Contacts of the helix formed by residues 593 - 605 (chain N) in PDB entry 2JA7
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 PRO 593 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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578N THR* 3.7 30.3 - - + +
580N VAL* 6.2 0.4 - - + -
590N HIS* 3.2 23.3 - - + +
591N ARG 2.8 11.0 - - - +
592N ASN* 1.3 80.4 - - - +
594N ALA* 1.3 55.9 + - + +
595N ARG 2.6 9.8 + - - -
596N LEU* 2.5 29.1 + - + +
597N MET* 2.7 14.1 + - + +
617N ARG* 2.9 40.4 - - + +
624N LEU* 6.1 4.0 - - + -
61U ASP* 5.1 2.7 - - - +
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Residues in contact with ALA 594 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592N ASN* 3.5 13.4 - - - +
593N PRO* 1.3 81.7 - - + +
595N ARG* 1.3 61.8 + - + +
597N MET* 3.9 3.6 - - - +
598N GLU* 3.7 18.7 + - - +
617N ARG* 2.9 25.7 + - - +
61U ASP* 4.0 17.0 - - + +
64U SER* 5.6 2.9 - - - +
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Residues in contact with ARG 595 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592N ASN* 3.7 21.8 + - - +
593N PRO 2.6 3.8 + - - -
594N ALA* 1.3 75.8 - - + +
596N LEU* 1.3 66.4 + - - +
597N MET 2.9 2.4 + - - -
598N GLU* 3.2 4.5 + - - +
599N THR* 2.8 32.0 + - - +
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Residues in contact with LEU 596 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557N PHE* 5.5 0.7 - - + -
558N LEU* 3.6 29.6 - - + -
561N TRP* 5.0 20.4 - - + +
563N MET* 6.0 2.5 - - + +
580N VAL* 4.4 3.8 - - + -
590N HIS* 3.5 44.8 + - + +
592N ASN 4.4 1.4 + - - -
593N PRO* 2.5 18.3 + - + +
595N ARG* 1.3 74.7 - - - +
597N MET* 1.3 66.0 + - - +
599N THR* 3.3 8.0 + - + -
600N LEU* 3.1 25.8 + - + +
624N LEU* 3.7 29.8 - - + -
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Residues in contact with MET 597 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593N PRO* 2.7 12.3 + - + +
594N ALA* 3.9 6.3 - - - +
595N ARG 2.9 0.6 + - - -
596N LEU* 1.3 73.8 - - - +
598N GLU* 1.3 55.7 + - - +
599N THR 2.5 4.4 + - - -
600N LEU* 2.5 40.9 + - + +
601N ARG* 3.0 36.8 + - + +
615N MET* 3.9 40.2 - - + +
616N ILE 4.8 0.2 - - - -
617N ARG* 3.8 34.1 - - + +
624N LEU* 3.3 30.5 - - + -
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Residues in contact with GLU 598 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594N ALA 3.7 11.9 + - - +
595N ARG* 3.2 6.0 + - - +
597N MET* 1.3 76.0 - - - +
599N THR* 1.3 56.7 + - - +
600N LEU 3.4 0.2 - - - -
601N ARG* 4.1 15.3 - - + +
602N THR* 2.7 35.9 + - - +
641N GLU* 4.3 13.0 - - - +
643N ASP* 5.5 1.9 - - - +
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Residues in contact with THR 599 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557N PHE* 4.5 12.8 - - + -
561N TRP* 3.4 46.6 - - + -
595N ARG* 2.8 23.3 + - - +
596N LEU* 3.3 10.8 - - + +
597N MET 2.5 5.9 + - - -
598N GLU* 1.3 75.9 - - - +
600N LEU* 1.3 60.2 + - + +
602N THR* 3.9 3.9 + - - -
603N LEU* 3.4 25.7 + - + +
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Residues in contact with LEU 600 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554N ILE* 5.6 4.5 - - + -
557N PHE* 3.7 33.4 - - + -
558N LEU* 4.1 8.1 - - + -
596N LEU* 3.1 33.2 + - + +
597N MET* 2.5 24.9 + - + +
599N THR* 1.3 70.3 - - + +
601N ARG* 1.3 57.6 + - - +
602N THR 3.1 2.2 - - - -
603N LEU* 2.7 27.4 + - - +
604N ARG* 3.0 8.1 + - - +
609N ILE* 3.6 16.5 - - + +
615N MET* 3.9 16.6 - - - -
624N LEU* 4.6 2.0 - - + -
626N ILE* 3.6 31.0 - - + -
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Residues in contact with ARG 601 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597N MET* 3.0 49.4 + - + +
598N GLU* 4.3 12.8 - - + +
600N LEU* 1.3 76.8 - - - +
602N THR* 1.3 59.0 + - - +
604N ARG* 3.6 3.6 + - - +
605N ARG* 2.9 64.8 + - - +
615N MET* 4.1 20.0 + - + -
617N ARG* 5.0 10.9 + - - +
691N GLU* 5.1 7.4 - - - +
697N GLU* 5.3 8.0 + - - +
700N SER* 4.8 17.6 + - - -
701N ILE* 5.9 1.8 - - - +
739N THR* 5.5 9.5 - - - +
740N HIS* 6.0 3.9 - - - -
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Residues in contact with THR 602 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598N GLU* 2.7 33.3 + - - +
599N THR* 4.1 4.5 - - - -
600N LEU 3.1 1.0 - - - -
601N ARG* 1.3 76.0 - - - +
603N LEU* 1.3 63.7 + - - +
605N ARG* 4.2 13.2 + - + +
606N LYS* 3.9 23.8 + - - +
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Residues in contact with LEU 603 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557N PHE* 3.4 43.5 - - + -
561N TRP* 6.1 2.2 - - + -
599N THR* 3.4 18.5 + - + +
600N LEU 2.7 14.9 + - - +
602N THR* 1.3 80.5 - - - +
604N ARG* 1.3 58.4 + - - +
606N LYS* 3.8 10.9 + - - +
607N GLY 3.5 2.1 + - - -
608N ASP* 3.1 65.5 + - + +
609N ILE* 3.3 25.3 + - + -
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Residues in contact with ARG 604 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600N LEU 3.0 8.1 + - - +
601N ARG* 3.9 6.7 - - - +
603N LEU* 1.3 75.1 - - - +
605N ARG* 1.3 55.7 + - - +
606N LYS 2.5 18.2 + - - -
607N GLY* 2.6 18.0 + - - -
609N ILE* 3.2 30.1 - - + +
610N ASN 4.2 1.6 + - - +
611N PRO* 3.7 29.5 + - + +
613N VAL* 2.6 31.3 + - - +
614N SER* 3.3 6.1 - - - +
615N MET* 3.5 26.1 - - + +
685N LEU* 5.3 2.5 - - + +
691N GLU* 2.4 51.3 + - - +
692N TYR 4.3 9.9 + - - -
697N GLU* 3.2 26.9 + - - -
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Residues in contact with ARG 605 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601N ARG* 2.9 55.4 + - - +
602N THR* 4.5 12.7 + - + +
603N LEU 3.6 0.2 - - - -
604N ARG* 1.3 73.7 - - + +
606N LYS* 1.3 56.5 + - - +
639N ILE* 3.8 36.2 - - + +
641N GLU* 3.8 21.8 + - - +
652N LYS* 4.9 9.3 - - - +
685N LEU* 3.6 11.6 - - - +
686N ASN 3.9 2.1 - - - -
687N GLU* 4.0 0.3 - - - -
688N GLY* 3.0 40.9 + - - -
691N GLU* 3.3 39.4 + - + -
740N HIS* 4.8 5.3 + - - -
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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
------------------------------------------------------------
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