Contacts of the helix formed by residues 617 - 629 (chain F) in PDB entry 6NYY
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 617 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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570E THR* 6.4 0.9 - - + -
641E ARG* 4.5 22.5 - - + +
642E ILE 3.4 12.3 - - - +
643E THR* 3.8 22.7 - - + +
587F HIS* 5.5 1.0 - - - -
615F LEU 4.4 3.4 - - - +
616F TYR* 1.3 78.5 - - - +
618F LYS* 1.3 64.9 + - - +
619F GLU* 3.5 13.1 + - - +
620F GLN* 3.2 37.7 + - - +
621F LEU* 3.3 21.3 + - - +
666F MET* 4.6 1.8 - - - -
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Residues in contact with LYS 618 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641E ARG* 6.1 0.2 - - - -
642E ILE* 3.2 26.3 + - + +
617F THR* 1.3 76.5 - - - +
619F GLU* 1.3 71.6 + - - +
621F LEU* 3.9 0.6 + - - -
622F LEU* 3.6 19.8 + - - +
660F GLN* 4.0 21.4 + - - +
666F MET* 3.7 51.4 + - + +
667F ASN* 4.7 5.5 + - - +
668F GLU* 5.4 2.2 - - - +
704F LEU* 5.9 4.3 - - - -
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Residues in contact with GLU 619 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640E GLY 4.9 4.9 - - - +
641E ARG* 3.7 32.9 - - - +
587F HIS* 4.3 14.1 - - + +
617F THR* 3.2 8.1 + - - +
618F LYS* 1.3 90.9 + - + +
620F GLN* 1.3 62.2 + - - +
621F LEU 3.3 1.3 - - - -
622F LEU* 3.8 10.7 - - + +
623F ASP* 3.3 29.6 + - - +
711F ARG* 5.3 4.5 + - - +
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Residues in contact with GLN 620 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567E GLU* 5.9 0.2 + - - -
587F HIS* 3.4 46.2 + - + +
613F GLN* 2.9 34.1 + - - +
615F LEU 3.4 16.0 + - - +
616F TYR* 3.4 12.3 - - + -
617F THR* 3.2 35.2 + - - +
619F GLU* 1.3 77.4 - - - +
621F LEU* 1.3 62.5 + - - +
623F ASP 4.0 0.9 + - - -
624F ARG* 3.7 24.9 + - - +
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Residues in contact with LEU 621 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644E THR* 4.7 1.6 - - + -
616F TYR* 3.8 28.9 - - + +
617F THR 3.3 13.2 + - - +
618F LYS 4.2 4.7 - - - +
619F GLU 3.3 0.2 - - - -
620F GLN* 1.3 77.9 - - - +
622F LEU* 1.3 63.0 + - - +
623F ASP 3.2 0.4 - - - -
624F ARG* 3.1 14.3 + - + +
625F MET* 3.1 24.7 + - - +
656F SER* 4.7 13.9 + - - +
660F GLN* 4.0 26.7 - - + +
664F PHE* 4.6 16.8 - - + -
666F MET* 3.8 28.7 - - - -
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Residues in contact with LEU 622 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618F LYS 3.6 15.7 + - - +
619F GLU* 3.6 11.5 + - + +
620F GLN 3.4 0.6 - - - -
621F LEU* 1.3 78.1 - - - +
623F ASP* 1.3 57.6 + - - +
624F ARG 3.2 0.2 - - - -
625F MET* 3.5 12.9 + - - +
626F CYS* 3.0 37.0 + - - -
660F GLN* 5.4 2.7 - - - +
704F LEU* 4.6 15.5 - - + -
707F ASP* 5.1 6.1 - - + +
708F ALA* 3.8 31.2 - - + +
711F ARG* 3.5 28.7 - - - +
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Residues in contact with ASP 623 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585F LEU* 3.7 27.2 - - + +
586F GLU* 4.4 2.8 + - - +
587F HIS* 3.1 57.9 + - + +
588F ALA* 4.3 6.4 - - - +
619F GLU* 3.3 9.4 + - - +
620F GLN 4.4 0.7 - - - +
621F LEU 3.2 1.0 - - - -
622F LEU* 1.3 75.6 - - - +
624F ARG* 1.3 60.0 + - - +
626F CYS* 5.1 0.2 - - - +
627F MET* 3.3 21.3 + - - +
711F ARG* 3.1 37.3 + - - -
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Residues in contact with ARG 624 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587F HIS 4.1 12.1 - - - +
588F ALA* 4.9 4.0 - - - -
589F ASP* 3.9 28.9 + - - +
608F TYR* 6.1 1.4 - - - -
610F PRO* 6.4 0.4 - - - +
616F TYR* 4.0 33.7 + - - -
620F GLN 3.7 15.7 - - - +
621F LEU* 3.1 15.2 + - - +
623F ASP* 1.3 81.4 - - - +
625F MET* 1.3 57.7 + - - +
626F CYS 3.4 0.2 - - - -
627F MET* 3.6 19.1 - - + +
628F THR* 2.6 35.7 + - - +
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Residues in contact with MET 625 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621F LEU 3.1 15.3 + - - +
622F LEU* 3.9 15.9 - - - +
624F ARG* 1.3 76.2 - - - +
626F CYS* 1.3 53.4 + - - +
628F THR* 3.2 1.3 + - - +
629F LEU* 2.7 41.5 + - - +
653F VAL* 3.8 23.8 - - + -
656F SER* 4.4 17.7 - - - +
657F ALA* 4.2 8.1 - - + -
660F GLN* 3.8 22.9 - - - +
704F LEU* 3.8 28.7 - - + +
705F ILE* 3.8 32.5 - - + -
708F ALA* 3.8 9.6 - - + -
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Residues in contact with CYS 626 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581F ALA* 4.0 4.7 - - - +
585F LEU* 3.7 22.4 - - + -
622F LEU* 3.0 23.9 + - - +
623F ASP* 4.4 0.7 - - - -
625F MET* 1.3 75.5 - - - +
627F MET* 1.3 61.6 + - - +
629F LEU* 4.0 0.7 - - - -
630F GLY* 3.4 12.1 + - - -
708F ALA* 3.3 31.9 - - - -
711F ARG* 3.7 31.0 - - + -
712F THR* 3.3 29.1 + - + +
715F LEU* 6.2 0.2 - - + -
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Residues in contact with MET 627 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578F HIS* 2.9 30.4 + - - +
581F ALA* 4.6 8.1 - - - +
582F GLY* 3.8 28.0 - - - +
585F LEU* 4.4 0.2 - - - +
588F ALA* 4.7 5.2 - - + -
589F ASP* 4.5 15.9 - - + +
608F TYR* 3.1 46.9 - - + -
623F ASP 3.3 20.5 + - - +
624F ARG* 3.8 20.9 - - + +
625F MET 3.2 0.8 - - - -
626F CYS* 1.3 78.4 - - - +
628F THR* 1.3 72.6 + - - +
630F GLY* 3.2 7.1 + - - -
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Residues in contact with THR 628 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578F HIS* 3.1 22.5 - - + -
624F ARG* 2.6 22.8 + - - +
625F MET* 3.9 2.7 - - - -
627F MET* 1.3 88.5 - - - +
629F LEU* 1.3 58.4 + - - +
630F GLY 3.1 1.7 + - - -
631F GLY 4.2 0.2 + - - -
632F ARG* 5.2 1.0 + - - +
649F ASP* 3.3 49.5 - - + +
652F LYS* 4.3 20.2 - - + +
653F VAL* 3.9 9.9 - - + -
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Residues in contact with LEU 629 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672A GLN* 4.8 3.4 - - + +
625F MET 2.7 23.4 + - - +
626F CYS 3.9 1.3 - - - -
628F THR* 1.3 70.3 - - - +
630F GLY* 1.3 60.6 + - - +
631F GLY 3.3 2.6 + - - -
632F ARG* 3.7 11.2 + - + +
633F VAL* 3.3 27.2 + - + +
649F ASP 5.9 0.2 - - - -
650F LEU* 3.7 30.3 - - + -
653F VAL* 3.9 17.3 - - + -
705F ILE* 3.9 17.0 - - + +
708F ALA* 3.7 37.5 - - + +
709F TYR* 3.8 16.6 - - + +
712F THR* 4.1 10.1 - - - +
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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