Contacts of the helix formed by residues 607 - 623 (chain C) in PDB entry 2FGJ
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 SER 607 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606C LEU* 1.3 76.3 - - - +
608C GLY* 1.3 66.5 + - - +
610C GLN* 2.9 43.5 + - - +
611C ARG* 2.9 12.2 + - - +
505D GLY* 3.8 2.6 + - - -
803D ATP 2.9 63.6 + - - -
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Residues in contact with GLY 608 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606C LEU 4.0 0.8 + - - -
607C SER* 1.3 71.1 - - - +
609C GLY* 1.3 56.6 + - - +
611C ARG* 3.3 23.0 + - - +
612C GLN* 2.9 30.7 + - - +
550D GLN* 5.8 6.3 - - - -
803D ATP 3.7 12.1 + - - -
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Residues in contact with GLY 609 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608C GLY* 1.3 69.0 - - - -
610C GLN* 1.3 58.9 + - - +
612C GLN* 3.6 4.4 - - - +
613C ARG* 3.0 36.7 + - - +
635C ALA 5.3 3.9 + - - -
636C LEU* 3.5 18.8 - - - +
504D SER* 3.4 10.3 - - - -
803D ATP 2.6 24.7 + - - -
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Residues in contact with GLN 610 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587C PHE* 3.4 57.6 - - + +
591C LEU* 5.7 3.4 - - - +
606C LEU* 4.0 9.2 - - + +
607C SER* 2.9 40.2 + - - +
609C GLY* 1.3 74.1 - - - +
611C ARG* 1.3 64.4 + - - +
613C ARG* 3.1 5.7 + - - +
614C ILE* 3.0 29.7 + - - +
504D SER* 3.6 10.3 + - - +
505D GLY* 4.5 8.2 - - - -
803D ATP 3.3 28.5 + - - -
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Residues in contact with ARG 611 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551C ASP* 4.0 17.2 + - - +
552C ASN* 2.6 36.8 + - - +
553C VAL* 4.0 3.8 + - - +
554C LEU* 3.9 22.8 - - + +
604C ALA* 3.3 30.6 + - + +
606C LEU* 3.9 26.2 + - + +
607C SER 2.9 15.2 + - - +
608C GLY* 3.5 20.7 + - - +
610C GLN* 1.3 74.3 - - - +
612C GLN* 1.3 58.5 + - - +
614C ILE* 3.3 5.6 + - - +
615C ALA* 3.0 28.3 + - - +
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Residues in contact with GLN 612 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548C VAL* 4.0 4.9 - - - +
549C LEU 2.7 26.9 + - - -
550C GLN* 2.8 24.6 + - - +
551C ASP* 4.2 0.2 - - - -
552C ASN* 3.1 20.0 + - - +
608C GLY 2.9 17.8 + - - +
609C GLY* 3.6 10.5 - - - +
610C GLN 3.2 0.2 - - - -
611C ARG* 1.3 78.1 + - - +
613C ARG* 1.3 57.4 + - - +
615C ALA* 3.3 6.8 + - - +
616C ILE* 3.1 32.1 + - + +
632C ALA* 2.9 35.8 + - - +
635C ALA* 6.6 0.2 - - + -
636C LEU* 4.9 9.2 - - + -
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Residues in contact with ARG 613 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582C ALA* 3.3 31.3 + - - +
583C GLY* 2.6 29.5 + - - -
584C ALA* 4.1 12.5 - - + +
586C ASP* 5.9 1.2 - - - +
587C PHE* 3.3 29.7 - - + +
609C GLY 3.0 20.7 + - - +
610C GLN* 3.1 6.9 + - - +
612C GLN* 1.3 73.2 - - - +
614C ILE* 1.3 64.6 + - - +
616C ILE* 3.4 6.3 + - + -
617C ALA* 3.2 17.0 + - - +
636C LEU* 3.9 27.6 - - + -
640C SER* 3.7 16.9 + - - -
644C ILE* 4.4 3.4 - - + -
504D SER* 3.0 38.6 + - - -
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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
----------------------------------------------------------
554C LEU* 3.8 24.0 - - + -
559C ILE* 4.2 15.0 - - + +
562C ASN* 4.7 9.4 - - + +
563C ILE* 4.0 20.7 - - + +
584C ALA* 4.1 3.8 - - + -
587C PHE* 3.7 15.3 - - + -
588C ILE* 3.5 33.4 - - + -
599C VAL* 5.8 0.7 - - + -
606C LEU* 4.5 11.4 - - + -
610C GLN 3.0 21.7 + - - +
611C ARG* 3.4 9.9 - - - +
612C GLN 3.3 0.2 - - - -
613C ARG* 1.3 74.6 - - - +
615C ALA* 1.3 57.9 + - - +
617C ALA* 3.0 9.8 + - - +
618C ARG* 2.9 24.9 + - - +
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Residues in contact with ALA 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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548C VAL* 4.3 8.0 - - + +
552C ASN* 3.4 39.3 - - + +
554C LEU* 4.6 4.0 - - + +
611C ARG 3.0 13.4 + - - +
612C GLN* 3.4 9.9 - - - +
614C ILE* 1.3 76.6 - - - +
616C ILE* 1.3 57.1 + - - +
618C ARG* 3.2 19.7 + - - +
619C ALA* 3.0 27.7 + - - +
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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
----------------------------------------------------------
548C VAL* 3.5 30.3 - - + -
581C LEU 5.5 0.2 - - - +
582C ALA* 3.8 18.6 - - + -
612C GLN* 3.1 17.1 + - + +
613C ARG* 3.5 12.8 - - + +
614C ILE 3.2 0.2 - - - -
615C ALA* 1.3 76.1 - - - +
617C ALA* 1.3 62.9 + - - +
619C ALA* 3.1 4.7 + - - +
620C LEU* 3.0 38.1 + - + +
629C PHE* 3.7 37.4 - - + -
632C ALA* 4.1 13.2 - - + +
633C THR* 5.3 1.6 - - + -
644C ILE* 4.6 17.9 - - + -
651C ILE* 5.6 1.3 - - + -
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Residues in contact with ALA 617 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563C ILE* 3.8 24.9 - - + -
578C ALA* 3.7 30.6 - - - +
579C ALA* 4.2 6.1 - - + -
582C ALA* 3.9 0.6 - - + +
584C ALA* 5.2 1.1 - - + -
613C ARG 3.2 9.6 + - - +
614C ILE* 3.0 10.2 + - - +
616C ILE* 1.3 78.9 - - - +
618C ARG* 1.3 62.9 + - - +
620C LEU* 3.3 5.4 + - - +
621C VAL* 3.0 27.7 + - - +
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Residues in contact with ARG 618 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552C ASN* 4.4 13.5 - - - +
553C VAL* 4.8 7.1 - - - +
554C LEU* 3.5 44.5 - - + +
555C LEU* 5.1 0.6 - - - +
562C ASN* 3.2 30.7 + - - +
563C ILE* 4.0 17.2 - - - +
565C LEU* 3.8 28.3 - - + +
614C ILE* 2.9 12.9 + - + +
615C ALA* 3.2 26.8 + - - +
617C ALA* 1.3 75.3 - - - +
619C ALA* 1.3 62.6 + - - +
621C VAL* 3.1 3.8 + - - +
622C ASN* 3.0 43.8 + - - +
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Residues in contact with ALA 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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546C GLY* 5.6 3.4 - - - -
547C VAL 5.3 3.4 - - - +
548C VAL* 3.5 30.3 - - + -
615C ALA 3.0 8.1 + - - +
616C ILE 3.5 8.1 - - - +
618C ARG* 1.3 76.6 - - - +
620C LEU* 1.3 61.9 + - - +
622C ASN* 3.3 15.1 + - - +
624C PRO* 3.3 26.8 - - + +
627C LEU* 3.7 18.8 - - + +
629C PHE* 5.4 0.4 - - + -
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Residues in contact with LEU 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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578C ALA* 3.8 31.2 - - + +
581C LEU* 4.0 24.5 - - + -
582C ALA 4.7 0.9 - - - +
616C ILE* 3.0 35.4 + - + +
617C ALA* 3.6 5.8 - - - +
618C ARG 3.2 0.2 - - - -
619C ALA* 1.3 76.3 - - - +
621C VAL* 1.3 52.6 + - - +
623C ASN* 2.6 33.8 + - - -
627C LEU* 3.6 27.8 - - + -
629C PHE* 5.5 0.4 - - + -
651C ILE* 3.8 25.6 - - + -
655C ARG* 4.1 15.5 + - - +
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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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563C ILE* 3.3 39.9 - - + +
564C SER* 4.4 3.1 - - - -
566C ALA* 5.1 0.3 - - - +
567C ASN* 4.5 17.3 + - + +
570C MET* 3.5 36.9 - - + +
574C LYS 4.7 1.8 - - - +
575C VAL* 4.7 4.3 - - - -
578C ALA* 3.9 15.7 - - + -
617C ALA 3.0 16.3 + - - +
618C ARG 3.1 4.2 + - - +
620C LEU* 1.3 74.3 - - - +
622C ASN* 1.3 66.5 + - - +
623C ASN* 3.1 10.8 + - - +
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Residues in contact with ASN 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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543C ARG 5.7 0.2 - - - +
565C LEU* 5.1 2.0 - - - +
566C ALA* 3.2 36.0 + - + +
618C ARG* 3.0 36.2 + - - +
619C ALA* 3.3 16.3 + - - +
621C VAL* 1.3 79.1 - - - +
623C ASN* 1.3 67.8 + - - +
624C PRO* 3.6 6.5 - - + +
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Residues in contact with ASN 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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543C ARG 4.8 2.4 - - - +
620C LEU 2.6 30.6 + - - -
621C VAL* 3.1 9.7 + - - +
622C ASN* 1.3 80.4 - - - +
624C PRO* 1.3 73.0 - - - +
625C LYS* 3.9 1.4 + - - +
655C ARG* 4.2 19.1 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
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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