Contacts of the helix formed by residues 412 - 423 (chain A) in PDB entry 6CNB
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 ASN 412 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406A GLU* 2.9 29.3 + - - -
407A LYS 3.7 16.6 + - - -
408A VAL* 3.9 14.8 - - + +
409A THR* 3.7 10.5 + - - +
411A TYR* 1.3 87.0 - - - +
413A ARG* 1.3 54.2 + - - +
414A HIS 3.5 1.1 - - - -
415A LYS* 3.1 9.5 + - - +
416A LEU* 2.7 48.0 + - + +
464A ARG* 4.3 7.5 + - - -
102F SER* 6.3 0.2 - - - +
115F THR* 4.6 1.8 - - - -
116F ASP* 3.9 21.8 + - - -
117F PRO* 4.9 3.4 - - - +
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Residues in contact with ARG 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A VAL* 3.9 19.0 - - + +
410A ARG* 4.7 16.6 + - - +
411A TYR 3.5 2.2 - - - -
412A ASN* 1.3 76.0 - - - +
414A HIS* 1.3 67.9 + - + +
416A LEU 2.5 24.1 + - - +
417A GLN* 2.5 45.8 + - + +
453A ALA 5.1 1.4 + - - -
454A LYS 5.0 4.8 + - - -
455A ASN 3.5 14.8 + - - -
456A LEU* 2.4 36.9 + - + +
457A GLN* 4.4 6.9 + - - +
458A ILE* 4.5 17.5 - - + +
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Residues in contact with HIS 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A TYR 5.1 1.4 + - - -
412A ASN 3.5 0.2 - - - -
413A ARG* 1.3 80.8 + - + +
415A LYS* 1.3 62.4 + - - +
417A GLN* 3.0 35.6 + - - +
418A GLU* 3.8 13.2 - - - +
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Residues in contact with LYS 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A TYR 5.3 0.9 + - - +
412A ASN* 3.1 12.8 + - - +
413A ARG 2.8 4.6 + - - -
414A HIS* 1.3 77.1 - - - +
416A LEU* 1.3 62.6 + - + +
418A GLU* 2.9 17.0 + - - +
419A LEU* 2.5 34.6 + - + +
464A ARG* 4.9 6.1 - - - +
115F THR* 4.6 29.4 - - + +
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Residues in contact with LEU 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A GLU* 4.1 10.1 - - + -
408A VAL* 3.6 26.2 - - + -
412A ASN* 2.7 25.2 + - + +
413A ARG 2.5 7.4 + - - +
415A LYS* 1.3 74.0 - - + +
417A GLN* 1.3 60.9 + - - +
418A GLU 3.0 1.6 - - - -
419A LEU* 2.7 28.1 + - + +
420A ILE* 2.9 18.6 + - + +
456A LEU* 4.2 13.5 - - + -
462A VAL* 3.3 36.3 - - + -
464A ARG* 3.3 35.0 - - - +
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Residues in contact with GLN 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A ARG* 2.5 52.2 + - + +
414A HIS* 3.0 37.7 + - - +
416A LEU* 1.3 72.8 - - - +
418A GLU* 1.3 59.0 + - + +
421A VAL* 4.3 6.9 + - - +
453A ALA* 3.5 38.7 - - - +
454A LYS* 5.6 11.6 + - + +
456A LEU* 3.8 15.2 - - + +
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Residues in contact with GLU 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414A HIS 3.8 12.8 - - - +
415A LYS* 2.9 16.3 + - - +
417A GLN* 1.3 80.3 - - + +
419A LEU* 1.3 82.8 + - - +
420A ILE 3.1 2.2 - - - -
421A VAL* 2.9 34.8 + - + +
422A ASN* 3.4 25.7 + - - +
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Residues in contact with LEU 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415A LYS* 2.5 20.8 + - + +
416A LEU* 2.7 22.3 + - + +
418A GLU* 1.3 81.3 + - - +
420A ILE* 1.3 61.8 + - + +
422A ASN* 3.7 5.9 + - - +
428A PRO* 3.1 32.3 - - + +
429A GLY* 3.5 32.6 - - - +
430A ALA* 3.7 6.9 + - + +
462A VAL* 5.8 1.3 - - + -
464A ARG* 3.6 40.4 - - + +
467A GLU* 4.2 9.4 - - + +
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Residues in contact with ILE 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416A LEU* 2.9 17.1 + - + +
417A GLN* 5.3 0.2 - - - -
419A LEU* 1.3 73.8 - - + +
421A VAL* 1.3 54.3 + - - +
422A ASN 2.9 4.9 - - - -
423A GLY* 2.6 31.7 + - - -
430A ALA* 3.8 12.8 - - + -
431A ASN 5.4 0.2 - - - +
432A TYR 5.4 0.4 - - - +
433A LEU* 4.0 21.3 - - + -
444A LEU* 4.0 24.1 - - + +
449A ARG* 4.0 21.5 - - + -
452A LEU* 4.7 6.3 - - + -
453A ALA* 4.1 22.7 - - + -
456A LEU* 5.6 5.6 - - + -
462A VAL* 3.5 31.0 - - + -
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Residues in contact with VAL 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A GLN 4.3 6.8 + - - +
418A GLU* 2.9 35.5 + - + +
420A ILE* 1.3 79.5 - - - +
422A ASN* 1.3 69.0 + - - +
423A GLY 3.4 0.2 - - - -
449A ARG* 4.4 14.3 + - + -
450A MET* 3.7 35.9 - - + +
453A ALA* 5.2 0.9 - - + +
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Residues in contact with ASN 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A GLU* 3.4 25.2 + - - +
419A LEU* 3.8 11.8 + - - +
420A ILE 2.8 1.6 + - - -
421A VAL* 1.3 86.7 - - - +
423A GLY* 1.3 63.5 + - - +
425A ASN* 3.7 6.8 + - - +
426A VAL* 3.5 30.2 - - + +
428A PRO* 2.5 35.7 + - - +
429A GLY* 4.2 0.4 - - - -
449A ARG* 3.7 7.0 + - - -
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Residues in contact with GLY 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A LEU 4.2 1.6 + - - -
420A ILE 2.6 21.7 + - - -
422A ASN* 1.3 77.8 - - - +
424A PRO* 1.3 75.4 - - - +
425A ASN 3.3 4.2 + - - -
426A VAL* 3.4 13.0 + - - +
430A ALA 3.4 11.1 + - - +
444A LEU* 4.6 1.3 - - - -
449A ARG* 3.4 14.8 - - - -
465A HIS* 3.8 3.3 - - - -
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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
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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