Contacts of the helix formed by residues 547 - 557 (chain A) in PDB entry 1OFD
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 ASN 547 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428A SER 3.8 9.3 + - - -
430A SER 3.1 23.7 + - - -
431A PHE* 3.5 38.6 - - + -
432A ALA 5.7 0.2 - - - +
545A LEU* 4.7 1.1 - - + -
546A VAL* 1.3 74.5 - - - +
548A GLU* 1.3 59.9 + - - +
549A VAL* 3.1 9.5 + - - +
550A GLU* 2.9 36.4 + - - +
551A LEU* 2.8 26.7 + - - +
665A CYS* 4.4 2.5 - - - -
670A LEU* 4.1 12.8 - - + -
704A ARG* 3.5 17.1 - - - +
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Residues in contact with GLU 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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432A ALA* 4.1 19.2 - - + +
436A LEU* 3.8 16.0 - - + +
547A ASN* 1.3 75.2 - - - +
549A VAL* 1.3 62.8 + - - +
551A LEU* 3.5 9.0 + - - +
552A GLN* 3.1 23.9 + - - +
603A ARG* 2.7 39.0 + - - -
665A CYS* 4.5 7.1 - - - -
667A TYR* 3.6 13.5 - - - +
670A LEU* 4.5 5.2 - - + +
674A ARG* 3.8 23.7 + - - +
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Residues in contact with VAL 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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428A SER* 3.6 24.2 - - - +
430A SER* 4.1 14.6 - - - +
431A PHE 4.2 2.7 - - - +
432A ALA* 4.1 22.9 - - + +
547A ASN* 3.1 8.0 + - - +
548A GLU* 1.3 76.9 - - - +
550A GLU* 1.3 60.7 + - - +
552A GLN* 3.4 6.1 + - - +
553A ALA* 3.1 23.3 + - + +
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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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426A VAL* 3.7 14.8 - - + +
427A ALA* 3.7 12.1 - - - -
428A SER* 2.8 41.9 + - - +
541A LEU* 6.0 0.4 - - + -
542A ARG* 4.4 3.6 + - - -
545A LEU 3.4 1.9 - - - +
546A VAL* 3.4 15.8 - - + +
547A ASN* 2.9 28.9 + - - +
549A VAL* 1.3 71.9 - - - +
551A LEU* 1.3 61.0 - - - +
553A ALA* 3.2 4.5 + - - +
554A ILE* 2.9 35.7 + - - +
704A ARG* 2.5 36.3 + - - -
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Residues in contact with LEU 551 (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 VAL* 4.2 10.9 - - + +
547A ASN 2.8 19.5 + - - +
548A GLU* 3.9 9.6 - - - +
549A VAL 3.4 0.2 - - - -
550A GLU* 1.3 73.8 - - - +
552A GLN* 1.3 61.3 + - - +
554A ILE* 3.3 14.0 + - + +
555A LYS* 3.1 52.0 + - + +
599A VAL* 4.5 11.9 - - + -
603A ARG* 3.9 13.0 - - - +
641A ILE* 4.2 25.4 - - + -
643A ASP* 3.8 24.7 - - - +
665A CYS* 4.0 11.9 - - + -
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Residues in contact with GLN 552 (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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548A GLU 3.1 17.9 + - - +
549A VAL* 3.8 5.4 - - - +
550A GLU 3.3 0.2 - - - -
551A LEU* 1.3 75.2 - - - +
553A ALA* 1.3 58.3 + - - +
555A LYS* 3.2 23.9 + - - +
556A THR* 3.0 36.6 + - - +
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Residues in contact with ALA 553 (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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424A GLN* 4.6 3.0 + - - +
426A VAL* 3.8 25.7 - - + +
549A VAL* 3.1 15.9 + - + +
550A GLU* 3.4 9.4 - - - +
552A GLN* 1.3 74.9 - - - +
554A ILE* 1.3 63.3 + - - +
556A THR* 3.5 8.0 - - - -
557A GLY* 3.0 20.4 + - - -
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Residues in contact with ILE 554 (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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426A VAL* 4.0 20.0 - - + -
522A LEU* 3.9 21.1 - - + -
539A ILE* 4.4 8.3 - - + +
541A LEU* 4.0 6.3 - - + -
546A VAL* 3.9 28.0 - - + -
550A GLU 2.9 20.8 + - - +
551A LEU* 3.6 12.6 - - + +
553A ALA* 1.3 77.2 - - - +
555A LYS* 1.3 63.5 + - + +
557A GLY* 3.0 13.3 + - - -
561A VAL* 3.6 12.8 - - + +
597A ILE* 3.8 29.4 - - + -
599A VAL* 5.9 0.7 - - + -
641A ILE* 3.9 21.5 - - + -
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Residues in contact with LYS 555 (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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551A LEU* 3.1 48.5 + - + +
552A GLN* 3.2 28.0 + - - +
554A ILE* 1.3 72.5 - - + +
556A THR* 1.3 66.9 + - - +
559A LEU 5.2 0.2 - - - +
561A VAL* 4.1 30.5 - - + +
563A GLU* 4.5 16.8 + - - -
599A VAL* 4.8 15.2 - - + +
601A THR* 5.9 0.4 + - - -
603A ARG* 5.6 0.6 - - - +
643A ASP* 5.0 4.6 + - - -
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Residues in contact with THR 556 (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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424A GLN* 6.0 0.9 - - - +
552A GLN* 3.0 23.7 + - - +
553A ALA* 3.5 11.6 - - - -
554A ILE 3.6 0.7 - - - -
555A LYS* 1.3 79.4 - - - +
557A GLY* 1.3 74.4 - - - +
559A LEU 4.4 3.3 - - - +
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Residues in contact with GLY 557 (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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424A GLN* 3.5 17.7 - - - -
539A ILE* 4.5 3.6 - - - -
553A ALA 3.0 8.7 + - - -
554A ILE 3.0 13.5 + - - -
556A THR* 1.3 97.3 - - - +
558A GLN* 1.3 63.7 + - - -
559A LEU 3.2 8.4 + - - +
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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