Contacts of the helix formed by residues 619 - 640 (chain C) in PDB entry 3T6A
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 619 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618C GLY* 1.3 77.6 + - - -
620C LEU* 1.3 65.8 + - - +
621C GLU* 3.4 16.1 + - - +
622C ASP* 2.9 47.5 + - - +
623C ARG* 3.0 14.7 + - - +
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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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619C THR* 1.3 72.2 - - - +
621C GLU* 1.3 75.7 + - - +
623C ARG* 3.1 39.5 + - - +
624C ALA* 2.9 20.4 + - - +
664C LYS* 3.9 16.6 - - + +
665C THR* 3.8 28.5 - - - +
668C ALA* 4.3 15.9 - - + -
672C GLN* 5.9 0.2 - - - +
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Residues in contact with GLU 621 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619C THR* 3.2 14.3 + - - +
620C LEU* 1.3 88.7 + - - +
622C ASP* 1.3 66.4 + - - +
624C ALA* 3.2 5.4 + - - +
625C ALA* 2.9 22.1 + - - +
672C GLN* 3.5 35.8 + - - +
673C TYR* 4.4 0.2 + - - -
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Residues in contact with ASP 622 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541C LYS* 5.8 1.6 - - - +
617C THR* 4.1 4.3 - - + -
618C GLY* 4.1 10.2 + - - +
619C THR* 2.9 42.3 + - - +
621C GLU* 1.3 77.7 - - - +
623C ARG* 1.3 57.4 + - - +
625C ALA* 3.1 9.4 + - - +
626C THR* 2.8 32.4 + - - -
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Residues in contact with ARG 623 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613C ILE* 3.5 38.3 - - + +
617C THR* 3.5 20.4 - - + +
618C GLY 4.4 6.3 + - - -
619C THR 3.0 11.7 + - - +
620C LEU* 3.2 41.3 - - - +
622C ASP* 1.3 75.2 - - - +
624C ALA* 1.3 65.0 + - - +
626C THR* 3.3 2.6 + - - -
627C LEU* 3.0 23.0 + - - +
662C LEU* 4.6 2.4 - - - +
664C LYS* 5.9 0.2 - - - +
665C THR* 2.9 21.1 + - + +
815C LEU* 3.6 39.0 + - - +
816C GLU* 3.0 34.4 + - - +
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Residues in contact with ALA 624 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620C LEU 2.9 8.0 + - - +
621C GLU* 3.2 10.5 + - - +
623C ARG* 1.3 75.6 - - - +
625C ALA* 1.3 56.9 + - - +
627C LEU* 3.2 6.0 + - - +
628C SER* 2.9 28.8 + - - -
665C THR* 4.1 10.4 - - - +
668C ALA* 3.7 30.5 - - + +
669C LEU* 4.0 13.3 - - - +
672C GLN* 4.6 1.8 - - - +
673C TYR* 3.9 15.1 - - + -
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Residues in contact with ALA 625 (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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621C GLU 2.9 11.4 + - - +
622C ASP* 3.1 13.2 + - - +
624C ALA* 1.3 77.2 - - - +
626C THR* 1.3 56.3 + - - +
628C SER* 3.4 3.5 + - - -
629C LYS* 3.0 28.6 + - - +
673C TYR* 3.1 29.6 - - + +
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Residues in contact with THR 626 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541C LYS* 2.7 31.6 + - - +
612C ASP* 3.0 37.0 - - - +
613C ILE* 4.5 3.8 - - + -
617C THR* 3.4 7.7 - - - +
622C ASP 2.8 13.7 + - - -
623C ARG 3.6 7.2 - - - -
625C ALA* 1.3 74.1 - - - +
627C LEU* 1.3 63.8 + - - +
629C LYS* 3.1 7.7 + - + +
630C ILE* 3.0 40.5 + - + +
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Residues in contact with LEU 627 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613C ILE* 3.9 18.8 - - + +
623C ARG 3.0 13.0 + - - +
624C ALA 3.3 9.9 - - - +
626C THR* 1.3 76.5 - - - +
628C SER* 1.3 61.9 + - - +
630C ILE* 3.4 7.2 + - + +
631C ILE* 3.1 29.9 + - + +
654C LEU* 3.4 33.9 - - + -
659C ILE* 5.2 2.0 - - + -
665C THR* 4.1 20.0 - - + -
666C TRP* 3.9 35.7 - - + -
669C LEU* 3.9 24.5 - - + -
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Residues in contact with SER 628 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624C ALA 2.9 14.2 + - - -
625C ALA* 3.5 9.0 - - - -
626C THR 3.2 0.2 - - - -
627C LEU* 1.3 76.8 - - - +
629C LYS* 1.3 62.8 + - - +
631C ILE* 3.3 2.6 + - - +
632C GLN* 2.9 35.2 + - - +
669C LEU* 3.9 10.2 - - - +
673C TYR* 3.5 40.2 - - - +
676C THR* 3.7 16.4 + - - +
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Residues in contact with LYS 629 (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 PHE* 3.0 29.6 + - + +
545C THR* 4.0 10.9 + - - +
547C ASN 3.0 21.4 + - - -
548C ASP* 4.4 0.8 - - - +
549C PRO* 4.3 21.7 - - + +
552C ILE* 4.0 12.6 - - + -
625C ALA 3.0 14.8 + - - +
626C THR* 3.1 12.5 + - + +
628C SER* 1.3 73.9 - - - +
630C ILE* 1.3 58.3 + - + +
632C GLN* 3.1 16.9 + - - +
633C VAL* 2.8 34.1 + - + +
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Residues in contact with ILE 630 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609C ILE* 3.7 31.6 - - + +
612C ASP* 5.0 4.0 - - + +
613C ILE* 3.3 40.6 - - + +
626C THR* 3.0 25.0 + - + +
627C LEU* 3.5 7.4 - - + +
629C LYS* 1.3 77.4 - - + +
631C ILE* 1.3 61.8 + - - +
633C VAL* 3.2 6.9 + - - +
634C ALA* 2.9 18.5 + - - +
650C LEU* 3.4 20.6 - - + +
654C LEU* 4.2 20.9 - - + -
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Residues in contact with ILE 631 (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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627C LEU* 3.1 20.3 + - + +
628C SER 3.3 1.5 + - - +
630C ILE* 1.3 75.4 - - - +
632C GLN* 1.3 57.6 + - - +
634C ALA* 3.1 9.2 + - - +
635C VAL* 2.9 26.9 + - - +
654C LEU* 3.8 20.9 - - + -
666C TRP* 4.6 2.5 - - + -
669C LEU* 3.9 23.6 - - + -
676C THR* 3.4 41.1 - - + +
679C LEU* 4.3 7.2 - - + -
680C TYR* 3.8 31.2 - - + -
684C LEU* 4.1 12.1 - - + -
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Residues in contact with GLN 632 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549C PRO* 3.8 27.1 - - + +
628C SER* 2.9 25.9 + - - +
629C LYS* 3.3 20.2 + - - +
631C ILE* 1.3 76.6 - - - +
633C VAL* 1.3 61.0 + - - +
635C VAL* 3.4 11.0 + - - +
636C GLU* 3.2 25.5 + - - +
676C THR* 4.2 18.3 + - + +
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Residues in contact with VAL 633 (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 PRO* 4.1 26.5 - - + +
552C ILE* 4.1 35.2 - - + -
553C ALA* 4.5 2.9 - - + +
556C VAL* 5.6 1.6 - - + -
629C LYS* 2.8 22.6 + - + +
630C ILE* 3.6 9.0 - - - +
632C GLN* 1.3 73.4 - - - +
634C ALA* 1.3 60.7 + - - +
636C GLU* 3.2 4.1 + - - +
637C LEU* 2.9 41.8 + - + +
650C LEU* 3.9 15.7 - - + -
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Residues in contact with ALA 634 (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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630C ILE 2.9 13.0 + - - +
631C ILE* 3.1 12.5 + - - +
633C VAL* 1.3 75.9 - - - +
635C VAL* 1.3 61.4 + - - +
637C LEU* 3.3 6.2 + - - +
638C LYS* 3.0 18.0 + - - +
647C PHE* 3.4 26.8 - - + -
650C LEU* 3.7 21.9 - - + +
651C MET* 4.7 5.8 - - - -
654C LEU* 5.6 1.8 - - + -
684C LEU* 4.1 14.8 - - + -
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Residues in contact with VAL 635 (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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631C ILE 2.9 17.6 + - - +
632C GLN* 3.5 11.7 - - - +
633C VAL 3.3 0.2 - - - -
634C ALA* 1.3 76.8 - - - +
636C GLU* 1.3 67.0 + - - +
638C LYS* 3.2 5.4 + - - +
639C ASP* 2.8 44.5 + - + +
679C LEU* 2.9 42.0 - - + -
684C LEU* 4.0 13.4 - - + +
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Residues in contact with GLU 636 (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 PRO* 3.8 7.6 - - + +
550C LYS* 3.1 50.5 + - - +
553C ALA* 3.6 19.1 - - + -
632C GLN 3.2 15.2 + - - +
633C VAL 3.2 7.2 + - - +
635C VAL* 1.3 80.9 - - + +
637C LEU* 1.3 63.3 + - - +
639C ASP* 5.3 0.2 - - - -
640C SER* 2.8 48.2 + - - -
641C MET* 2.9 9.9 + - - +
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Residues in contact with LEU 637 (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 ALA* 3.6 34.1 - - + +
556C VAL* 4.1 17.5 - - + -
557C LEU 4.6 0.2 - - - +
633C VAL* 2.9 33.6 + - + +
634C ALA 3.5 5.4 - - - +
636C GLU* 1.3 76.2 - - - +
638C LYS* 1.3 57.3 + - - +
641C MET* 3.6 7.2 - - + -
642C GLY 2.8 8.3 + - - -
643C ASP* 2.8 51.7 + - + +
646C SER* 4.0 29.6 - - - +
647C PHE* 4.0 6.3 - - + +
650C LEU* 4.2 14.1 - - + -
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Residues in contact with LYS 638 (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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634C ALA 3.0 15.6 + - - +
635C VAL* 3.7 4.3 - - - +
637C LEU* 1.3 77.8 - - - +
639C ASP* 1.3 89.4 + - - +
642C GLY* 3.3 20.0 + - - -
643C ASP 4.9 0.4 - - - +
644C LEU* 5.0 4.0 - - - -
647C PHE* 3.9 20.6 - - + -
683C GLN* 5.5 4.1 - - - +
684C LEU* 4.5 16.3 - - + +
687C PHE* 3.4 57.5 - - + -
701C PRO* 3.3 29.4 - - + +
702C PRO* 4.9 2.8 - - - +
703C ASN 5.3 0.2 + - - -
704C ASN 4.7 0.2 - - - +
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Residues in contact with ASP 639 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635C VAL* 2.8 31.3 + - + +
638C LYS* 1.3 109.7 + - - +
640C SER* 1.3 62.7 + - - +
702C PRO* 3.6 29.6 - - + +
703C ASN* 3.4 22.7 + - - +
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Residues in contact with SER 640 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550C LYS* 3.4 15.6 + - - -
636C GLU* 2.8 41.1 + - - -
639C ASP* 1.3 82.7 + - - +
641C MET* 1.3 75.3 + - - -
642C GLY 3.5 0.2 - - - -
703C ASN* 2.6 30.2 + - - +
764C ILE* 3.4 9.7 - - - +
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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
------------------------------------------------------------
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