Contacts of the helix formed by residues 619 - 640 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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618A GLY* 1.3 80.0 + - - +
620A LEU* 1.3 60.0 + - - +
621A GLU* 3.6 16.5 + - - +
622A ASP* 3.1 25.2 + - + +
623A ARG* 3.0 30.3 + - - +
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Residues in contact with LEU 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619A THR* 1.3 73.4 - - - +
621A GLU* 1.3 74.7 + - - +
623A ARG* 3.1 39.7 + - - +
624A ALA* 2.9 27.7 + - - +
664A LYS* 3.7 25.8 - - + +
665A THR* 3.3 31.4 - - - +
668A ALA* 4.5 12.8 - - + -
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Residues in contact with GLU 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619A THR* 3.3 17.7 + - - +
620A LEU* 1.3 92.1 + - + +
622A ASP* 1.3 57.5 - - - +
624A ALA* 3.5 6.7 + - - +
625A ALA* 2.9 29.8 + - - +
668A ALA* 5.7 4.2 - - + +
672A GLN* 6.5 0.9 - - + -
673A TYR* 4.7 2.6 + - - -
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Residues in contact with ASP 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A LYS* 4.9 4.0 + - - -
616A CYS 4.2 2.9 - - - +
617A THR* 3.5 14.0 - - - +
618A GLY 3.5 17.4 + - - +
619A THR* 3.1 29.3 + - - +
621A GLU* 1.3 73.1 - - - +
623A ARG* 1.3 64.2 + - - +
625A ALA* 3.5 6.9 + - - +
626A THR* 2.8 30.5 + - - -
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Residues in contact with ARG 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A ILE* 3.4 36.9 - - + +
617A THR* 3.5 19.7 - - - +
618A GLY 4.0 5.1 + - - -
619A THR 3.0 23.2 + - - +
620A LEU* 3.1 30.4 + - - +
622A ASP* 1.3 78.0 - - - +
624A ALA* 1.3 57.5 + - - +
626A THR* 3.1 6.6 + - - -
627A LEU* 2.9 26.9 + - - +
662A LEU* 4.7 6.8 - - - +
664A LYS* 6.0 0.2 - - - +
665A THR* 3.1 20.9 + - + +
815A LEU* 3.8 43.6 + - - +
816A GLU* 3.0 33.7 + - - +
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Residues in contact with ALA 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A LEU 2.9 15.9 + - - +
621A GLU* 3.9 5.4 - - - +
623A ARG* 1.3 76.7 - - - +
625A ALA* 1.3 57.3 + - - +
627A LEU* 3.1 7.3 + - - +
628A SER* 3.0 24.8 + - - -
665A THR* 3.9 17.8 - - + +
668A ALA* 3.8 27.4 - - + -
669A LEU* 3.7 13.7 - - - +
673A TYR* 4.1 11.8 - - + -
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Residues in contact with ALA 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621A GLU 2.9 18.3 + - - +
622A ASP* 3.8 10.1 - - - +
623A ARG 3.3 0.2 - - - -
624A ALA* 1.3 75.5 - - - +
626A THR* 1.3 58.0 + - - +
628A SER* 3.4 2.6 + - - -
629A LYS* 3.0 28.2 + - - +
673A TYR* 3.5 27.6 - - + +
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Residues in contact with THR 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541A LYS* 3.2 22.7 + - - +
544A PHE* 4.5 2.0 - - + -
612A ASP* 3.9 29.4 - - - +
613A ILE* 4.0 8.1 - - + -
617A THR* 3.3 10.3 - - - +
622A ASP* 2.8 18.8 + - - -
623A ARG* 3.1 11.2 + - - -
625A ALA* 1.3 74.3 - - - +
627A LEU* 1.3 61.5 + - - +
629A LYS* 3.2 7.5 + - - +
630A ILE* 2.9 51.6 + - + +
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Residues in contact with LEU 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A ILE* 3.5 33.9 - - + -
623A ARG 2.9 10.7 + - - +
624A ALA 3.1 9.2 + - - +
626A THR* 1.3 78.0 - - - +
628A SER* 1.3 61.2 + - - +
630A ILE* 3.4 6.3 + - - +
631A ILE* 3.1 28.8 + - + +
654A LEU* 3.7 17.0 - - + -
659A ILE* 4.5 5.6 - - + -
662A LEU* 6.4 0.4 - - + -
665A THR* 3.8 28.5 - - + +
666A TRP* 3.9 43.1 - - + -
669A LEU* 4.3 12.8 - - + -
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Residues in contact with SER 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624A ALA 3.0 8.9 + - - -
625A ALA 3.6 7.9 - - - -
627A LEU* 1.3 74.9 - - - +
629A LYS* 1.3 66.1 + - - +
631A ILE* 3.1 4.9 + - - +
632A GLN* 2.9 34.7 + - - +
669A LEU* 3.7 21.2 - - - +
673A TYR* 3.5 28.3 - - - +
676A THR* 3.7 21.0 + - - +
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Residues in contact with LYS 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544A PHE* 3.1 36.0 + - + -
545A THR* 3.3 25.3 + - - +
547A ASN 3.2 23.0 + - - -
549A PRO* 3.8 27.8 - - + -
552A ILE* 4.3 3.4 - - - -
625A ALA 3.0 17.2 + - - +
626A THR* 3.2 6.7 + - - +
628A SER* 1.3 76.4 - - - +
630A ILE* 1.3 57.6 + - - +
632A GLN* 3.2 12.6 + - - +
633A VAL* 2.9 35.8 + - + +
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Residues in contact with ILE 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544A PHE* 3.9 17.3 - - + -
609A ILE* 3.8 27.1 - - + +
612A ASP* 4.3 6.1 - - - +
613A ILE* 3.3 38.8 - - + -
626A THR* 2.9 28.2 + - + +
627A LEU* 3.6 6.1 - - - +
628A SER 3.2 0.2 - - - -
629A LYS* 1.3 75.4 - - - +
631A ILE* 1.3 57.1 + - - +
633A VAL* 3.2 8.8 + - - +
634A ALA* 2.9 25.3 + - - +
650A LEU* 3.6 15.1 - - + +
654A LEU* 3.8 26.7 - - + -
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Residues in contact with ILE 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627A LEU* 3.1 17.0 + - + +
628A SER 3.1 5.6 + - - +
630A ILE* 1.3 75.1 - - - +
632A GLN* 1.3 57.8 + - - +
634A ALA* 3.2 6.8 + - - +
635A VAL* 2.9 31.6 + - + +
654A LEU* 3.9 19.5 - - + -
666A TRP* 4.8 4.3 - - + -
669A LEU* 3.9 25.8 - - + -
676A THR* 3.7 24.9 - - + +
679A LEU* 5.3 1.6 - - + -
680A TYR* 3.7 31.4 - - + +
684A LEU* 3.8 23.3 - - + -
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Residues in contact with GLN 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549A PRO* 4.1 19.4 - - + +
628A SER* 2.9 24.6 + - - +
629A LYS* 3.2 26.9 + - - +
631A ILE* 1.3 73.2 - - - +
633A VAL* 1.3 66.4 + - - +
635A VAL* 3.3 9.3 + - - +
636A GLU* 3.0 25.8 + - - +
676A THR* 4.4 19.0 + - + +
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Residues in contact with VAL 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544A PHE* 4.2 12.6 - - + -
549A PRO* 3.9 29.2 - - + +
552A ILE* 4.0 34.3 - - + -
553A ALA* 4.8 2.5 - - + -
556A VAL* 5.7 2.5 - - + -
629A LYS* 2.9 19.9 + - + +
630A ILE* 3.2 8.9 + - - +
632A GLN* 1.3 77.4 - - - +
634A ALA* 1.3 57.5 + - - +
636A GLU* 3.1 5.4 + - - +
637A LEU* 2.9 37.2 + - + +
650A LEU* 3.8 16.2 - - + -
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Residues in contact with ALA 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630A ILE 2.9 13.6 + - - +
631A ILE* 3.6 11.7 - - - +
632A GLN 3.2 0.2 - - - -
633A VAL* 1.3 75.1 - - - +
635A VAL* 1.3 57.7 + - - +
637A LEU* 3.3 4.6 + - - +
638A LYS* 3.0 24.3 + - - +
647A PHE* 3.3 31.5 - - + -
650A LEU* 3.8 21.9 - - + +
651A MET* 4.8 7.0 - - - -
654A LEU* 5.5 2.5 - - + -
684A LEU* 4.6 7.0 - - + -
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Residues in contact with VAL 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631A ILE* 2.9 20.3 + - + +
632A GLN* 3.3 12.1 + - - +
634A ALA* 1.3 76.9 - - - +
636A GLU* 1.3 60.9 + - + +
638A LYS* 3.4 4.1 + - - +
639A ASP* 2.9 45.8 + - + +
679A LEU* 3.5 34.5 - - + -
684A LEU* 3.9 21.3 - - + -
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Residues in contact with GLU 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549A PRO* 3.9 8.1 - - + +
550A LYS* 2.8 67.0 + - - +
553A ALA* 3.7 17.0 - - + -
632A GLN 3.0 16.0 + - - +
633A VAL 3.1 7.2 + - - +
635A VAL* 1.3 77.2 - - + +
637A LEU* 1.3 61.3 + - - +
640A SER* 2.9 41.6 + - - -
641A MET* 3.0 10.6 + - - +
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Residues in contact with LEU 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553A ALA* 3.7 33.7 - - + +
556A VAL* 4.0 19.3 - - + -
633A VAL* 2.9 22.6 + - + +
634A ALA* 3.6 7.2 - - - +
636A GLU* 1.3 76.0 - - - +
638A LYS* 1.3 56.8 + - - +
641A MET* 4.0 3.8 - - + -
642A GLY 2.8 26.0 + - - -
643A ASP* 2.9 37.4 + - + +
646A SER* 3.9 10.3 - - - +
647A PHE* 3.8 21.5 - - + +
650A LEU* 3.9 24.9 - - + -
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Residues in contact with LYS 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634A ALA 3.0 17.0 + - - +
635A VAL* 3.9 3.6 - - - +
636A GLU 3.3 0.2 - - - -
637A LEU* 1.3 80.8 - - - +
639A ASP* 1.3 88.3 + - - +
642A GLY* 3.4 14.9 + - - -
643A ASP 5.0 0.7 - - - +
644A LEU* 5.1 3.4 - - + -
647A PHE* 3.8 15.9 - - + -
683A GLN* 5.5 4.4 + - - +
684A LEU* 4.1 23.2 - - + +
687A PHE* 3.5 57.1 - - + +
701A PRO* 3.4 25.6 - - + +
702A PRO* 5.0 2.4 - - - +
704A ASN 4.6 0.3 - - - +
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Residues in contact with ASP 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635A VAL* 2.9 31.0 + - + +
638A LYS* 1.3 108.1 + - - +
640A SER* 1.3 63.0 + - - +
684A LEU* 6.0 0.9 - - - +
701A PRO* 4.2 0.2 - - - -
702A PRO* 3.3 34.6 - - + +
703A ASN* 3.2 23.8 + - - +
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Residues in contact with SER 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A LYS* 3.2 21.7 + - - -
636A GLU* 2.9 33.9 + - - -
638A LYS 3.5 0.2 - - - -
639A ASP* 1.3 83.6 + - - +
641A MET* 1.3 69.1 + - - +
642A GLY 3.5 0.2 - - - -
703A ASN* 2.7 28.4 + - - +
764A ILE* 3.2 13.7 - - - +
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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