Contacts of the helix formed by residues 596 - 603 (chain A) in PDB entry 2RD0
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 GLU 596 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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594A LYS* 3.0 41.1 + - - +
595A PRO* 1.3 80.7 - - - +
597A GLN* 1.3 86.6 + - - +
599A MET* 3.6 16.1 - - - +
631A TYR* 5.5 9.8 - - - +
994A HIS* 5.0 9.9 + - - +
996A ASN* 3.2 17.7 + - - +
997A LEU* 3.3 50.7 + - + +
1000A ASN* 3.4 18.0 + - - +
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Residues in contact with GLN 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563A GLU* 3.9 31.3 + - + +
566A PRO* 5.9 5.6 - - + +
593A ILE* 3.6 20.0 - - + -
594A LYS* 2.8 34.9 + - + +
596A GLU* 1.3 94.0 - - - +
598A ALA* 1.3 57.1 + - - +
599A MET 2.8 11.6 + - - -
600A GLU* 2.9 28.2 + - - +
601A LEU* 4.3 3.3 + - - +
996A ASN* 3.3 14.8 + - - +
1000A ASN* 4.7 4.5 - - - +
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Residues in contact with ALA 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593A ILE* 3.5 12.5 - - + +
594A LYS 2.7 19.3 + - - +
595A PRO* 3.7 9.0 - - + -
596A GLU 3.4 0.4 - - - -
597A GLN* 1.3 71.6 - - - +
599A MET* 1.3 58.1 + - - +
600A GLU 3.4 0.2 - - - -
601A LEU* 4.0 12.9 - - + +
602A LEU* 4.4 1.7 - - - +
615A ALA* 3.5 28.0 - - - +
618A CYS* 3.5 35.9 - - + -
619A LEU* 4.4 5.3 - - + +
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Residues in contact with MET 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595A PRO 3.1 21.6 + - - +
596A GLU* 3.6 12.1 - - - +
597A GLN 2.8 0.6 + - - -
598A ALA* 1.3 75.5 - - - +
600A GLU* 1.3 63.7 + - - +
601A LEU 2.9 6.1 - - - -
602A LEU* 2.8 24.5 + - - +
603A ASP 4.0 1.2 + - - -
619A LEU* 4.6 9.0 - - + -
623A LEU* 5.0 9.2 - - + -
631A TYR* 3.3 48.7 - - + -
635A LEU* 3.9 30.5 - - + -
997A LEU* 5.9 2.9 - - - -
1000A ASN* 5.3 3.4 - - + -
1001A LEU* 4.8 7.9 - - - -
1004A MET* 3.6 35.2 - - + +
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Residues in contact with GLU 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539A PRO* 3.3 35.4 - - + +
566A PRO* 3.5 30.1 - - - +
567A LYS* 5.7 2.7 + - - +
570A LEU* 5.6 1.6 - - - +
596A GLU 4.3 1.0 + - - -
597A GLN* 2.9 17.5 + - - +
599A MET* 1.3 80.2 - - - +
601A LEU* 1.3 57.9 + - + +
602A LEU 3.1 4.7 + - - -
603A ASP* 3.1 34.7 - - - +
606A TYR* 3.1 26.4 + - + -
1000A ASN* 3.3 28.5 + - - +
1004A MET* 5.3 0.9 - - - -
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Residues in contact with LEU 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565A LEU* 4.3 9.4 - - + -
566A PRO* 4.1 19.7 - - + -
569A LEU* 3.8 14.6 - - + -
593A ILE* 5.6 2.9 - - + -
597A GLN 4.6 4.0 - - - +
598A ALA* 4.0 18.6 - - - +
599A MET 2.9 0.8 - - - -
600A GLU* 1.3 77.5 - - + +
602A LEU* 1.3 67.2 + - - +
603A ASP 3.6 0.4 - - - -
606A TYR* 3.5 55.5 - - + +
611A VAL* 4.0 11.9 - - + +
612A ARG* 3.9 5.5 - - - +
614A PHE* 4.1 30.5 - - + -
615A ALA* 3.8 16.6 - - + -
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Residues in contact with LEU 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598A ALA 4.4 2.7 - - - +
599A MET* 2.8 14.2 + - - +
601A LEU* 1.3 90.5 - - - +
603A ASP* 1.3 61.3 + - - +
612A ARG* 2.7 50.3 + - + +
615A ALA* 3.7 21.5 - - + -
616A VAL* 4.7 5.2 - - + -
619A LEU* 3.8 29.4 - - + -
635A LEU* 4.4 9.2 - - + -
638A VAL* 3.2 27.8 - - + +
641A TYR* 3.9 2.4 - - - -
642A GLU* 5.3 0.7 - - - +
649A LEU* 4.1 24.5 - - + -
1004A MET* 5.3 1.8 - - + -
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Residues in contact with ASP 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599A MET 4.0 2.0 + - - -
600A GLU* 3.3 19.1 + - - +
602A LEU* 1.3 79.2 - - - +
604A CYS* 1.3 62.9 + - - +
605A ASN* 3.0 18.3 + - - +
606A TYR* 3.1 26.5 + - - -
612A ARG* 2.7 22.7 + - - -
638A VAL* 4.1 3.1 - - - +
641A TYR* 3.9 8.1 - - - -
1003A SER* 4.1 24.3 - - - +
1004A MET* 4.4 11.9 - - + +
1016A PHE* 3.7 22.4 - - - -
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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