Contacts of the helix formed by residues 541 - 550 (chain B) in PDB entry 3HN8
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 ASP 541 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298B CYS* 5.0 1.9 - - - -
421B LEU* 5.6 0.5 - - - -
422B GLU* 3.4 36.0 + - - +
534B ARG* 6.1 0.4 - - - +
539B ALA* 3.8 3.6 - - - +
540B ALA* 1.3 77.6 - - + +
542B PRO* 1.3 77.5 - - - +
543B HIS* 3.0 26.7 + - - +
544B GLY* 2.7 32.5 + - - +
545B ARG* 3.3 6.8 + - - +
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Residues in contact with PRO 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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295B GLY* 5.4 4.4 - - - -
297B PRO* 3.9 40.2 - - + +
298B CYS* 4.7 11.2 - - + -
422B GLU* 6.6 0.2 - - - -
540B ALA 3.4 8.5 - - - +
541B ASP* 1.3 90.7 - - - +
543B HIS* 1.3 52.5 + - - +
545B ARG* 3.0 32.8 + - - +
546B GLU* 2.7 38.0 + - - +
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Residues in contact with HIS 543 (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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298B CYS* 3.6 9.4 - - - -
419B ASP* 4.0 12.1 - - + -
420B ILE 6.1 0.2 - - - +
421B LEU* 3.5 21.3 - - + +
422B GLU 6.4 0.2 - - - +
541B ASP* 3.0 18.2 + - - +
542B PRO* 1.3 79.6 - - - +
544B GLY* 1.3 61.2 + - - +
546B GLU* 3.4 21.4 + - + +
547B HIS* 3.4 10.4 + - - +
561B HIS* 3.8 26.4 + + - -
562B TRP 2.7 30.6 + - - -
563B HIS* 3.4 23.0 + + - -
564B GLN 5.6 0.2 - - - -
700B ZN 2.2 39.7 - - - -
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Residues in contact with GLY 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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534B ARG 3.8 18.6 - - - -
535B VAL* 2.9 33.9 - - - +
536B GLY 3.5 1.3 + - - -
539B ALA* 4.4 2.9 - - - -
541B ASP* 2.7 24.3 + - - +
543B HIS* 1.3 77.1 - - - +
545B ARG* 1.3 56.8 + - - -
547B HIS 3.6 2.8 + - - -
548B TRP 3.7 0.3 + - - -
563B HIS* 4.0 9.2 - - - -
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Residues in contact with ARG 545 (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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297B PRO* 5.5 6.1 - - - +
536B GLY 3.0 26.2 + - - +
537B PRO* 4.3 4.3 - - + -
538B GLU 4.7 4.9 - - - +
539B ALA* 2.9 30.6 + - + +
540B ALA 3.9 8.5 + - - -
541B ASP 3.3 3.1 + - - +
542B PRO* 3.4 38.9 - - - +
544B GLY* 1.3 73.9 - - - +
546B GLU* 1.3 61.3 + - - +
547B HIS 3.1 1.3 - - - -
548B TRP* 3.8 1.5 - - - +
549B ALA* 2.8 29.9 + - - +
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Residues in contact with GLU 546 (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 GLY* 2.9 39.9 + - - +
298B CYS* 4.0 3.3 - - - +
419B ASP* 2.9 11.9 - - - +
542B PRO 2.7 16.3 + - - +
543B HIS* 3.4 18.1 + - + +
545B ARG* 1.3 74.0 - - - +
547B HIS* 1.3 62.4 + - + +
549B ALA* 3.4 8.3 - - - +
550B GLU* 3.0 41.5 + - - +
561B HIS* 4.3 10.0 - - - +
700B ZN 2.7 32.1 - - - -
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Residues in contact with HIS 547 (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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435B PHE* 3.2 38.4 - + - -
437B LEU* 3.6 10.4 - - + +
535B VAL* 3.6 5.2 - - + +
543B HIS* 3.4 15.0 + - + +
544B GLY 3.7 6.7 - - - +
545B ARG 3.1 0.2 - - - -
546B GLU* 1.3 82.6 - - + +
548B TRP* 1.3 59.8 + - - +
550B GLU* 3.6 4.9 + - - +
551B MET* 3.1 22.7 + - - +
559B VAL* 3.0 32.9 + - + +
561B HIS* 3.2 35.4 - + + +
563B HIS* 2.7 24.5 + - + -
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Residues in contact with TRP 548 (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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437B LEU* 3.7 11.4 - - + +
446B LEU* 3.8 12.9 - - + +
473B LEU* 5.7 0.2 - - + -
509B VAL* 2.6 48.7 - - + -
510B GLU* 3.9 4.0 - - - -
512B VAL* 3.3 32.3 - - + -
513B GLY* 4.1 2.7 - - - -
514B LEU* 3.2 19.8 - - + +
535B VAL* 3.7 28.1 + - + +
536B GLY* 3.3 24.5 - - - +
537B PRO* 3.8 13.2 - - + -
544B GLY 3.7 2.2 + - - -
545B ARG 3.4 5.0 + - - +
547B HIS* 1.3 76.3 - - - +
549B ALA* 1.3 63.1 + - - +
551B MET* 3.3 29.5 + - + +
552B LEU* 3.0 52.0 + - + +
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Residues in contact with ALA 549 (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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545B ARG 2.8 20.0 + - - +
546B GLU* 3.4 11.2 - - - +
547B HIS 3.2 0.2 - - - -
548B TRP* 1.3 79.8 - - - +
550B GLU* 1.3 56.3 + - - +
552B LEU* 2.8 24.4 - - - +
553B ALA* 4.0 5.4 - - - +
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Residues in contact with GLU 550 (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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546B GLU* 3.0 30.7 + - - +
547B HIS* 3.6 9.4 - - - +
549B ALA* 1.3 73.9 - - - +
551B MET* 1.3 57.5 + - - +
552B LEU 2.8 14.5 - - - +
553B ALA* 4.7 2.0 - - - -
554B ASN* 3.3 25.3 - - - +
559B VAL* 3.7 22.0 - - + +
561B HIS* 2.6 36.6 + - - -
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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