Contacts of the helix formed by residues 569 - 578 (chain C) in PDB entry 2DB3
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 LYS 569 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403C ARG* 6.2 1.1 - - - +
406C ASP* 5.3 9.7 + - - +
567C PRO* 3.6 6.4 - - - +
568C SER* 1.3 91.7 + - - +
570C ILE* 1.3 66.9 + - + +
571C ASP* 3.3 7.6 - - + +
572C ASP* 3.1 26.3 + - + +
573C TYR 3.5 3.1 + - - -
601C ILE* 3.6 3.4 - - - -
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Residues in contact with ILE 570 (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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569C LYS* 1.3 71.5 - - - +
571C ASP* 1.3 79.5 + - - +
573C TYR* 2.8 34.7 + - + +
574C VAL* 3.0 10.7 + - - +
601C ILE* 3.5 19.4 - - + +
604C ASP* 3.8 31.5 + - + +
605C LEU* 3.7 34.8 - - + +
608C ILE* 3.8 29.6 - - + -
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Residues in contact with ASP 571 (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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402C ASP* 4.6 0.9 - - - +
434C THR* 3.3 35.6 + - + +
435C PHE 4.9 0.3 + - - -
436C PRO* 3.2 31.1 - - - +
459C GLY* 4.6 7.8 - - - +
551C ARG* 4.9 6.3 - - - +
569C LYS* 3.3 6.2 - - + +
570C ILE* 1.3 92.6 - - - +
572C ASP* 1.3 61.4 + - - +
574C VAL* 3.3 5.6 + - - +
575C HIS* 3.1 31.2 + - + -
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Residues in contact with ASP 572 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547C SER* 2.7 26.1 + - - -
550C SER* 3.2 23.6 + - - -
551C ARG* 5.2 6.2 + - - +
567C PRO* 3.5 20.2 - - + +
569C LYS* 3.1 17.7 + - + +
570C ILE 3.1 0.8 - - - -
571C ASP* 1.3 76.6 - - - +
573C TYR* 1.3 65.7 + - - +
575C HIS* 3.4 5.9 + - - +
576C ARG* 3.0 33.0 + - - +
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Residues in contact with TYR 573 (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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467C GLN* 2.7 42.9 + - - +
469C ILE* 3.8 10.3 - - + +
563C ASN* 3.8 16.2 - - - -
566C MET* 4.0 17.3 - - + -
567C PRO* 3.7 17.6 - - + +
569C LYS 3.5 2.4 + - - -
570C ILE* 2.8 27.2 + - + +
572C ASP* 1.3 78.5 - - - +
574C VAL* 1.3 71.0 + - + +
576C ARG* 3.1 5.9 + - - +
577C ILE* 3.0 43.9 + - + +
589C ALA* 5.4 0.5 - - - +
591C SER* 3.4 24.5 + - - -
601C ILE* 4.9 1.8 - - + -
605C LEU* 3.7 19.5 - - + +
608C ILE* 3.9 12.3 - - + -
609C LEU* 4.2 0.3 - - - +
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Residues in contact with VAL 574 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C THR* 4.0 12.5 + - + +
433C ALA* 4.9 3.8 - - + +
434C THR* 4.1 14.1 - - + -
459C GLY 3.5 21.3 - - - +
460C GLY 3.8 19.5 - - - +
461C ALA* 4.1 12.7 - - + +
462C CYS 5.3 1.3 + - - +
570C ILE 3.0 14.5 + - - +
571C ASP* 3.6 9.2 - - - +
573C TYR* 1.3 84.5 - - + +
575C HIS* 1.3 62.2 + - - +
577C ILE* 3.6 8.0 - - - +
578C GLY* 3.3 17.8 + - - -
608C ILE* 3.7 25.4 - - + -
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Residues in contact with HIS 575 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C THR* 4.2 7.0 - - - +
400C GLU* 3.3 24.9 + - - -
432C SER* 3.9 4.3 - - - -
433C ALA* 3.8 27.3 - - + +
434C THR* 2.8 29.8 + - + +
550C SER* 3.2 16.2 - - - +
551C ARG* 3.2 36.6 + - + +
571C ASP 3.1 26.4 + - - +
572C ASP* 3.9 6.3 - - - +
574C VAL* 1.3 76.2 - - - +
576C ARG* 1.3 61.6 + - - +
578C GLY 3.1 4.0 + - - -
579C ARG* 2.9 34.6 + - - +
2903C ANP 4.7 1.7 + - - -
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Residues in contact with ARG 576 (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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495C PHE* 3.6 38.6 + - + +
496C VAL 4.0 19.2 + - - -
497C GLU* 4.9 7.3 + - - +
547C SER* 2.9 29.5 + - - +
550C SER* 3.4 20.2 - - - -
561C VAL* 3.6 10.2 - - + +
563C ASN* 2.9 30.0 + - - +
565C ASP* 3.0 24.7 + - - +
567C PRO* 3.5 20.7 - - - +
572C ASP* 3.0 28.1 + - - +
573C TYR* 3.1 6.3 + - - +
575C HIS* 1.3 76.9 - - - +
577C ILE* 1.3 62.8 + - - +
578C GLY 3.0 1.1 + - - -
579C ARG* 3.2 20.8 + - - +
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Residues in contact with ILE 577 (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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461C ALA* 4.1 13.5 - - + -
462C CYS* 5.2 2.9 - - + +
465C VAL* 3.6 15.8 - - + +
467C GLN* 3.4 40.8 - - + +
561C VAL* 4.0 8.7 - - + -
563C ASN* 3.6 24.2 - - - +
573C TYR* 3.0 34.4 + - + +
574C VAL* 3.6 11.7 - - - +
576C ARG* 1.3 74.9 - - - +
578C GLY* 1.3 60.6 + - - +
579C ARG 3.1 4.7 + - - -
580C THR* 3.4 23.0 - - - +
589C ALA* 3.8 21.8 - - + -
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Residues in contact with GLY 578 (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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291C THR* 3.2 25.6 + - - -
462C CYS* 5.5 0.9 - - - -
465C VAL* 4.8 3.4 - - - -
574C VAL 3.3 7.6 + - - -
575C HIS 3.1 8.0 + - - -
576C ARG 3.0 2.0 - - - -
577C ILE* 1.3 75.5 - - - +
579C ARG* 1.3 64.0 + - - +
580C THR 3.0 15.1 + - - +
582C ARG* 2.9 26.2 + - - +
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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