Contacts of the helix formed by residues 599 - 614 (chain O) in PDB entry 5A31
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 599 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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777A THR* 4.8 0.2 - - + -
945A GLU* 3.0 52.5 - - + +
946A THR* 4.2 8.7 - - - +
947A LEU 5.2 1.1 - - - +
1788A PRO* 4.2 14.1 - - + +
591O TYR* 3.3 37.2 - - + -
596O SER* 2.8 42.3 + - - +
598O THR* 1.3 78.5 - - - +
600O ALA* 1.3 59.6 + - - +
602O PRO* 3.1 15.1 - - - +
603O MET* 4.1 6.4 - - - +
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Residues in contact with ALA 600 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588O ALA* 4.0 13.2 - - - +
591O TYR* 3.7 22.8 - - + +
592O TRP* 4.4 12.3 - - + +
597O PRO 3.1 15.9 + - - +
599O ILE* 1.3 80.9 - - - +
601O LEU* 1.3 63.1 + - - +
603O MET* 3.0 21.1 + - - +
604O LEU* 3.1 27.4 + - + +
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Residues in contact with LEU 601 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1750A PHE* 4.0 24.9 - - + -
1754A PHE* 4.6 8.1 - - + -
1787A LEU* 4.6 8.3 - - + -
1791A ILE* 5.0 3.6 - - + -
592O TRP* 5.0 2.5 - - + -
597O PRO 4.2 10.1 - - - +
598O THR* 3.0 33.5 + - + +
600O ALA* 1.3 77.6 - - - +
602O PRO* 1.3 62.9 - - + +
604O LEU* 3.3 10.0 + - + +
605O LEU* 2.9 45.0 + - + +
627O LEU* 5.3 1.1 - - + -
630O ALA* 3.9 28.5 - - + -
634O LEU* 4.1 23.3 - - + -
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Residues in contact with PRO 602 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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945A GLU* 4.8 10.1 - - - +
1746A ALA* 5.2 4.7 - - + +
1784A PRO 5.7 1.1 - - - +
1787A LEU* 5.4 4.3 - - + -
1788A PRO* 3.9 28.0 - - + -
598O THR 3.4 7.0 - - - +
599O ILE* 3.1 15.5 - - - +
601O LEU* 1.3 94.1 - - + +
603O MET* 1.3 65.2 + - - +
605O LEU* 4.0 8.7 - - + +
606O GLN* 3.2 27.9 + - - +
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Residues in contact with MET 603 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942A ARG* 3.4 36.6 - - - +
945A GLU* 4.9 11.9 - - - +
584O LEU* 3.4 35.0 - - + +
587O VAL* 4.0 15.9 - - + -
588O ALA* 4.2 13.9 - - + -
591O TYR* 3.9 33.2 - - + -
599O ILE 4.1 6.7 - - - +
600O ALA* 3.0 10.8 + - - +
602O PRO* 1.3 80.8 - - - +
604O LEU* 1.3 58.6 + - - +
606O GLN* 3.4 8.2 + - - +
607O ALA* 3.0 31.0 + - - +
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Residues in contact with LEU 604 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585O LEU* 4.4 13.0 - - + -
588O ALA* 3.5 24.2 - - + -
592O TRP* 4.1 24.7 - - + +
600O ALA* 3.1 23.0 + - + +
601O LEU* 3.5 8.7 - - - +
603O MET* 1.3 81.5 - - - +
605O LEU* 1.3 57.0 + - - +
607O ALA* 3.4 5.4 + - - +
608O LEU* 2.8 32.4 + - - +
623O THR* 3.7 8.5 + - - +
626O ASN* 3.9 34.1 - - + +
627O LEU* 3.8 24.5 - - + -
630O ALA* 4.8 2.7 - - + -
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Residues in contact with LEU 605 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1746A ALA* 3.9 26.0 - - + +
1747A LEU* 6.4 0.2 - - + -
1749A SER* 3.8 37.0 - - - +
1750A PHE* 3.7 28.0 - - + +
1753A TYR* 5.0 0.2 - - + -
1754A PHE* 4.4 6.5 - - + -
1787A LEU* 6.0 1.6 - - + -
601O LEU* 2.9 31.9 + - + +
602O PRO* 4.0 7.0 - - + +
604O LEU* 1.3 76.1 - - - +
606O GLN* 1.3 59.3 + - - +
608O LEU* 3.2 5.8 + - - +
609O ALA* 2.8 32.6 + - - +
627O LEU* 4.3 24.2 - - + -
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Residues in contact with GLN 606 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942A ARG* 4.4 16.4 + - - +
1745A PRO* 5.8 1.1 - - - +
1746A ALA* 4.8 15.6 - - + +
572O GLN* 5.0 11.1 - - - +
580O VAL* 5.8 0.4 - - - +
584O LEU* 4.0 26.7 - - + +
602O PRO 3.2 17.1 + - - +
603O MET* 3.6 9.1 - - - +
605O LEU* 1.3 78.2 - - - +
607O ALA* 1.3 56.7 + - - +
609O ALA* 3.5 4.6 + - - +
610O LEU* 3.0 39.5 + - + +
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Residues in contact with ALA 607 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581O ILE* 3.9 11.0 - - + +
584O LEU* 4.0 22.0 - - + +
585O LEU* 3.4 32.8 - - + -
603O MET 3.0 18.2 + - - +
604O LEU 3.5 4.0 - - - +
606O GLN* 1.3 75.7 - - - +
608O LEU* 1.3 58.9 + - - +
610O LEU* 3.3 6.0 - - - +
611O SER* 2.9 30.3 + - - -
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Residues in contact with LEU 608 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1749A SER* 3.1 28.0 - - - +
1753A TYR* 4.0 7.9 - - + +
604O LEU 2.8 18.3 + - - +
605O LEU* 3.4 6.3 - - + +
607O ALA* 1.3 74.0 - - - +
609O ALA* 1.3 67.4 + - - +
611O SER* 3.1 6.4 + - - +
612O LYS* 3.1 48.4 + - + +
620O ALA* 4.7 0.7 - - - +
623O THR* 3.4 20.8 + - + +
624O VAL* 3.4 31.0 - - + -
627O LEU* 3.7 24.9 - - + -
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Residues in contact with ALA 609 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1745A PRO* 3.7 39.0 - - + +
1749A SER* 4.7 7.4 - - - -
605O LEU 2.8 19.0 + - - +
606O GLN 4.0 3.4 - - - +
608O LEU* 1.3 77.2 - - - +
610O LEU* 1.3 62.6 + - - +
612O LYS* 3.3 10.9 + - - +
613O GLU* 3.2 30.0 + - + +
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Residues in contact with LEU 610 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577O THR* 4.0 11.0 - - + +
580O VAL* 4.2 20.4 - - + -
581O ILE* 3.5 25.4 - - + -
584O LEU* 4.9 5.8 - - + -
606O GLN* 3.0 29.1 + - + +
607O ALA 3.3 7.2 - - - +
609O ALA* 1.3 77.4 - - - +
611O SER* 1.3 62.0 + - - +
613O GLU* 3.1 9.3 + - - +
614O TYR* 3.1 44.9 + - + +
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Residues in contact with SER 611 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581O ILE* 3.8 25.1 - - - -
607O ALA 2.9 17.3 + - - -
608O LEU* 3.1 11.8 + - - -
610O LEU* 1.3 73.9 - - - +
612O LYS* 1.3 58.7 + - - +
614O TYR 4.5 0.2 - - - +
615O ARG* 2.8 23.0 + - - -
616O LEU* 2.9 36.5 + - - +
620O ALA* 3.2 25.0 - - - +
623O THR* 4.0 0.3 - - - +
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Residues in contact with LYS 612 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1749A SER* 4.4 3.2 + - - -
1752A GLU* 5.3 3.2 + - - -
1753A TYR* 3.0 31.4 + - - +
608O LEU* 3.1 42.2 + - + +
609O ALA* 3.8 7.3 - - - +
610O LEU 3.3 0.2 - - - -
611O SER* 1.3 83.1 + - - +
613O GLU* 1.3 61.1 + - + +
615O ARG* 3.6 15.8 + - - +
620O ALA* 5.0 8.5 - - + -
624O VAL* 5.5 0.7 - - - -
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Residues in contact with GLU 613 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1745A PRO* 4.0 24.3 - - - +
391O ALA 4.0 7.6 - - - +
392O GLY* 4.6 2.1 - - - -
609O ALA* 3.2 17.7 + - - +
610O LEU* 3.1 14.1 + - - +
612O LYS* 1.3 78.8 - - + +
614O TYR* 1.3 74.1 + - + +
615O ARG* 3.4 7.2 + - - +
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Residues in contact with TYR 614 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389O ALA 4.7 1.0 - - - +
390O PHE 3.5 21.5 - - - +
391O ALA* 3.5 19.1 - - - +
392O GLY* 4.0 8.1 + - - -
432O TYR* 4.1 4.7 - - - -
577O THR* 3.4 39.8 + - + -
610O LEU* 3.1 36.4 + - + +
613O GLU* 1.3 93.2 + - + +
615O ARG* 1.3 70.0 + - - +
616O LEU* 3.2 24.5 - - + +
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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