Contacts of the helix formed by residues 615 - 624 (chain C) in PDB entry 2JLF
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 615 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613C GLU 4.8 2.7 - - - +
614C LEU* 1.3 78.8 - - - +
616C PRO* 1.4 73.3 - - - +
617C ILE* 3.0 11.6 + - - +
618C ASP* 2.9 40.6 + - - +
619C LEU* 3.4 22.7 + - - +
636C ASP 4.9 3.6 + - - +
638C SER* 3.4 14.1 - - - +
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Residues in contact with PRO 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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553C SER* 3.3 27.8 - - - -
556C ASP* 3.6 45.5 - - + +
557C THR* 5.5 2.9 - - - +
615C THR* 1.4 94.3 - - - +
617C ILE* 1.3 65.1 + - + +
619C LEU* 3.6 2.4 + - + -
620C GLU* 3.5 10.5 + - - +
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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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305C THR* 4.9 11.9 - - - +
306C THR* 5.3 8.5 - - + -
615C THR* 3.0 6.9 + - - +
616C PRO* 1.3 79.6 - - + +
618C ASP* 1.3 70.5 + - - +
619C LEU 3.0 2.0 - - - -
620C GLU* 2.7 20.8 + - - +
621C VAL* 2.8 20.5 + - + -
632C TRP* 3.5 60.6 - - + +
636C ASP* 3.9 28.7 - - + +
637C VAL* 4.6 4.5 - - + -
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Residues in contact with ASP 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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614C LEU* 4.0 12.8 - - + -
615C THR* 2.9 44.8 + - - +
617C ILE* 1.3 72.0 - - - +
619C LEU* 1.3 57.7 + - - +
621C VAL* 3.5 6.8 + - - +
622C LEU* 3.0 33.8 + - - +
636C ASP 4.2 1.4 - - - +
637C VAL* 3.6 14.6 - - - +
638C SER* 2.5 46.2 + - - -
641C ILE* 3.7 15.0 - - + +
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Residues in contact with LEU 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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549C LEU* 3.7 24.5 - - + +
552C ALA* 3.4 32.5 - - + +
553C SER* 3.9 15.5 - - - +
611C LEU* 4.0 20.2 - - + -
614C LEU* 3.3 35.7 - - + +
615C THR 3.4 14.5 + - - +
616C PRO* 3.7 7.2 - - + +
617C ILE 2.8 4.2 + - - -
618C ASP* 1.3 71.3 - - - +
620C GLU* 1.3 66.4 + - - +
622C LEU* 3.0 7.1 + - - +
623C ALA* 2.8 25.7 + - - +
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Residues in contact with GLU 620 (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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524C ASN* 4.4 6.2 + - - -
550C ALA* 4.5 14.3 - - - +
553C SER* 3.3 23.6 + - - +
554C MET* 5.0 0.5 + - - -
557C THR* 3.8 28.4 + - - +
558C TYR* 4.8 8.1 + - - -
616C PRO 3.5 8.9 + - - +
617C ILE 2.7 11.5 + - - +
619C LEU* 1.3 76.7 - - - +
621C VAL* 1.3 60.4 + - - +
623C ALA* 3.4 7.2 + - - +
624C ASP* 3.1 23.6 + - - +
627C LYS* 3.3 26.0 + - - +
632C TRP* 3.9 26.0 - - + -
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Residues in contact with VAL 621 (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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617C ILE* 2.8 18.9 + - + +
618C ASP* 3.5 10.1 - - - +
620C GLU* 1.3 76.4 - - - +
622C LEU* 1.3 55.9 + - - +
624C ASP 2.8 36.8 + - - -
625C PRO* 2.9 6.1 - - - +
627C LYS* 4.9 3.4 - - + -
628C LEU* 3.8 24.2 - - + -
632C TRP* 3.8 26.7 - - + -
637C VAL* 4.1 23.8 - - + -
641C ILE* 5.0 2.7 - - + -
645C LEU* 3.5 24.2 - - + -
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Residues in contact with LEU 622 (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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545C PRO* 3.4 13.7 - - - +
546C PHE* 3.3 39.8 + - + -
549C LEU* 3.6 28.0 - - + -
598C LEU* 3.8 25.6 - - + -
614C LEU* 4.0 9.9 - - + -
618C ASP 3.0 21.0 + - - +
619C LEU* 3.0 4.2 + - - +
621C VAL* 1.3 77.0 - - - +
623C ALA* 1.3 59.1 + - - +
641C ILE* 3.9 27.8 - - + -
644C VAL* 4.2 15.9 - - + -
645C LEU* 4.3 18.2 - - + -
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Residues in contact with ALA 623 (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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544C ARG* 3.7 23.2 + - - +
545C PRO* 4.5 1.6 - - - -
546C PHE 3.9 15.5 - - - +
547C PRO* 4.2 7.5 - - + +
549C LEU* 4.5 0.4 - - - +
550C ALA* 3.7 37.7 - - + +
619C LEU 2.8 16.0 + - - +
620C GLU* 3.7 6.3 - - - +
622C LEU* 1.3 77.4 - - - +
624C ASP* 1.3 63.3 + - + +
625C PRO* 4.4 0.7 - - - -
627C LYS* 6.0 0.2 - - - +
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Residues in contact with ASP 624 (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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524C ASN* 6.0 0.3 - - - -
543C LYS 4.2 7.1 - - - +
544C ARG* 5.6 3.5 - - + +
620C GLU 3.1 9.4 + - - +
621C VAL* 2.8 11.7 + - - +
622C LEU 3.2 1.0 + - - -
623C ALA* 1.3 81.8 - - + +
625C PRO* 1.3 63.5 - - - +
626C ASN* 3.0 28.5 + - - +
627C LYS* 3.2 47.9 + - - +
630C TYR* 4.1 5.2 + - - -
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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