Contacts of the helix formed by residues 605 - 619 (chain C) in PDB entry 3J8B
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 LEU 605 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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594C MET* 5.0 12.1 - - + +
595C GLU* 6.2 0.7 - - - -
598C SER* 4.1 12.7 - - - -
603C LEU 3.5 2.3 + - - -
604C ASP* 1.3 71.3 - - - +
606C PRO* 1.3 63.6 - - - +
608C VAL* 3.0 10.2 + - + -
609C HIS* 2.9 30.9 + - + +
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Residues in contact with PRO 606 (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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604C ASP* 3.1 6.4 - - + +
605C LEU* 1.3 77.3 - - - +
607C THR* 1.3 60.4 + - - +
609C HIS* 4.8 2.1 - - + +
610C SER* 3.2 21.8 + - - -
304E ASP* 5.8 0.5 - - - +
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Residues in contact with THR 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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603C LEU* 4.8 11.0 - - - -
604C ASP* 2.9 14.4 + - - +
606C PRO* 1.3 78.4 - - - +
608C VAL* 1.3 58.7 + - - +
610C SER* 3.3 5.5 + - - -
611C ILE* 2.9 32.4 + - - +
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Residues in contact with VAL 608 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594C MET* 5.1 14.4 - - + +
597C LEU* 5.8 4.5 - - + -
598C SER* 5.2 4.3 - - - +
603C LEU* 4.7 11.6 - - + +
604C ASP 3.3 4.0 + - - +
605C LEU* 3.0 17.6 + - + +
607C THR* 1.3 79.7 - - - +
609C HIS* 1.3 65.6 + - - +
611C ILE* 3.2 4.6 + - - +
612C ILE* 2.9 27.3 + - - +
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Residues in contact with HIS 609 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594C MET* 5.9 6.8 - - + +
605C LEU* 2.9 17.7 + - + +
606C PRO* 4.8 2.5 - - + +
608C VAL* 1.3 73.3 - - - +
610C SER* 1.3 57.4 + - - +
612C ILE* 4.7 3.8 - - - -
613C SER* 2.9 35.6 + - - -
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Residues in contact with SER 610 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606C PRO 3.2 21.2 + - - -
607C THR* 3.3 6.4 + - - -
608C VAL 3.1 0.4 - - - -
609C HIS* 1.3 77.8 - - - +
611C ILE* 1.3 56.7 + - - +
613C SER* 4.8 0.7 - - - -
614C LYS* 2.9 33.6 + - - +
302E ASN 3.6 9.2 - - - +
303E PHE* 3.8 11.6 - - - +
304E ASP* 4.4 22.2 - - - -
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Residues in contact with ILE 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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575C GLU* 5.7 8.5 - - + +
578C LEU* 6.4 2.0 - - + -
579C ARG* 6.0 6.5 - - + +
607C THR 2.9 19.7 + - - +
608C VAL* 3.7 4.7 - - - +
610C SER* 1.3 72.1 - - - +
612C ILE* 1.3 58.2 + - - +
614C LYS* 3.7 4.4 - - - +
615C MET* 2.9 32.3 + - - +
302E ASN 5.4 0.2 - - - -
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Residues in contact with ILE 612 (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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582C LEU* 6.2 3.8 - - + -
608C VAL 2.9 16.8 + - - +
609C HIS* 4.0 4.9 - - - +
611C ILE* 1.3 77.9 - - - +
613C SER* 1.3 56.4 + - - +
615C MET* 3.8 4.2 - - - +
616C ILE* 2.9 33.1 + - - +
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Residues in contact with SER 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 HIS 2.9 19.9 + - - -
610C SER* 4.0 2.5 - - - -
612C ILE* 1.3 73.8 - - - +
614C LYS* 1.3 66.7 + - - +
616C ILE* 3.4 5.6 + - - +
617C ILE* 2.9 26.4 + - - +
625C LEU* 5.9 7.6 - - - -
303E PHE* 4.5 9.4 - - - -
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Residues in contact with LYS 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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610C SER 2.9 13.7 + - - +
611C ILE* 3.7 4.7 - - - +
613C SER* 1.3 77.9 - - - +
615C MET* 1.3 57.3 + - - +
617C ILE* 3.2 5.5 + - - +
618C ASN* 2.9 30.4 + - - +
301E VAL 5.0 2.5 - - - +
302E ASN* 3.1 35.2 - - + +
303E PHE* 3.5 9.8 - - + +
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Residues in contact with MET 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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579C ARG* 6.3 3.4 - - + -
611C ILE 2.9 19.4 + - - +
612C ILE* 3.8 4.9 - - - +
614C LYS* 1.3 75.5 - - - +
616C ILE* 1.3 53.6 + - - +
618C ASN* 3.0 6.8 + - - +
619C GLU* 2.8 39.2 + - + +
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Residues in contact with ILE 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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612C ILE 2.9 22.2 + - - +
613C SER* 3.8 5.8 - - - +
615C MET* 1.3 72.2 - - - +
617C ILE* 1.3 56.9 + - - +
620C GLU* 3.1 9.4 + - - -
621C LEU* 3.0 47.3 + - + +
623C ALA* 4.5 18.8 - - + +
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Residues in contact with ILE 617 (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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613C SER 2.9 17.7 + - - +
614C LYS* 3.6 5.6 - - - +
616C ILE* 1.3 76.8 - - - +
618C ASN* 1.3 61.6 + - - +
620C GLU* 3.8 7.2 + - - +
347E ILE* 6.5 1.3 - - + -
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Residues in contact with ASN 618 (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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497C ARG* 4.6 3.8 - - - +
614C LYS 2.9 16.7 + - - +
615C MET* 3.6 7.4 - - - +
617C ILE* 1.3 79.0 - - - +
619C GLU* 1.3 59.2 + - + +
620C GLU* 3.3 1.3 + - - +
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Residues in contact with GLU 619 (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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495C ALA* 5.3 11.5 - - + +
497C ARG* 3.5 30.9 - - + +
615C MET* 2.8 17.0 + - + +
618C ASN* 1.3 76.1 - - + +
620C GLU* 1.3 70.3 + - - +
621C LEU* 3.1 11.7 + - + +
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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