Contacts of the helix formed by residues 567 - 580 (chain B) 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 PHE 567 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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552B ASN* 3.2 8.5 - - - +
566B ARG* 1.3 134.2 - - + +
568B PRO* 1.3 71.8 - - + +
569B THR 3.5 1.3 - - - -
570B LYS* 3.8 21.0 + - + -
571B PHE* 3.3 18.4 + - - +
279N GLU* 3.7 31.6 - - + +
282N LEU* 3.7 28.7 - - + -
283N LEU* 3.8 29.8 - - + -
286N ASP* 5.4 0.2 - - + -
384N LYS 4.2 7.0 - - - -
385N GLY* 4.1 19.1 - - - -
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Residues in contact with PRO 568 (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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552B ASN* 3.7 22.2 - - + +
553B TYR* 3.5 44.4 - - + +
565B ILE* 4.8 7.4 - - + +
566B ARG* 3.9 0.8 - - - +
567B PHE* 1.3 86.2 - - - +
569B THR* 1.3 73.8 + - - +
571B PHE* 3.1 11.7 + - + +
572B VAL* 2.9 27.5 + - + +
592B SER* 5.6 1.1 - - - +
599B VAL* 5.6 6.3 - - + -
275N GLU* 5.5 4.5 - - - +
279N GLU* 3.9 7.9 - - + +
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Residues in contact with THR 569 (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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553B TYR* 5.7 1.0 - - - -
568B PRO* 1.3 82.4 - - - +
570B LYS* 1.3 61.6 + - - +
572B VAL* 3.0 11.7 + - + +
573B THR* 2.9 30.9 + - - +
592B SER* 5.5 4.2 + - - -
275N GLU* 4.2 14.9 + - + +
276N ALA* 5.6 7.4 - - + +
279N GLU* 3.1 28.1 + - - +
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Residues in contact with LYS 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B LEU* 5.2 8.7 - - - +
567B PHE* 4.2 22.4 - - + +
568B PRO 3.3 0.4 - - - -
569B THR* 1.3 79.1 - - - +
571B PHE* 1.3 64.9 + - - +
573B THR* 3.9 5.4 - - - +
574B GLN* 2.9 50.5 + - + +
279N GLU* 3.2 10.7 + - + +
283N LEU* 4.9 25.8 - - + -
382N ILE* 5.8 6.2 + - + +
419N THR* 5.4 9.3 - - - +
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Residues in contact with PHE 571 (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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533B CYS* 4.0 14.8 - - - -
536B LEU* 3.3 48.7 - - + -
538B VAL* 3.8 17.3 - - + -
555B VAL* 4.5 9.6 - - + -
565B ILE* 4.0 24.9 - - + -
567B PHE 3.3 12.8 + - - +
568B PRO 3.1 11.8 + - - +
570B LYS* 1.3 80.5 - - - +
572B VAL* 1.3 71.2 + - + +
574B GLN* 3.4 2.4 - - - +
575B PHE* 2.9 30.3 + + + +
590B ILE* 4.0 20.0 - - + -
599B VAL* 4.6 10.1 - - + -
601B ILE* 3.9 21.5 - - + -
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Residues in contact with VAL 572 (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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568B PRO* 2.9 22.5 + - + +
569B THR* 3.0 12.5 + - + +
571B PHE* 1.3 77.6 - - + +
573B THR* 1.3 65.0 + - - +
575B PHE* 2.8 14.6 + - - +
576B ARG* 2.9 47.6 + - - +
590B ILE* 4.3 14.8 - - + +
592B SER* 4.6 18.4 - - - +
599B VAL* 3.9 28.7 - - + -
656B ASP* 5.7 0.4 - - - +
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Residues in contact with THR 573 (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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569B THR* 2.9 25.3 + - - +
570B LYS* 4.0 5.8 - - - -
572B VAL* 1.3 74.1 - - - +
574B GLN* 1.3 65.3 + - - +
576B ARG* 4.1 10.1 + - - +
577B HIS* 2.9 27.8 + - + +
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Residues in contact with GLN 574 (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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536B LEU* 3.9 17.4 - - + +
570B LYS* 2.9 48.0 + - + +
571B PHE* 3.4 5.6 - - - +
573B THR* 1.3 80.3 - - - +
575B PHE* 1.3 63.8 + - - +
577B HIS* 3.2 6.6 + - - +
578B LEU* 3.1 25.0 + - + +
419N THR* 5.1 4.9 - - - +
420N PRO 3.8 11.1 + - - -
421N GLN* 3.9 3.8 - - - +
422N ILE* 3.2 50.9 + - + +
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Residues in contact with PHE 575 (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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529B ILE* 3.6 35.2 - - + -
532B LEU* 4.0 17.5 - - + -
533B CYS* 6.1 3.1 - - - -
536B LEU* 4.3 10.2 - - + +
571B PHE* 2.9 19.3 + + + +
572B VAL 2.8 13.9 + - - +
574B GLN* 1.3 67.5 - - - +
576B ARG* 1.3 59.3 + - - +
578B LEU* 2.7 36.1 + - + +
579B ARG* 2.9 18.4 + - + -
584B VAL* 4.6 7.9 - - + -
588B ILE* 3.7 29.2 - - + -
590B ILE* 3.5 37.9 - - + -
601B ILE* 4.4 17.3 - - + -
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Residues in contact with ARG 576 (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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572B VAL* 2.9 47.4 + - - +
573B THR* 4.1 9.0 + - - +
575B PHE* 1.3 78.3 - - - +
577B HIS* 1.3 61.9 + - - +
579B ARG* 3.2 24.0 + - - +
580B ARG* 3.1 35.8 + - + +
590B ILE* 3.4 33.3 + - + +
591B TYR* 4.6 4.4 - - - +
614B ILE* 6.1 2.5 - - + -
647B GLU* 5.3 4.5 - - - +
653B GLU* 3.5 23.1 + - - +
656B ASP* 4.8 7.5 + - - +
657B SER* 6.1 0.2 - - - -
672B HIS* 5.3 9.4 - - - -
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Residues in contact with HIS 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B THR* 2.9 23.4 + - + +
574B GLN* 3.2 8.3 - - - +
576B ARG* 1.3 75.3 - - - +
578B LEU* 1.3 68.7 + - + +
580B ARG* 3.1 32.2 - - - +
581B THR* 3.7 15.4 + - + -
422N ILE* 3.2 33.7 + - + +
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Residues in contact with LEU 578 (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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532B LEU* 4.6 29.2 - - + -
536B LEU* 5.0 9.2 - - + -
574B GLN* 3.1 14.6 + - + +
575B PHE* 2.7 24.8 + - + +
577B HIS* 1.3 75.1 - - - +
579B ARG* 1.3 60.3 + - - +
581B THR* 3.0 1.1 + - - -
582B GLY* 2.7 34.6 + - - +
583B LYS* 3.5 13.4 + - + +
584B VAL* 5.9 2.5 - - + -
422N ILE* 4.3 26.9 - - + -
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Residues in contact with ARG 579 (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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575B PHE* 2.9 19.1 + - + +
576B ARG* 3.2 30.6 + - - +
578B LEU* 1.3 76.3 - - - +
580B ARG* 1.3 61.8 + - - +
581B THR* 2.9 10.2 + - - +
583B LYS 3.5 14.8 - - - +
584B VAL* 3.4 19.0 - - + +
585B SER* 4.3 15.6 - - - -
586B GLU 3.3 16.7 + - - +
587B PHE 3.3 23.1 - - - -
588B ILE* 3.9 13.8 + - - -
589B SER* 4.7 8.0 - - - +
590B ILE* 5.2 5.9 - - - +
647B GLU* 3.4 43.5 + - - +
648B TYR 3.6 13.0 + - - +
649B LEU* 4.8 6.1 - - - +
653B GLU* 5.1 7.3 + - - +
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Residues in contact with ARG 580 (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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576B ARG* 3.1 28.7 + - + +
577B HIS* 3.1 29.5 - - + +
579B ARG* 1.3 77.2 - - - +
581B THR* 1.3 66.5 + - - +
614B ILE* 3.5 46.9 - - + +
616B SER* 5.6 0.8 - - - -
621B ARG* 2.9 45.5 - - - +
641B LEU* 3.1 22.1 - - - +
644B GLY* 3.4 22.3 + - - -
646B VAL 5.7 0.2 - - - +
647B GLU* 5.1 17.4 - - + +
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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