Contacts of the helix formed by residues 551 - 555 (chain C) in PDB entry 5DO7
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 551 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547C GLY 3.8 4.9 - - - -
548C PHE 4.8 6.2 + - - -
550C ARG* 1.3 69.8 - - - +
552C ILE* 1.3 53.0 + - - +
553C GLN* 2.7 3.7 + - + +
554C GLU* 2.4 53.3 + - + +
555C MET 4.4 0.4 - - - -
611C LYS* 3.9 38.2 + - - +
612C THR* 4.1 19.9 - - - +
446D MET* 3.3 16.4 - - - +
447D ASP* 2.9 32.6 + - - +
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Residues in contact with ILE 552 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544C VAL 4.5 3.6 - - - +
545C GLY 5.2 2.7 - - - +
547C GLY* 3.9 20.5 + - - +
550C ARG 2.6 12.9 + - - -
551C ASN* 1.3 66.4 - - - +
553C GLN* 1.3 75.2 + - + +
555C MET* 2.8 35.5 + - + +
560C LYS* 4.3 9.6 - - + +
563C SER* 3.3 32.8 - - - +
564C TYR* 5.2 4.5 - - + -
569C LYS* 3.5 34.1 - - + +
573C GLU* 4.2 9.6 - - - +
612C THR 3.4 19.2 + - - +
613C CYS* 4.9 3.6 - - + -
614C PRO* 5.6 1.6 - - + -
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Residues in contact with GLN 553 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648A LEU* 3.4 55.8 - - - +
551C ASN* 2.7 5.2 + - + +
552C ILE* 1.3 82.8 - - + +
554C GLU* 1.3 59.9 + - - +
555C MET 3.4 0.3 + - - -
560C LYS* 3.6 28.2 + - - +
564C TYR* 5.7 0.2 + - - -
611C LYS 5.6 4.0 - - - +
612C THR 4.9 5.6 - - - +
614C PRO* 4.3 21.3 - - + +
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Residues in contact with GLU 554 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550C ARG* 3.1 29.7 + - - +
551C ASN* 2.4 42.8 + - + +
553C GLN* 1.3 69.6 - - - +
555C MET* 1.3 61.4 + - - +
556C PRO* 3.9 0.5 - - - +
440D SER* 6.2 0.3 - - - -
441D ILE* 4.5 25.7 - - + +
442D GLN 3.4 21.0 - - - +
444D SER* 3.8 8.4 + - - -
446D MET* 5.0 2.3 - - - +
447D ASP* 3.3 14.9 - - - +
617D LEU* 3.4 20.3 - - - +
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Residues in contact with MET 555 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543C LEU 5.0 0.2 - - - +
544C VAL* 3.5 33.0 - - - +
550C ARG* 3.5 46.4 - - + +
551C ASN 3.6 0.8 + - - -
552C ILE* 2.8 30.3 + - - +
554C GLU* 1.3 76.5 - - - +
556C PRO* 1.4 75.3 - - + +
557C ILE 3.6 1.2 + - - -
559C PHE* 3.4 28.9 - - - +
560C LYS* 3.5 38.1 + - - +
563C SER* 4.9 0.7 - - - -
434D LEU* 4.6 5.8 - - + -
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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