82.4 + - - +
421B LEU* 1.3 57.2 + - - +
423B VAL* 3.6 8.5 + - - +
424B TYR* 3.0 28.1 + - - +
439B MET* 5.1 3.2 - - - +
442B LEU* 3.4 39.1 + - + +
443B PHE* 3.4 26.8 - - + +
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Residues in contact with LEU 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B ILE* 4.5 2.5 - - + -
417B LEU* 3.5 42.8 - - + -
418B GLU* 3.5 19.3 + - + +
419B ARG 3.1 0.4 - - - -
420B ASN* 1.3 76.1 - - - +
422B LYS* 1.3 58.4 + - - +
424B TYR* 3.1 2.1 + - + +
425B ILE* 2.8 58.7 + - + +
443B PHE* 3.3 40.7 - - + +
444B TRP* 3.8 26.9 - - + +
455B VAL* 4.3 10.8 - - + -
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Residues in contact with LYS 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B GLU* 2.6 27.1 + - - -
293B GLU* 2.7 27.1 + - - -
295B LEU* 3.9 12.7 - - + +
396B TYR* 3.3 38.4 + - + +
413B VAL* 4.1 5.1 - - + +
414B ASN* 2.7 27.5 + - - +
417B LEU* 3.7 34.5 - - + +
418B GLU 3.1 10.4 + - - +
419B ARG* 3.1 11.6 + - + +
421B LEU* 1.3 79.1 - - - +
423B VAL* 1.3 59.6 + - - +
425B ILE* 4.5 1.1 - - - -
426B LYS* 3.3 17.9 + - - +
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Residues in contact with VAL 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 3.9 37.2 - - + +
419B ARG* 3.0 25.8 + - + +
420B ASN* 3.6 10.5 - - - +
422B LYS* 1.3 73.9 - - - +
424B TYR* 1.3 58.4 + - - +
426B LYS* 3.0 3.7 + - - +
427B THR* 2.7 48.3 + - - +
439B MET* 3.9 18.6 - - + -
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Residues in contact with TYR 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B GLY 2.6 29.8 + - - -
420B ASN 3.0 18.9 + - - +
421B LEU 3.1 2.9 + - - +
423B VAL* 1.3 73.7 - - - +
425B ILE* 1.3 63.1 + - + +
427B THR* 3.2 1.0 + - - -
428B VAL* 2.7 57.3 + - + +
435B THR* 4.0 10.8 - - + -
439B MET* 3.9 21.5 - - + -
440B TYR* 3.6 27.1 - + - -
443B PHE* 3.4 47.8 - + + -
452B LYS 4.7 2.9 - - - -
455B VAL* 4.8 7.2 - - + -
456B ASN* 2.7 28.5 + - - -
459B LEU* 5.1 1.3 - - + -
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Residues in contact with ILE 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B ILE* 3.7 29.4 - - + -
396B TYR* 3.8 24.0 - - + -
397B ILE* 3.3 29.4 - - + -
400B VAL* 5.9 0.7 - - + -
417B LEU* 4.9 2.0 - - + -
421B LEU* 2.8 48.0 + - + +
422B LYS* 4.1 3.1 - - - +
424B TYR* 1.3 77.0 - - + +
426B LYS* 1.3 54.5 + - - +
428B VAL* 3.1 2.8 + - - +
429B ALA* 2.8 34.7 + - + +
455B VAL* 4.1 18.4 - - + -
459B LEU* 3.8 13.4 - - + +
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Residues in contact with LYS 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B LYS 5.1 4.6 + - - -
292B SER 5.4 0.2 + - - -
293B GLU 3.3 22.4 + - - +
294B SER* 5.1 0.4 - - - +
295B LEU* 4.2 29.8 - - + +
323B TYR* 3.9 38.1 + - - -
324B GLU* 4.6 7.2 + - - -
332B GLN 5.2 2.6 + - - -
396B TYR* 3.9 17.5 - - + +
400B VAL* 4.3 15.2 - - + +
422B LYS 3.3 15.8 + - - +
423B VAL* 3.0 5.1 + - - +
425B ILE* 1.3 81.9 - - - +
427B THR* 1.3 54.8 + - - +
429B ALA* 4.3 4.5 - - - +
430B CYS* 2.8 50.9 + - + +
431B TYR* 6.2 2.0 - - + -
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Residues in contact with THR 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B LEU 5.2 6.3 + - - -
423B VAL* 2.7 30.1 + - - +
424B TYR 3.7 0.2 - - - -
426B LYS* 1.3 72.0 - - - +
428B VAL* 1.3 56.6 + - - +
431B TYR* 2.7 58.5 + - + +
432B PRO 2.8 1.0 - - - -
434B LYS* 4.0 8.3 - - + -
435B THR* 3.8 16.4 - - - +
439B MET* 3.4 36.3 - - + +
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Residues in contact with VAL 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B SER* 2.7 51.0 + - - +
213B GLY* 3.6 19.7 - - - +
424B TYR* 2.7 44.2 + - + +
425B ILE 3.6 3.4 - - - +
427B THR* 1.3 72.9 - - - +
429B ALA* 1.3 54.1 + - - +
432B PRO* 3.4 12.2 - - - +
435B THR* 3.5 17.5 - - + +
456B ASN* 3.6 19.1 - - - +
459B LEU* 3.7 15.7 - - + -
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Residues in contact with ALA 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B SER* 4.1 2.5 - - - -
397B ILE* 4.5 9.4 - - + -
400B VAL* 5.4 1.8 - - + -
401B PHE* 3.7 21.1 - - + -
425B ILE* 2.8 21.2 + - + +
426B LYS* 3.8 5.8 - - - +
428B VAL* 1.3 74.8 - - - +
430B CYS* 1.3 67.0 + - - +
432B PRO* 4.3 0.8 - - - +
459B LEU* 3.8 18.4 - - + -
463B ARG* 3.2 31.8 + - - +
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Residues in contact with CYS 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B HIS* 4.4 6.6 - - - -
167B ALA 6.0 0.4 - - - -
168B HIS* 4.6 8.0 + - - +
323B TYR* 3.6 39.8 + - + +
400B VAL* 3.6 31.2 - - - -
401B PHE* 4.4 3.6 - - - -
426B LYS* 2.8 30.4 + - + +
429B ALA* 1.3 81.3 - - - +
431B TYR* 1.3 80.7 + - + +
432B PRO* 3.3 7.9 - - - +
433B GLU* 4.0 2.6 - - - +
463B ARG* 5.6 0.9 - - - +
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Residues in contact with TYR 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B HIS* 6.4 0.7 - + - -
322B GLY* 3.6 14.5 - - - -
323B TYR* 3.3 23.5 + + + -
324B GLU* 2.7 48.2 + - + +
326B PHE* 5.1 4.8 - + - -
426B LYS* 5.3 2.5 - - - -
427B THR* 2.7 21.4 + - + +
430B CYS* 1.3 92.6 - - + +
432B PRO* 1.3 66.2 - - - +
433B GLU* 3.1 21.1 - - - -
434B LYS* 2.8 36.1 + - + +
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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