Contacts of the helix formed by residues 606 - 627 (chain H) in PDB entry 6OD3
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 THR 606 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604H PRO* 2.8 26.3 + - + +
605H GLN* 1.3 76.4 - - - +
607H LYS* 1.3 65.7 + - - +
608H LEU* 3.6 7.5 + - - +
609H LEU* 3.2 22.7 + - - +
610H ILE* 3.0 23.6 + - - +
701H EDO 4.3 6.3 - - - -
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Residues in contact with LYS 607 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584G ILE* 4.0 19.5 - - + -
581H VAL* 6.0 2.0 - - - +
584H ILE* 4.5 6.3 - - - -
585H ASN* 2.9 29.7 + - - +
588H PHE* 3.4 47.6 - - + -
606H THR* 1.3 74.5 - - - +
608H LEU* 1.3 62.0 + - - +
611H LEU* 3.2 30.7 + - - +
701H EDO 3.3 26.1 + - - +
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Residues in contact with LEU 608 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581G VAL 3.4 23.1 - - - +
582G ARG* 3.6 23.1 - - + +
583G ASP 3.5 22.7 - - - +
584G ILE* 4.0 14.9 - - + +
587G ALA* 4.1 4.7 - - + -
606H THR* 3.2 7.7 + - - +
607H LYS* 1.3 79.8 - - - +
609H LEU* 1.3 63.0 + - - +
611H LEU* 3.4 6.0 + - - +
612H HIS* 3.0 45.7 + - + +
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Residues in contact with LEU 609 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601H SER* 5.7 0.4 - - - +
603H LYS* 3.7 46.7 - - + +
604H PRO 3.4 21.1 - - - +
605H GLN* 3.8 11.0 - - + -
606H THR* 3.2 19.0 + - - +
608H LEU* 1.3 80.5 - - - +
610H ILE* 1.3 56.7 + - - +
612H HIS* 3.3 9.4 + - + -
613H GLN* 2.8 62.7 + - + +
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Residues in contact with ILE 610 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588H PHE* 3.6 41.7 - - + +
589H LYS* 5.5 0.4 - - - -
591H LEU* 3.9 15.9 - - + +
592H GLY* 3.7 32.3 - - - +
595H VAL* 5.0 1.1 - - + +
605H GLN* 3.9 27.8 - - + +
606H THR 3.0 21.0 + - - +
607H LYS 3.9 4.0 - - - +
608H LEU 3.3 0.2 - - - -
609H LEU* 1.3 75.7 - - - +
611H LEU* 1.3 58.4 + - - +
613H GLN* 3.2 11.3 + - - +
614H ALA* 2.8 28.8 + - - +
701H EDO 4.2 10.3 - - - -
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Residues in contact with LEU 611 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584G ILE* 3.9 11.0 - - + -
587G ALA* 3.7 32.8 - - + +
588G PHE* 3.6 47.8 - - + +
591G LEU* 3.9 17.0 - - + +
611G LEU* 3.9 9.9 - - + -
588H PHE* 3.7 21.8 - - + -
591H LEU* 4.8 1.1 - - + -
607H LYS 3.2 18.1 + - - +
608H LEU* 3.7 4.7 - - - +
609H LEU 3.2 0.2 - - - -
610H ILE* 1.3 76.8 - - - +
612H HIS* 1.3 61.9 + - - +
614H ALA* 3.3 5.9 + - - +
615H VAL* 3.1 29.6 + - - +
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Residues in contact with HIS 612 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580G ARG 4.8 1.1 - - - -
581G VAL* 2.6 57.5 + - + +
587G ALA* 4.0 17.4 - - + +
608H LEU* 3.0 39.0 + - + +
609H LEU* 3.8 10.3 - - + +
611H LEU* 1.3 78.1 - - - +
613H GLN* 1.3 62.5 + - - +
615H VAL* 3.5 9.5 + - - +
616H ALA* 3.2 21.7 + - - +
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Residues in contact with GLN 613 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595H VAL* 3.4 17.3 - - + +
599H LEU* 3.7 30.9 - - + +
601H SER* 4.9 13.5 - - - -
605H GLN* 3.0 32.1 + - - +
609H LEU* 2.8 46.4 + - + +
610H ILE* 3.2 13.4 + - - +
612H HIS* 1.3 75.2 - - - +
614H ALA* 1.3 64.6 + - - +
616H ALA* 3.3 4.7 + - - +
617H VAL* 3.0 28.2 + - - +
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Residues in contact with ALA 614 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591G LEU* 4.3 15.3 - - + -
614G ALA* 5.0 0.9 - - + -
618G ILE* 4.6 4.5 - - + -
591H LEU* 3.8 35.2 - - + -
595H VAL* 3.9 10.0 - - + +
610H ILE 2.8 16.2 + - - +
611H LEU 3.3 4.9 + - - +
613H GLN* 1.3 75.0 - - - +
615H VAL* 1.3 62.3 + - - +
617H VAL* 3.4 2.6 + - - +
618H ILE* 3.1 32.5 + - + +
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Residues in contact with VAL 615 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587G ALA* 4.9 3.6 - - + +
590G GLU* 4.8 6.7 - - + -
591G LEU* 4.0 31.0 - - + +
594G MET* 3.6 28.4 - - - +
611H LEU 3.1 18.5 + - - +
612H HIS* 3.8 11.4 - - - +
613H GLN 3.2 0.4 - - - -
614H ALA* 1.3 77.1 - - - +
616H ALA* 1.3 61.9 + - - +
618H ILE 3.5 0.2 + - - -
619H LEU* 3.1 37.0 + - + +
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Residues in contact with ALA 616 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599H LEU* 5.2 9.2 - - + -
612H HIS 3.2 16.5 + - - +
613H GLN* 3.3 5.8 + - - +
615H VAL* 1.3 78.5 - - - +
617H VAL* 1.3 59.9 + - + +
619H LEU* 3.6 7.4 + - - +
620H SER* 2.9 34.9 + - - +
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Residues in contact with VAL 617 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618G ILE* 4.2 16.2 - - + -
595H VAL* 3.9 19.5 - - + -
598H HIS* 3.8 41.3 - - + -
599H LEU* 4.0 18.4 - - + -
613H GLN 3.0 16.6 + - - +
614H ALA 3.9 3.8 - - - +
616H ALA* 1.3 74.6 - - - +
618H ILE* 1.3 60.0 + - - +
620H SER* 3.3 5.5 + - - -
621H LEU* 2.9 44.8 + - + +
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Residues in contact with ILE 618 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568E MET* 6.3 0.9 - - - -
591G LEU* 3.9 15.0 - - + -
594G MET* 3.7 25.6 - - + +
595G VAL* 3.9 26.9 - - + -
614G ALA* 4.6 6.1 - - + +
617G VAL* 4.1 15.0 - - + -
618G ILE* 3.7 24.9 - - + -
621G LEU* 3.8 20.4 - - + +
614H ALA 3.1 19.1 + - - +
617H VAL* 1.3 76.6 - - - +
619H LEU* 1.3 58.3 + - + +
621H LEU* 4.6 0.4 - - - -
622H GLU* 2.9 32.2 + - + +
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Residues in contact with LEU 619 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594G MET* 3.7 20.9 - - + -
615H VAL* 3.1 35.6 + - + +
616H ALA* 3.9 6.7 - - - +
618H ILE* 1.3 78.7 - - + +
620H SER* 1.3 62.5 + - - +
622H GLU* 3.9 5.9 - - + +
623H GLN* 3.1 23.4 + - - +
626H ARG* 5.6 0.7 + - - -
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Residues in contact with SER 620 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616H ALA* 2.9 19.7 + - - +
617H VAL* 3.3 6.0 + - - -
619H LEU* 1.3 76.8 - - - +
621H LEU* 1.3 65.2 + - - +
623H GLN* 3.4 7.1 + - - +
624H GLN* 3.3 27.3 + - - +
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Residues in contact with LEU 621 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618G ILE* 4.0 9.6 - - + +
621G LEU* 3.7 35.9 - - + +
622G GLU* 3.9 22.7 - - + -
625G VAL* 4.4 14.9 - - + +
598H HIS* 3.9 20.9 - - + +
617H VAL* 2.9 38.5 + - + +
620H SER* 1.3 77.0 - - - +
622H GLU* 1.3 64.5 + - - +
624H GLN* 3.3 9.0 + - + +
625H VAL* 3.2 27.4 + - - +
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Residues in contact with GLU 622 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621G LEU* 4.2 12.7 - - + +
618H ILE* 2.9 22.6 + - + +
619H LEU* 3.9 7.2 - - + +
621H LEU* 1.3 78.2 - - - +
623H GLN* 1.3 56.9 + - - +
625H VAL* 3.5 6.8 + - - +
626H ARG* 3.0 45.2 + - - +
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Residues in contact with GLN 623 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619H LEU 3.1 17.0 + - - +
620H SER* 3.7 7.0 - - - +
621H LEU 3.2 0.4 - - - -
622H GLU* 1.3 76.0 - - - +
624H GLN* 1.3 68.9 + - - +
626H ARG* 3.0 29.8 + - - +
627H GLU* 2.9 37.7 + - + +
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Residues in contact with GLN 624 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625G VAL* 4.2 23.1 - - + +
620H SER 3.3 14.6 + - - +
621H LEU* 3.3 12.2 + - + +
623H GLN* 1.3 88.8 - - - +
625H VAL* 1.3 60.9 + - - +
627H GLU* 3.5 7.6 + - - +
628H ARG* 3.3 21.1 + - - +
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Residues in contact with VAL 625 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621G LEU* 4.2 11.0 - - + +
624G GLN* 3.3 41.7 - - + +
625G VAL* 3.7 21.5 - - + +
621H LEU 3.2 18.2 + - - +
622H GLU* 4.0 5.8 - - - +
623H GLN 3.3 0.2 - - - -
624H GLN* 1.3 75.5 - - - +
626H ARG* 1.3 61.6 + - - +
628H ARG* 3.4 20.0 + - + +
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Residues in contact with ARG 626 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619H LEU* 5.6 0.6 + - - +
622H GLU* 3.0 36.2 + - - +
623H GLN* 3.0 49.6 + - - +
624H GLN 3.3 0.2 - - - -
625H VAL* 1.3 79.2 - - - +
627H GLU* 1.3 55.8 + - - +
628H ARG 3.2 6.2 + - - -
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Residues in contact with GLU 627 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623H GLN* 2.9 30.7 + - + +
624H GLN* 3.5 10.1 + - - +
625H VAL 3.3 0.2 - - - -
626H ARG* 1.3 75.3 - - - +
628H ARG* 1.3 59.6 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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