Contacts of the strand formed by residues 543 - 548 (chain A) in PDB entry 6N8Q
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 543 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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541A ALA* 4.1 3.1 + - + +
542A VAL* 1.3 70.3 - - - +
544A GLN* 1.3 61.3 + - - +
545A VAL* 4.4 6.5 - - + +
580A PHE 3.3 13.2 + - - +
581A VAL* 3.5 12.3 - - + +
582A LEU 2.9 29.9 + - - +
619A ARG* 2.7 52.8 + - - +
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Residues in contact with GLN 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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468A VAL 5.3 0.2 - - - +
542A VAL* 2.8 30.8 + - - +
543A GLU* 1.3 72.0 - - - +
545A VAL* 1.3 63.6 + - - +
563A ARG* 4.4 13.9 - - - +
566A ALA* 3.5 33.9 + - + +
567A ARG 3.8 15.7 + - - +
568A SER* 4.3 13.7 + - - +
582A LEU* 3.6 16.7 - - + +
584A GLN* 6.5 0.2 - - + -
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Residues in contact with VAL 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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543A GLU* 4.0 8.7 - - + +
544A GLN* 1.3 80.1 - - - +
546A GLU* 1.3 71.6 + - - +
563A ARG* 6.3 0.9 - - - -
581A VAL* 4.0 12.3 - - + -
582A LEU 2.9 7.4 + - - +
583A VAL* 3.2 5.5 - - - -
584A GLN* 2.8 27.9 + - - +
614A PHE* 3.5 33.9 - - + -
619A ARG 3.6 22.0 - - - +
620A ARG* 5.1 0.2 - - - -
621A GLN* 4.3 10.1 - - + +
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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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545A VAL* 1.3 79.9 - - - +
547A ALA* 1.3 62.9 + - - +
548A ASP* 3.8 23.1 + - - +
563A ARG* 4.4 13.7 + - - +
584A GLN* 3.4 12.1 - - - +
586A GLN* 3.3 34.0 + - + +
621A GLN* 3.5 16.1 + - - +
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Residues in contact with ALA 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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546A GLU* 1.3 72.1 - - - +
548A ASP* 1.3 62.6 + - - +
549A LEU* 3.3 8.3 + - + +
551A GLN* 5.6 0.4 - - - +
583A VAL* 4.1 11.9 - - + -
584A GLN 3.1 10.6 + - - +
585A CYS* 3.7 5.3 - - - -
586A GLN* 2.9 22.9 + - - +
605A PHE* 4.2 13.0 - - + -
621A GLN* 3.3 31.4 - - - +
624A VAL* 4.4 10.1 - - + -
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Residues in contact with ASP 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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546A GLU* 3.8 15.7 + - - +
547A ALA* 1.3 69.1 - - - +
549A LEU* 1.3 61.1 + - - +
550A LEU* 3.3 27.7 - - - +
551A GLN* 3.3 61.0 + - + +
586A GLN* 3.4 24.8 - - - +
624A VAL* 3.3 12.1 - - - +
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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