Contacts of the helix formed by residues 602 - 616 (chain C) in PDB entry 2IY1
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 ASP 602 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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463C LEU* 4.0 7.0 - - - +
466C LEU* 6.0 0.2 - - - -
597C GLN* 4.2 2.6 - - + +
599C ASN* 2.6 33.7 + - - +
601C SER* 1.3 75.0 - - - +
603C ALA* 1.3 65.9 + - - +
604C GLY 3.2 2.9 - - - -
605C MET* 2.8 19.1 + - + +
606C PHE* 2.9 32.1 + - + -
624C GLN* 2.9 14.1 + - - +
627C MET* 3.5 15.0 - - + +
628C PRO* 5.6 0.2 - - - +
631C ARG* 2.7 36.1 + - - +
92D GLY 3.5 0.8 + - - -
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Residues in contact with ALA 603 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533C HIS* 3.3 32.8 - - + +
534C TRP* 3.7 17.3 - - - +
551C SER* 3.7 5.0 + - - -
597C GLN* 3.5 11.2 + - - +
601C SER 3.4 1.2 - - - -
602C ASP* 1.3 75.0 - - - +
604C GLY* 1.3 56.9 + - - +
606C PHE* 3.2 4.2 + - - +
607C ALA* 3.0 28.2 + - - +
92D GLY* 3.2 26.3 + - - +
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Residues in contact with GLY 604 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466C LEU* 3.9 19.2 - - - +
471C ILE* 4.2 4.7 - - - -
534C TRP* 3.5 30.3 - - - -
601C SER 4.7 2.4 + - - -
602C ASP 3.2 1.0 - - - -
603C ALA* 1.3 77.7 - - - +
605C MET* 1.3 57.7 + - - +
607C ALA* 3.2 3.2 + - - +
608C CYS* 3.0 34.0 + - - -
91D GLY 4.8 1.2 + - - -
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Residues in contact with MET 605 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460C LEU* 3.7 18.2 - - - -
466C LEU* 3.7 33.3 - - + +
602C ASP* 2.8 15.3 + - - +
604C GLY* 1.3 72.2 - - - +
606C PHE* 1.3 58.8 + - - +
608C CYS* 3.4 2.0 + - - +
609C LYS* 2.9 43.7 + - + +
627C MET* 3.7 15.5 - - - -
630C PHE* 3.4 42.0 - - + -
631C ARG* 3.8 22.9 - - + +
634C MET* 3.7 24.5 - - + -
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Residues in contact with PHE 606 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551C SER* 3.3 23.8 - - - +
595C PRO* 3.4 36.8 - - + -
596C GLN 3.6 7.0 - - - -
597C GLN* 3.5 36.6 - - + -
602C ASP* 2.9 22.0 + - + -
603C ALA 3.6 2.2 - - - +
605C MET* 1.3 73.2 - - - +
607C ALA* 1.3 56.8 + - - +
609C LYS* 3.2 0.8 + - - -
610C TYR* 2.7 49.7 + + + +
622C PHE* 3.7 19.3 - + - -
624C GLN* 3.8 19.1 - - - -
627C MET* 3.6 32.8 - - + -
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Residues in contact with ALA 607 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471C ILE* 5.3 5.4 - - + -
475C MET* 4.3 5.5 - - + +
527C PRO* 6.1 2.0 - - + -
534C TRP* 4.5 9.2 - - + +
535C CYS* 4.3 20.2 - - - +
536C LEU* 3.8 13.5 - - + +
603C ALA 3.0 13.3 + - - +
604C GLY* 3.2 12.8 + - - +
606C PHE* 1.3 74.9 - - - +
608C CYS* 1.3 64.5 + - - +
610C TYR* 3.5 12.1 - - - +
611C ALA* 3.1 24.4 + - - +
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Residues in contact with CYS 608 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466C LEU* 4.5 6.1 - - - -
471C ILE* 3.9 37.2 - - - -
474C TYR* 3.2 44.7 - - + -
475C MET* 4.2 6.5 - - - -
604C GLY 3.0 23.2 + - - +
605C MET* 3.8 4.0 - - - +
607C ALA* 1.3 77.0 - - - +
609C LYS* 1.3 58.5 + - - +
611C ALA* 3.4 2.8 + - - +
612C ASP* 3.0 21.5 + - - +
634C MET* 3.9 16.6 - - + -
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Residues in contact with LYS 609 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474C TYR* 3.6 11.7 + - - +
605C MET* 2.9 28.7 + - + +
608C CYS* 1.3 74.8 - - - +
610C TYR* 1.3 68.8 + - - +
612C ASP* 3.1 25.1 + - - +
613C CYS* 3.1 25.1 + - - -
622C PHE* 3.7 26.7 - - + -
627C MET* 4.4 1.3 - - + -
630C PHE* 3.6 51.9 + - + -
633C ARG* 3.9 17.4 - - - +
634C MET* 4.0 21.2 - - + +
637C GLU* 4.6 7.7 + - - -
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Residues in contact with TYR 610 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536C LEU* 3.9 9.9 - - + -
549C TYR* 3.7 24.2 - + + -
550C ASP 4.3 0.2 - - - -
551C SER* 3.2 33.1 - - - -
594C ILE* 3.3 30.1 - - + +
595C PRO* 2.6 36.7 + - + -
606C PHE* 2.7 37.2 + + + +
607C ALA* 3.5 10.1 - - - +
609C LYS* 1.3 74.4 - - - +
611C ALA* 1.3 61.8 + - - +
613C CYS* 3.2 3.6 + - - +
614C ILE* 3.0 33.1 + - + +
620C ILE* 4.2 14.3 - - + +
622C PHE* 3.5 22.0 - + - -
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Residues in contact with ALA 611 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475C MET* 3.9 13.5 - - + -
478C LEU* 3.6 18.2 - - + -
525C LEU* 4.2 13.0 - - + -
536C LEU* 3.9 13.2 - - + +
607C ALA 3.1 15.0 + - - +
608C CYS 3.6 5.6 - - - +
609C LYS 3.2 0.2 - - - -
610C TYR* 1.3 79.3 - - - +
612C ASP* 1.3 56.0 + - - +
614C ILE* 3.3 6.1 + - - +
615C THR* 2.9 36.9 + - - +
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Residues in contact with ASP 612 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474C TYR* 3.4 24.9 + - + +
478C LEU* 4.0 7.1 - - - +
481C ARG* 2.9 35.8 + - - +
608C CYS 3.0 8.2 + - - +
609C LYS* 3.1 30.0 + - - +
611C ALA* 1.3 74.1 - - - +
613C CYS* 1.3 66.7 + - - +
615C THR* 3.1 17.2 + - - -
616C LYS* 3.2 27.6 + - - +
633C ARG* 4.5 6.3 + - - -
643C LEU* 5.1 1.7 - - - +
644C LEU 5.4 0.4 - - - +
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Residues in contact with CYS 613 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609C LYS* 3.1 12.8 + - - +
610C TYR 3.6 6.7 - - - +
612C ASP* 1.3 83.2 - - - +
614C ILE* 1.3 58.7 + - - +
616C LYS* 3.1 13.5 + - - +
617C ASP 3.0 21.0 + - - -
618C ARG* 3.1 28.6 + - + +
619C PRO 4.0 8.5 - - - -
620C ILE* 4.0 17.9 - - + -
621C ASN* 3.9 20.9 - - - -
622C PHE* 4.0 12.3 - - - -
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Residues in contact with ILE 614 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523C ILE* 3.9 19.5 - - + +
525C LEU* 5.1 0.7 - - + -
536C LEU* 4.3 4.0 - - + -
538C VAL* 4.2 26.0 - - + -
540C ASP* 5.4 3.1 - - - +
549C TYR* 3.5 46.4 - - + +
610C TYR* 3.0 29.2 + - + +
611C ALA* 3.7 6.5 - - - +
612C ASP 3.3 0.4 - - - -
613C CYS* 1.3 78.6 - - + +
615C THR* 1.3 62.3 + - + +
617C ASP* 3.0 26.7 + - - +
618C ARG 4.9 2.2 - - - +
620C ILE* 5.0 8.7 - - + -
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Residues in contact with THR 615 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478C LEU* 4.2 12.6 - - + +
481C ARG* 2.7 30.1 + - - -
482C SER* 5.8 1.6 - - - -
487C LEU* 4.3 11.1 - - - +
488C PRO* 3.3 27.9 - - - +
490C VAL* 3.8 26.5 - - + -
523C ILE* 4.5 3.8 - - + -
525C LEU* 3.9 29.4 - - + -
611C ALA 2.9 22.7 + - - +
612C ASP* 3.1 1.7 + - - -
614C ILE* 1.3 75.7 - - - +
616C LYS* 1.3 57.8 + - - +
617C ASP 3.4 0.2 - - - -
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Residues in contact with LYS 616 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481C ARG* 3.7 30.1 - - - +
487C LEU* 4.6 19.7 - - + +
488C PRO* 4.8 2.2 - - - +
612C ASP* 3.2 35.9 + - - +
613C CYS* 3.1 14.7 + - - +
615C THR* 1.3 76.9 - - - +
617C ASP* 1.3 71.0 + - - +
618C ARG* 3.4 28.7 + - + +
633C ARG* 5.4 2.0 - - - +
644C LEU 4.4 10.9 + - - -
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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