Contacts of the helix formed by residues 526 - 536 (chain B) in PDB entry 6CNC
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 526 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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525B GLU* 1.3 83.3 - - - +
527B GLU* 1.3 96.8 + - - +
528B PRO 3.4 1.6 - - - -
529B ILE* 3.0 23.4 - - - +
530B LYS* 3.2 23.9 + - - +
557B LEU* 4.0 14.7 - - + +
558B ASN* 4.5 17.5 - - - +
603B THR* 4.8 2.0 - - + -
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Residues in contact with GLU 527 (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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525B GLU* 4.5 3.0 + - - +
526B GLU* 1.3 90.0 + - - +
528B PRO* 1.3 74.7 - - + +
530B LYS* 2.9 33.4 + - - +
531B LYS* 2.9 47.7 + - - +
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Residues in contact with PRO 528 (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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525B GLU* 3.4 30.7 - - + +
526B GLU 3.6 1.6 - - - -
527B GLU* 1.3 95.0 - - + +
529B ILE* 1.3 63.1 + - - +
531B LYS* 3.6 11.3 - - + +
532B LEU* 2.9 26.1 + - - +
583B LYS* 4.6 19.8 - - - +
584B VAL* 6.3 0.7 - - + -
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Residues in contact with ILE 529 (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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524B ASP* 5.6 0.4 - - - +
525B GLU* 4.1 12.9 - - - +
526B GLU* 3.0 27.4 - - - +
528B PRO* 1.3 77.7 - - - +
530B LYS* 1.3 56.8 + - - +
532B LEU* 4.0 7.2 - - + -
533B CYS* 2.9 28.3 + - + +
557B LEU* 4.3 17.7 - - + -
575B PHE* 3.3 37.2 - - + -
584B VAL* 3.4 26.8 - - + +
588B ILE* 3.8 26.0 - - + -
601B ILE* 4.7 9.4 - - + -
603B THR* 5.0 3.6 - - - -
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Residues in contact with LYS 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B GLU* 3.2 24.6 + - - +
527B GLU* 2.9 33.4 + - - +
529B ILE* 1.3 76.2 - - - +
531B LYS* 1.3 56.8 + - - +
533B CYS* 2.7 29.9 + - + +
534B TYR* 2.8 50.2 + - + -
557B LEU* 4.1 18.8 - - + -
562B ILE* 3.4 28.8 - - + +
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Residues in contact with LYS 531 (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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527B GLU* 2.9 46.5 + - - +
528B PRO* 3.6 13.7 - - + +
530B LYS* 1.3 74.7 - - - +
532B LEU* 1.3 60.2 + - - +
534B TYR* 3.3 18.4 + - + +
535B VAL* 2.9 31.6 + - + +
312N ARG* 4.8 17.6 - - - +
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Residues in contact with LEU 532 (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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528B PRO 2.9 19.8 + - - +
529B ILE* 3.6 23.6 - - + +
531B LYS* 1.3 76.0 - - - +
533B CYS* 1.3 59.7 + - - +
535B VAL* 2.7 42.1 + - + +
536B LEU* 2.9 18.2 + - + +
575B PHE* 4.5 9.2 - - + -
578B LEU* 4.3 27.4 - - + -
583B LYS* 4.3 21.1 - - + -
584B VAL* 4.1 15.5 - - + -
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Residues in contact with CYS 533 (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* 2.9 15.9 + - + +
530B LYS* 2.7 20.0 + - + +
532B LEU* 1.3 72.9 - - - +
534B TYR* 1.3 59.3 + - + +
536B LEU* 3.4 12.5 + - - +
537B GLY 3.7 0.7 + - - -
538B VAL* 3.1 47.2 + - + +
555B VAL* 4.5 14.6 - - - -
557B LEU* 6.4 0.4 - - + -
562B ILE* 5.6 6.3 - - + -
571B PHE* 3.8 21.3 - - + -
575B PHE* 6.2 4.3 - - + -
601B ILE* 4.6 7.9 - - + -
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Residues in contact with TYR 534 (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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530B LYS* 2.8 71.1 + - + -
531B LYS* 3.3 16.2 - - + +
533B CYS* 1.3 74.1 - - + +
535B VAL* 1.3 66.0 + - + +
537B GLY* 2.9 15.8 + - - -
538B VAL* 3.5 19.6 + - + +
539B GLU* 5.1 0.2 - - - -
540B ASP* 3.3 49.1 + - + -
562B ILE* 3.3 18.3 - - + +
155M ASN* 5.6 6.1 - - + -
308N GLN* 4.9 4.8 - - - +
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Residues in contact with VAL 535 (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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531B LYS* 2.9 22.6 + - + +
532B LEU* 2.7 32.3 + - + +
534B TYR* 1.3 72.7 - - + +
536B LEU* 1.3 56.2 + - - +
537B GLY* 3.1 4.4 + - - -
310N PRO* 4.0 32.3 - - + +
311N THR* 4.3 22.7 - - + +
312N ARG* 6.3 1.1 - - + -
418N VAL 4.8 0.2 - - - +
419N THR* 3.6 10.9 + - - +
420N PRO* 4.4 10.3 - - + +
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Residues in contact with LEU 536 (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* 2.9 17.8 + - + +
533B CYS* 3.4 6.2 + - - +
534B TYR 3.1 0.8 - - - -
535B VAL* 1.3 74.9 - - - +
537B GLY* 1.3 56.3 + - - +
538B VAL 3.8 1.3 - - - -
565B ILE* 3.6 7.4 - - + +
570B LYS* 5.3 5.1 + - - +
571B PHE* 3.3 46.7 - - + +
574B GLN* 3.9 28.3 - - + +
575B PHE* 4.3 17.3 - - + +
578B LEU* 4.4 18.6 - - + -
419N THR* 3.0 28.2 + - + +
420N PRO 5.8 0.2 - - - +
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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