Contacts of the helix formed by residues 601 - 612 (chain B) 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 ILE 601 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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566B MET* 4.0 30.7 - - + -
567B PRO* 3.4 28.7 - - + +
568B SER 4.4 8.1 - - - +
569B LYS 3.8 4.3 - - - +
570B ILE* 3.8 42.2 - - + +
573B TYR* 5.0 0.2 - - + -
593B PHE* 4.2 3.6 - - + -
598B ASP* 3.3 26.4 + - + +
599B ARG 3.2 1.2 - - - -
600B ALA* 1.3 78.0 - - - +
602B ALA* 1.3 65.0 + - - +
603B ALA 3.4 1.3 - - - -
604B ASP* 3.5 8.4 + - + +
605B LEU* 3.0 17.1 + - + +
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Residues in contact with ALA 602 (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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593B PHE* 3.9 24.2 - - + -
598B ASP 3.7 0.6 + - - -
599B ARG* 3.4 13.7 + - - +
600B ALA 3.5 0.2 - - - -
601B ILE* 1.3 77.3 - - - +
603B ALA* 1.3 67.8 + - - +
605B LEU* 2.9 8.7 + - - +
606B VAL* 2.9 28.2 + - - +
620B LEU* 3.7 25.1 - - + +
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Residues in contact with ALA 603 (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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599B ARG 4.9 0.8 + - - -
600B ALA 4.9 5.3 + - - +
601B ILE 3.4 0.6 - - - -
602B ALA* 1.3 79.9 - - - +
604B ASP* 1.3 67.9 + - - +
606B VAL* 3.1 20.6 + - - +
607B LYS* 3.2 14.7 + - + +
620B LEU 5.1 0.9 + - - -
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Residues in contact with ASP 604 (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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570B ILE* 3.7 38.4 + - + +
600B ALA 4.9 7.0 - - - +
601B ILE* 3.5 11.2 + - + +
602B ALA 3.2 0.6 - - - -
603B ALA* 1.3 80.0 - - - +
605B LEU* 1.3 60.5 + - - +
607B LYS* 3.4 25.0 + - - +
608B ILE* 2.9 33.6 + - + +
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Residues in contact with LEU 605 (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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469B ILE* 3.9 22.0 - - + -
566B MET* 4.1 21.1 - - + -
570B ILE* 3.9 7.1 - - + +
573B TYR* 3.8 42.2 - - + +
593B PHE* 4.6 4.5 - - + -
601B ILE 3.0 14.8 + - - +
602B ALA* 2.9 9.9 + - - +
604B ASP* 1.3 77.0 - - - +
606B VAL* 1.3 60.7 + - - +
608B ILE* 3.5 1.3 + - + -
609B LEU* 3.0 45.9 + - + +
620B LEU* 3.8 29.6 - - + -
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Residues in contact with VAL 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602B ALA 2.9 16.4 + - - +
603B ALA* 3.1 12.3 + - - +
605B LEU* 1.3 77.7 - - - +
607B LYS* 1.3 63.0 + - + +
609B LEU* 3.1 9.2 + - - +
610B GLU* 2.9 53.2 + - + +
616B VAL* 3.9 24.2 - - + +
620B LEU* 4.0 24.7 - - + +
621B ARG* 4.6 12.3 - - + +
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Residues in contact with LYS 607 (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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603B ALA* 3.2 12.0 + - + +
604B ASP* 3.7 27.8 + - - +
606B VAL* 1.3 79.2 - - + +
608B ILE* 1.3 62.6 + - + +
610B GLU* 3.8 11.8 - - - +
611B GLY* 2.8 30.0 + - - -
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Residues in contact with ILE 608 (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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459B GLY 4.2 14.8 - - - +
460B GLY* 5.0 4.0 - - - -
461B ALA* 4.1 15.9 + - + +
467B GLN* 3.7 9.0 - - - +
570B ILE* 3.6 28.5 - - + -
573B TYR* 3.6 29.2 - - + -
574B VAL* 3.7 20.4 - - + -
604B ASP* 2.9 16.2 + - + +
605B LEU* 3.9 5.8 - - + +
606B VAL 3.3 0.2 - - - -
607B LYS* 1.3 80.0 - - + +
609B LEU* 1.3 56.6 + - - +
611B GLY* 3.6 1.7 + - - -
612B SER* 2.7 34.1 + - - -
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Residues in contact with LEU 609 (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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467B GLN* 3.4 37.5 - - + +
469B ILE* 4.3 12.6 - - + -
573B TYR* 4.5 0.2 - - - +
605B LEU* 3.0 36.3 + - + +
606B VAL 3.1 3.3 + - - +
608B ILE* 1.3 78.4 - - - +
610B GLU* 1.3 62.2 + - - +
612B SER* 3.2 11.3 + - - -
613B GLY 3.3 0.2 + - - -
614B GLN* 3.0 36.9 + - + +
615B THR 4.0 13.7 - - - +
616B VAL* 4.1 16.6 - - + -
617B PRO* 4.0 6.5 - - + -
620B LEU* 3.7 28.3 - - + -
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Residues in contact with GLU 610 (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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606B VAL* 2.9 34.9 + - - +
607B LYS* 3.8 11.1 - - - +
609B LEU* 1.3 70.8 - - - +
611B GLY* 1.3 53.4 - - - +
612B SER 2.8 15.8 + - - -
613B GLY* 2.8 15.4 + - - -
614B GLN 4.5 5.2 - - - +
616B VAL* 3.8 13.7 - - + -
621B ARG* 3.5 18.9 + - - -
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Residues in contact with GLY 611 (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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457B ILE* 5.9 7.4 - - - +
460B GLY* 6.4 1.3 - - - -
461B ALA 5.4 1.4 - - - +
607B LYS 2.8 22.0 + - - -
608B ILE* 3.9 2.2 - - - -
610B GLU* 1.3 71.2 - - - +
612B SER* 1.3 57.6 + - - +
613B GLY 3.6 0.4 - - - -
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Residues in contact with SER 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B ALA* 3.8 24.7 - - - +
463B SER* 3.7 27.0 - - - -
467B GLN* 3.4 24.5 + - - -
608B ILE 2.7 22.4 + - - -
609B LEU 3.3 4.6 + - - -
610B GLU 2.8 2.8 + - - -
611B GLY* 1.3 76.3 - - - +
613B GLY* 1.3 64.1 + - - +
614B GLN* 3.0 14.2 + - - +
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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