Contacts of the helix formed by residues 541 - 550 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A CYS* 5.1 1.9 - - - -
421A LEU* 5.7 0.7 - - - -
422A GLU* 3.4 35.2 + - - +
534A ARG* 6.1 0.6 - - - +
539A ALA* 3.8 3.2 - - - +
540A ALA* 1.3 78.1 - - + +
542A PRO* 1.3 78.7 - - - +
543A HIS* 3.0 26.7 + - - +
544A GLY* 2.7 32.8 + - - +
545A ARG* 3.3 6.9 + - - +
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Residues in contact with PRO 542 (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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295A GLY* 5.3 3.5 - - - -
297A PRO* 3.9 40.4 - - + +
298A CYS* 4.7 11.7 - - + -
422A GLU* 6.6 0.2 - - - -
540A ALA 3.4 8.2 - - - +
541A ASP* 1.3 88.1 - - - +
543A HIS* 1.3 52.1 + - - +
545A ARG* 3.0 33.6 + - - +
546A GLU* 2.7 37.5 + - - +
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Residues in contact with HIS 543 (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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298A CYS* 3.6 8.8 - - - -
419A ASP* 4.0 11.2 - - + -
420A ILE 6.1 0.2 - - - +
421A LEU* 3.5 21.1 - - + +
541A ASP* 3.0 19.5 + - - +
542A PRO* 1.3 78.3 - - - +
544A GLY* 1.3 61.9 + - - +
546A GLU* 3.3 21.0 + - - +
547A HIS* 3.4 10.4 + - - +
561A HIS* 3.8 27.3 + + + -
562A TRP 2.7 28.9 + - - -
563A HIS* 3.4 22.2 + + - -
564A GLN 5.6 0.2 - - - -
700A ZN 2.2 39.9 - - - -
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Residues in contact with GLY 544 (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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534A ARG 3.8 18.8 - - - -
535A VAL* 2.9 33.9 - - - +
536A GLY 3.5 1.1 + - - -
539A ALA* 4.4 3.1 - - - -
541A ASP* 2.7 24.6 + - - +
543A HIS* 1.3 75.5 - - - +
545A ARG* 1.3 58.1 + - - -
547A HIS 3.6 2.4 + - - -
548A TRP 3.7 0.5 + - - -
563A HIS* 4.1 9.6 + - - -
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Residues in contact with ARG 545 (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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297A PRO* 5.5 5.5 - - - +
536A GLY 3.0 26.5 - - - +
537A PRO* 4.3 4.0 - - + -
538A GLU 4.7 4.7 - - - +
539A ALA* 2.9 30.3 + - + +
540A ALA 3.9 8.9 + - - -
541A ASP 3.3 3.9 + - - +
542A PRO* 3.4 38.7 - - - +
544A GLY* 1.3 72.9 - - - +
546A GLU* 1.3 60.0 + - - +
547A HIS 3.1 1.8 - - - -
548A TRP* 3.8 1.7 - - - +
549A ALA* 2.8 29.3 + - - +
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Residues in contact with GLU 546 (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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295A GLY* 2.9 40.0 + - - +
298A CYS* 4.0 4.0 - - - +
419A ASP* 2.9 10.6 - - - +
542A PRO 2.7 16.8 + - - +
543A HIS* 3.3 19.4 + - + +
545A ARG* 1.3 74.0 - - - +
547A HIS* 1.3 63.1 + - + +
549A ALA* 3.4 8.1 - - - +
550A GLU* 3.0 41.5 + - - +
561A HIS* 4.3 9.5 - - - +
700A ZN 2.6 31.7 - - - -
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Residues in contact with HIS 547 (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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435A PHE* 3.2 38.4 - + - -
437A LEU* 3.6 11.5 - - + +
535A VAL* 3.6 5.5 - - + +
543A HIS 3.5 14.4 - - - +
544A GLY 3.7 6.3 - - - +
545A ARG 3.1 0.4 - - - -
546A GLU* 1.3 82.6 - - + +
548A TRP* 1.3 59.6 + - - +
550A GLU* 3.6 4.8 + - - +
551A MET* 3.1 23.0 + - - +
559A VAL* 3.0 33.9 + - + +
561A HIS* 3.3 34.3 - + + +
563A HIS* 2.7 24.7 + + + -
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Residues in contact with TRP 548 (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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437A LEU* 3.7 11.2 - - + +
446A LEU* 3.8 13.8 - - + +
473A LEU* 5.7 0.2 - - + -
509A VAL* 2.6 49.6 - - + -
510A GLU* 3.9 4.7 - - - -
512A VAL* 3.3 30.1 - - + -
513A GLY* 4.0 3.1 - - - -
514A LEU* 3.2 20.0 - - + +
535A VAL* 3.7 28.6 + - + +
536A GLY* 3.3 23.3 - - - +
537A PRO* 3.9 14.1 - - + -
544A GLY 3.7 2.0 + - - -
545A ARG 3.4 5.3 + - - +
546A GLU 3.4 0.2 - - - -
547A HIS* 1.3 77.2 - - - +
549A ALA* 1.3 64.5 + - - +
551A MET* 3.3 27.9 + - + +
552A LEU* 3.0 52.8 + - + +
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Residues in contact with ALA 549 (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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545A ARG 2.8 19.6 + - - +
546A GLU* 3.4 11.2 - - - +
548A TRP* 1.3 79.3 - - - +
550A GLU* 1.3 58.0 + - - +
552A LEU* 2.8 25.0 + - - +
553A ALA* 4.0 5.5 - - - +
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Residues in contact with GLU 550 (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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546A GLU* 3.0 31.5 + - - +
547A HIS* 3.6 9.6 - - - +
549A ALA* 1.3 74.7 - - + +
551A MET* 1.3 59.0 + - - +
552A LEU 2.8 13.6 - - - +
553A ALA* 4.8 2.2 - - - -
554A ASN* 3.3 25.7 - - - +
559A VAL* 3.7 20.8 - - + +
561A HIS* 2.6 35.5 + - - -
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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