Contacts of the helix formed by residues 533 - 545 (chain B) in PDB entry 2C6N
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 SER 533 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B LEU* 4.1 8.1 - - - +
519B ALA* 3.9 24.7 - - - -
530B ILE* 3.2 16.4 + - - +
531B TYR 3.0 6.2 + - - -
532B ARG* 1.3 75.1 - - - +
534B THR* 1.3 59.7 + - - +
535B LYS* 4.6 1.8 - - - -
536B ALA* 3.7 18.4 - - - +
537B GLY* 3.1 22.2 + - - -
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Residues in contact with THR 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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303B SER 4.4 4.7 - - - +
304B LEU 4.1 9.2 - - - +
305B GLU* 3.7 36.6 - - + +
532B ARG 2.9 11.4 + - - +
533B SER* 1.3 70.7 - - - +
535B LYS* 1.3 68.9 + - - +
536B ALA 3.1 0.2 - - - -
537B GLY* 3.1 0.7 + - - -
538B ALA* 2.8 27.3 + - - +
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Residues in contact with LYS 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B GLU* 3.4 34.9 - - - +
519B ALA* 5.1 1.8 - - - -
533B SER* 5.1 1.1 - - - -
534B THR* 1.3 85.4 + - - +
536B ALA* 1.3 61.9 + - - +
538B ALA* 3.6 7.4 + - - +
539B LYS* 3.4 15.2 + - - +
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Residues in contact with ALA 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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304B LEU* 5.7 0.2 - - + -
515B LEU* 3.8 34.9 - - + +
518B GLU* 4.3 5.8 + - - -
519B ALA* 4.4 1.6 - - + -
530B ILE* 4.4 11.2 - - + -
533B SER* 3.5 21.7 + - - +
534B THR 3.1 0.4 - - - -
535B LYS* 1.3 75.5 - - - +
537B GLY* 1.3 57.4 - - - +
538B ALA 3.0 1.3 - - - -
539B LYS* 2.5 34.2 + - - +
540B LEU* 2.9 11.9 + - - +
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Residues in contact with GLY 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LEU* 3.5 38.0 - - - +
533B SER 3.1 9.8 + - - -
534B THR 3.5 0.7 - - - -
536B ALA* 1.3 78.1 - - - +
538B ALA* 1.3 50.0 + - - +
540B LEU* 3.2 7.6 + - - +
541B ARG* 2.6 43.5 + - - +
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Residues in contact with ALA 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LEU 4.5 0.4 + - - -
534B THR 2.8 15.9 + - - +
535B LYS* 3.7 7.6 - - - +
537B GLY* 1.3 77.4 - - - +
539B LYS* 1.3 61.8 + - - +
541B ARG* 3.2 5.8 + - - +
542B LYS* 3.1 27.6 + - - +
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Residues in contact with LYS 539 (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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514B ALA 5.8 1.3 - - - +
515B LEU* 6.2 2.5 - - + -
518B GLU* 4.8 18.8 - - + +
535B LYS 3.4 9.9 + - - +
536B ALA* 2.5 24.6 + - - +
538B ALA* 1.3 74.7 - - - +
540B LEU* 1.3 56.4 + - - -
542B LYS* 3.8 9.4 + - - +
543B VAL* 3.6 19.4 - - - +
559B MET* 4.1 19.5 - - + +
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Residues in contact with LEU 540 (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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301B PHE* 6.1 1.3 - - + -
304B LEU* 5.9 4.5 - - + -
391B ILE* 4.0 18.8 - - + +
394B VAL* 5.8 5.2 - - + -
395B LEU* 4.2 26.2 - - + -
511B PHE* 6.1 2.2 - - + -
515B LEU* 6.5 1.1 - - + -
536B ALA 2.9 8.6 + - - +
537B GLY* 3.7 9.9 - - - +
539B LYS* 1.3 76.7 - - - +
541B ARG* 1.3 74.3 + - + +
542B LYS 2.9 1.5 + - - -
543B VAL* 3.5 16.0 + - + -
544B LEU* 3.1 41.2 - - + +
559B MET* 4.6 16.8 - - + +
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Residues in contact with ARG 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B PHE* 2.6 39.6 + - - -
304B LEU* 4.4 10.3 + - - +
305B GLU* 3.3 8.6 - - - +
306B LEU* 2.5 53.3 - - + +
307B SER 3.7 7.1 + - - +
367B GLN* 3.4 30.7 - - - +
371B GLN* 3.9 22.7 - - - +
395B LEU* 5.9 0.2 - - - +
537B GLY* 2.6 33.0 + - - +
538B ALA* 3.2 6.1 + - - +
540B LEU* 1.3 83.3 - - - +
542B LYS* 1.3 61.1 + - - +
543B VAL 3.2 0.9 - - - -
544B LEU* 3.8 14.7 - - - +
545B GLN* 3.3 30.6 + - + +
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Residues in contact with LYS 542 (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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538B ALA 3.1 16.4 + - - +
539B LYS* 4.0 9.2 - - - +
540B LEU 2.9 1.6 - - - -
541B ARG* 1.3 80.1 - - - +
543B VAL* 1.3 61.3 + - + +
545B GLN* 4.2 7.6 + - + +
546B ALA* 3.9 14.6 + - - +
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Residues in contact with VAL 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B TYR* 3.8 10.9 + - - +
383B ALA* 5.8 1.2 - - - +
387B PHE* 5.3 14.1 - - + -
391B ILE* 4.6 6.7 - - + -
511B PHE* 5.5 1.8 - - + -
539B LYS 3.6 15.9 - - - +
540B LEU* 3.5 26.0 - - + +
542B LYS* 1.3 78.4 - - + +
544B LEU* 1.3 77.9 + - + +
545B GLN 3.3 0.2 - - - -
546B ALA* 3.1 19.4 + - - +
547B GLY 3.7 2.9 + - - +
555B VAL* 4.4 18.1 - - + +
558B ASP* 6.4 0.2 - - + -
559B MET* 3.8 34.8 - - + -
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Residues in contact with LEU 544 (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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367B GLN* 3.7 26.0 - - + +
368B TYR* 3.4 36.4 - - + +
371B GLN* 3.4 35.4 - - + -
372B TYR* 3.6 9.4 - - - +
391B ILE* 3.3 38.4 - - + -
540B LEU* 3.1 28.9 + - + +
541B ARG* 4.1 8.5 - - - +
543B VAL* 1.3 83.1 - - + +
545B GLN* 1.3 58.5 + - - +
546B ALA 2.9 5.9 + - - -
547B GLY 3.0 11.3 + - - -
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Residues in contact with GLN 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B LEU* 6.3 0.6 - - - +
371B GLN* 3.4 38.5 + - - +
372B TYR* 4.4 6.5 - - - +
374B ASP* 6.2 0.5 - - - +
375B LEU* 6.0 1.2 - - - +
541B ARG* 3.3 20.3 + - - +
542B LYS* 4.5 6.5 - - + +
543B VAL 3.3 0.2 - - - -
544B LEU* 1.3 78.2 - - - +
546B ALA* 1.3 59.6 + - - +
547B GLY 3.3 0.4 - - - -
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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