Contacts of the helix formed by residues 547 - 557 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428B SER 3.8 4.4 + - - -
430B SER 3.1 24.5 + - - -
431B PHE* 3.6 33.8 - - + -
432B ALA 5.5 0.2 - - - +
545B LEU* 4.2 1.5 - - + +
546B VAL* 1.3 74.9 - - - +
548B GLU* 1.3 60.3 + - - +
549B VAL* 3.1 7.9 + - - +
550B GLU* 2.8 46.3 + - - +
551B LEU* 2.9 27.2 + - - +
665B CYS* 4.3 2.9 - - - -
670B LEU* 3.9 14.1 - - + -
704B ARG* 3.6 26.1 - - - +
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Residues in contact with GLU 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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432B ALA* 4.0 20.3 - - + +
436B LEU* 3.9 13.4 - - + +
547B ASN* 1.3 76.3 - - - +
549B VAL* 1.3 62.4 + - - +
551B LEU* 3.5 9.6 + - - +
552B GLN* 3.1 25.1 + - - +
603B ARG* 2.6 42.4 + - - -
665B CYS* 4.5 4.7 - - - -
667B TYR* 3.5 13.2 - - - +
670B LEU* 4.4 4.3 - - + +
674B ARG* 3.8 23.8 + - - +
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Residues in contact with VAL 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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428B SER* 3.7 22.0 - - - +
430B SER* 3.9 17.3 - - - +
431B PHE 4.1 3.1 - - - +
432B ALA* 4.1 23.1 - - + +
547B ASN* 3.1 7.0 + - - +
548B GLU* 1.3 76.1 - - - +
550B GLU* 1.3 59.1 + - - +
552B GLN* 3.5 6.5 + - - +
553B ALA* 3.0 27.5 + - + +
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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
----------------------------------------------------------
426B VAL* 3.6 18.1 - - + +
427B ALA* 3.8 8.1 - - - +
428B SER* 2.9 40.0 + - - +
541B LEU* 5.9 0.9 - - + -
542B ARG* 4.4 4.9 + - - +
545B LEU 3.4 0.9 - - - +
546B VAL* 3.3 15.4 - - + -
547B ASN* 2.8 29.3 + - - +
549B VAL* 1.3 74.5 - - - +
551B LEU* 1.3 59.4 + - - +
553B ALA* 3.1 5.9 + - - +
554B ILE* 2.8 33.9 + - - +
704B ARG* 2.3 36.6 + - - -
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Residues in contact with LEU 551 (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 VAL* 4.1 19.0 - - + +
547B ASN 2.9 17.6 + - - +
548B GLU* 3.8 9.6 - - - +
550B GLU* 1.3 75.5 - - - +
552B GLN* 1.3 58.4 + - - +
554B ILE* 3.2 11.3 + - + +
555B LYS* 3.0 60.7 + - + +
599B VAL* 4.5 12.1 - - + -
603B ARG* 4.0 12.1 - - - +
641B ILE* 4.3 22.7 - - + -
643B ASP* 3.8 23.3 - - - +
665B CYS* 4.0 9.4 - - + -
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Residues in contact with GLN 552 (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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548B GLU 3.1 18.3 + - - +
549B VAL* 3.8 5.6 - - - +
551B LEU* 1.3 74.1 - - - +
553B ALA* 1.3 66.1 + - - +
555B LYS* 3.3 20.4 + - - +
556B THR* 3.1 39.0 + - - +
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Residues in contact with ALA 553 (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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424B GLN* 4.5 3.3 + - - +
426B VAL* 3.8 24.5 - - + +
549B VAL* 3.0 16.7 + - + +
550B GLU* 3.3 10.1 - - - +
552B GLN* 1.3 76.3 - - - +
554B ILE* 1.3 60.3 + - - +
556B THR* 3.4 8.0 + - - +
557B GLY* 3.1 20.6 + - - -
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Residues in contact with ILE 554 (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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426B VAL* 3.9 19.1 - - + -
522B LEU* 4.0 20.6 - - + -
539B ILE* 4.4 9.6 - - + +
541B LEU* 4.0 13.2 - - + -
546B VAL* 4.0 20.6 - - + -
550B GLU 2.8 22.2 + - - +
551B LEU* 3.2 11.0 + - + +
553B ALA* 1.3 76.2 - - - +
555B LYS* 1.3 64.3 + - + +
557B GLY* 3.0 14.0 + - - -
561B VAL* 3.6 11.4 - - + +
597B ILE* 3.8 29.2 - - + -
599B VAL* 6.1 0.9 - - + -
641B ILE* 4.0 22.0 - - + -
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Residues in contact with LYS 555 (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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551B LEU* 3.0 50.5 + - + +
552B GLN* 3.3 23.3 + - - +
554B ILE* 1.3 76.4 - - + +
556B THR* 1.3 58.3 + - - +
557B GLY 3.8 0.5 + - - +
559B LEU 5.2 1.0 - - - +
561B VAL* 4.0 34.7 - - + +
563B GLU* 4.6 17.5 + - - -
599B VAL* 4.7 17.9 - - + -
601B THR* 5.9 0.2 + - - -
603B ARG* 5.7 0.8 - - - +
643B ASP* 5.0 4.9 + - - -
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Residues in contact with THR 556 (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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552B GLN* 3.1 32.1 + - - +
553B ALA* 3.7 7.6 - - - +
554B ILE 3.1 0.6 - - - -
555B LYS* 1.3 78.0 - - - +
557B GLY* 1.3 69.3 + - - +
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Residues in contact with GLY 557 (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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424B GLN* 3.6 16.8 - - - -
539B ILE* 4.7 3.6 - - - -
553B ALA 3.1 12.0 + - - -
554B ILE 3.0 12.2 + - - -
556B THR* 1.3 87.5 - - - +
558B GLN* 1.3 64.4 + - - -
559B LEU 3.2 11.4 + - - +
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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