Contacts of the helix formed by residues 598 - 610 (chain B) in PDB entry 1DQA
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 ARG 598 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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596B LEU* 3.2 3.8 - - - +
597B PRO* 1.3 99.0 + - + +
599B ALA* 1.3 60.3 + - - +
600B CYS* 3.9 7.0 - - + +
601B ASP* 2.9 34.9 + - - +
602B SER* 3.0 11.6 + - - -
641B ARG* 3.6 13.1 - - - +
709C GLU* 3.5 23.1 - - - +
711C VAL* 3.8 17.8 - - - +
784C SER* 3.9 15.8 + - - -
792C TYR* 3.8 28.4 - - - +
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Residues in contact with ALA 599 (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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598B ARG* 1.3 68.9 - - - +
600B CYS* 1.3 66.7 + - - +
602B SER* 3.0 10.8 + - - -
603B ALA* 2.9 26.5 + - - +
640B GLY* 3.5 25.4 - - - +
641B ARG* 3.8 3.2 - - - +
707C VAL* 3.7 26.9 - - + +
708C CYS* 5.2 0.9 - - - -
709C GLU* 2.8 27.5 + - + +
792C TYR* 4.1 1.6 - - - +
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Residues in contact with CYS 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B ARG* 3.1 5.4 - - + -
599B ALA* 1.3 77.0 - - - +
601B ASP* 1.3 64.0 + - - +
603B ALA* 3.6 3.5 + - - +
604B GLU* 3.2 20.8 + - - +
580C SER* 3.6 23.3 - - - -
581C SER* 5.3 0.2 - - - -
582C ARG* 3.5 57.0 + - - +
709C GLU* 3.0 20.4 + - - +
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Residues in contact with ASP 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B LEU* 3.6 20.6 - - + -
597B PRO* 3.5 15.6 - - - +
598B ARG* 2.9 36.3 + - - +
600B CYS* 1.3 79.5 - - - +
602B SER* 1.3 65.0 + - - +
603B ALA 3.2 0.2 - - - -
604B GLU* 3.0 25.3 + - - +
605B VAL* 3.0 16.6 + - - +
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Residues in contact with SER 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B LEU* 3.8 16.9 - - - +
598B ARG 3.0 5.3 + - - -
599B ALA* 3.0 12.3 + - - -
601B ASP* 1.3 75.6 - - - +
603B ALA* 1.3 54.9 + - - +
605B VAL* 3.2 4.9 + - - +
606B LYS* 2.9 24.9 + - - +
638B ILE* 3.4 20.9 - - - +
640B GLY 2.9 23.3 + - - -
641B ARG 3.6 23.3 - - - -
642B ASN 4.2 2.0 - - - -
643B LEU* 4.2 8.2 - - - +
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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
----------------------------------------------------------
599B ALA 2.9 17.9 + - - +
600B CYS 3.6 5.8 - - - +
602B SER* 1.3 78.5 + - - +
604B GLU* 1.3 57.5 + - - +
606B LYS* 3.3 3.9 + - - +
607B ALA* 3.0 28.8 + - - +
638B ILE* 3.5 11.2 - - + -
582C ARG* 4.0 19.5 - - + -
584C LEU* 3.7 25.9 - - + +
707C VAL* 4.8 1.1 - - + -
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Residues in contact with GLU 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B CYS 3.2 10.6 + - - +
601B ASP* 3.0 20.1 + - - +
603B ALA* 1.3 80.5 - - - +
605B VAL* 1.3 56.3 + - - +
607B ALA* 3.3 7.0 + - + +
608B TRP* 2.9 29.5 + - + +
675B PHE* 4.2 22.3 - - + -
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Residues in contact with VAL 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B LEU* 4.0 20.6 - - + -
601B ASP 3.0 13.2 + - - +
602B SER* 3.2 8.3 + - - +
604B GLU* 1.3 75.0 - - - +
606B LYS* 1.3 57.7 + - - +
608B TRP* 3.2 7.2 + - - +
609B LEU* 2.9 37.8 + - + +
643B LEU* 3.4 23.6 - - + -
671B LEU* 4.2 24.7 - - + -
675B PHE* 3.7 33.0 - - + -
678B MET* 5.3 1.6 - - + -
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Residues in contact with LYS 606 (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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602B SER 2.9 12.7 + - - +
603B ALA 3.5 8.5 - - - +
604B GLU 3.3 0.2 - - - -
605B VAL* 1.3 77.8 - - - +
607B ALA* 1.3 62.6 + - - +
609B LEU* 3.3 11.1 + - - +
610B GLU* 2.7 55.0 + - - +
636B THR* 3.2 41.6 + - - +
637B SER* 4.5 5.4 - - - +
638B ILE* 3.8 23.8 - - + +
643B LEU* 4.4 7.1 - - + +
584C LEU* 4.4 33.3 + - + +
585C ALA* 5.4 4.6 - - - +
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Residues in contact with ALA 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 3.0 16.5 + - - +
604B GLU* 3.6 7.9 - - + +
606B LYS* 1.3 76.2 - - - +
608B TRP* 1.3 62.9 + - - +
610B GLU* 3.1 20.3 + - - +
611B THR* 3.4 17.7 + - - +
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Residues in contact with TRP 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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604B GLU* 2.9 15.0 + - + +
605B VAL 3.4 7.2 - - - +
607B ALA* 1.3 77.6 - - - +
609B LEU* 1.3 71.3 + - + +
611B THR* 2.8 33.9 + - + -
613B GLU 5.6 0.2 - - - -
614B GLY* 3.5 38.3 - - - -
617B VAL* 4.2 11.9 - - + -
618B ILE* 3.9 13.5 - - + -
671B LEU* 3.6 25.6 - - + -
674B TYR* 3.6 48.5 - + - -
675B PHE* 3.7 25.6 - + + -
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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
----------------------------------------------------------
605B VAL* 2.9 32.7 + - + +
606B LYS* 3.3 5.4 + - - +
608B TRP* 1.3 88.5 - - + +
610B GLU* 1.3 60.9 + - - +
611B THR 3.3 7.3 + - - +
615B PHE* 3.9 17.7 + - - +
618B ILE* 3.6 32.1 - - + -
634B LEU* 4.0 24.2 - - + +
636B THR* 3.9 25.6 - - + -
643B LEU* 4.4 3.6 - - + -
645B ILE* 4.0 26.5 - - + -
647B PHE* 6.4 0.9 - - + -
671B LEU* 4.0 9.0 - - + -
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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
----------------------------------------------------------
606B LYS* 2.7 52.4 + - - +
607B ALA* 3.1 12.1 + - - +
608B TRP 3.1 0.8 - - - -
609B LEU* 1.3 78.7 - - + +
611B THR* 1.3 62.1 + - - +
612B SER 4.0 0.3 + - - -
615B PHE* 5.7 0.2 - - - -
636B THR* 3.2 13.2 + - + +
584C LEU 4.6 7.4 - - - +
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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