Contacts of the helix formed by residues 619 - 640 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618B GLY* 1.3 75.2 + - - -
620B LEU* 1.3 76.2 + - - +
621B GLU* 3.0 19.4 + - + +
622B ASP* 2.8 49.8 + - - +
623B ARG* 3.1 27.5 + - - +
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Residues in contact with LEU 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619B THR* 1.3 79.0 + - - +
621B GLU* 1.3 56.6 + - - +
623B ARG* 3.4 22.5 + - - +
624B ALA* 3.1 24.9 + - - +
664B LYS* 3.8 23.6 - - + +
665B THR* 3.4 43.7 - - - +
668B ALA* 4.1 17.3 - - + -
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Residues in contact with GLU 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619B THR* 3.0 16.7 + - + +
620B LEU* 1.3 82.4 - - - +
622B ASP* 1.3 60.0 + - - +
624B ALA* 3.7 5.7 + - - +
625B ALA* 3.2 24.4 + - - +
668B ALA* 5.8 1.1 - - - -
672B GLN* 5.9 10.5 + - + +
673B TYR* 4.9 3.0 + - - +
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Residues in contact with ASP 622 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617B THR* 4.1 4.7 - - + -
618B GLY* 3.5 16.5 + - - +
619B THR* 2.8 39.4 + - - +
621B GLU* 1.3 77.9 - - - +
623B ARG* 1.3 60.4 + - - +
624B ALA 3.2 0.2 - - - -
625B ALA* 3.7 7.0 - - - +
626B THR* 2.9 34.6 + - - -
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Residues in contact with ARG 623 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B ILE* 3.4 37.8 - - + +
617B THR* 3.7 19.2 + - + +
618B GLY 5.0 2.6 + - - -
619B THR* 3.1 12.5 + - - +
620B LEU* 3.6 41.5 - - - +
621B GLU 3.4 0.2 - - - -
622B ASP* 1.3 77.9 - - - +
624B ALA* 1.3 57.6 + - - +
626B THR* 3.3 2.6 + - - -
627B LEU* 2.9 29.6 + - - +
662B LEU* 4.5 5.5 - - - +
664B LYS* 5.1 1.0 - - - +
665B THR* 2.8 24.4 + - + +
815B LEU* 3.8 40.6 + - - +
816B GLU* 2.6 38.4 + - - +
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Residues in contact with ALA 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620B LEU 3.1 13.8 + - - +
621B GLU* 3.8 7.2 - - + +
623B ARG* 1.3 79.5 - - - +
625B ALA* 1.3 56.1 + - - +
627B LEU* 3.3 5.4 + - - +
628B SER* 2.9 29.5 + - - -
665B THR* 4.1 10.7 - - + +
668B ALA* 4.0 25.1 - - + -
669B LEU* 3.9 15.7 - - - +
672B GLN* 5.7 1.1 - - + -
673B TYR* 4.0 11.2 - - + -
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Residues in contact with ALA 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621B GLU 3.2 14.8 + - - +
622B ASP* 3.3 8.2 + - - +
624B ALA* 1.3 79.1 - - - +
626B THR* 1.3 56.2 + - - +
628B SER* 3.4 3.8 + - - -
629B LYS* 3.0 26.5 + - - +
673B TYR* 3.3 29.1 - - + +
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Residues in contact with THR 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541B LYS* 2.7 32.6 + - - +
612B ASP* 4.0 16.8 - - - +
613B ILE* 3.9 12.1 - - + -
617B THR* 3.8 9.9 - - - +
622B ASP* 2.9 20.6 + - - +
623B ARG 3.4 5.2 - - - -
625B ALA* 1.3 73.6 - - - +
627B LEU* 1.3 67.1 + - - +
629B LYS* 2.9 8.1 + - - +
630B ILE* 2.9 45.6 + - + +
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Residues in contact with LEU 627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613B ILE* 3.7 13.6 - - + +
623B ARG 2.9 17.4 + - - +
624B ALA 3.5 6.5 - - - +
626B THR* 1.3 75.6 - - - +
628B SER* 1.3 61.4 + - - +
630B ILE* 3.5 7.0 + - - +
631B ILE* 3.1 30.3 + - + +
654B LEU* 3.2 36.8 - - + -
659B ILE* 4.9 3.4 - - + -
665B THR* 4.1 19.7 - - + -
666B TRP* 3.9 42.4 - - + +
669B LEU* 4.1 20.0 - - + -
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Residues in contact with SER 628 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624B ALA 2.9 17.4 + - - -
625B ALA 3.5 5.4 - - - -
626B THR 3.1 0.2 - - - -
627B LEU* 1.3 76.5 - - - +
629B LYS* 1.3 63.3 + - - +
631B ILE* 3.3 3.5 + - - +
632B GLN* 3.1 34.2 + - - +
669B LEU* 3.8 10.7 - - - +
673B TYR* 3.3 43.0 - - - +
676B THR* 4.1 11.2 + - - +
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Residues in contact with LYS 629 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544B PHE* 2.7 33.4 - - + +
545B THR* 3.8 16.0 + - - +
547B ASN 3.0 20.2 + - - -
549B PRO* 4.1 17.3 - - + +
552B ILE* 4.2 12.1 - - + -
625B ALA 3.0 12.4 + - - +
626B THR* 2.9 10.5 + - + +
628B SER* 1.3 73.2 + - - +
630B ILE* 1.3 66.9 + - + +
632B GLN* 3.1 18.9 + - - +
633B VAL* 3.0 29.1 + - + +
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Residues in contact with ILE 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609B ILE* 3.9 32.1 - - + +
612B ASP* 4.6 9.0 - - - +
613B ILE* 3.2 42.4 - - + -
626B THR* 2.9 27.1 + - + +
627B LEU* 3.6 7.0 - - - +
629B LYS* 1.3 76.1 - - + +
631B ILE* 1.3 62.4 + - - +
633B VAL* 3.2 9.1 + - - +
634B ALA* 3.0 20.7 + - + +
650B LEU* 3.9 17.4 - - + +
654B LEU* 4.1 21.1 - - + -
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Residues in contact with ILE 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627B LEU* 3.1 22.5 + - + +
628B SER 3.7 1.8 - - - +
629B LYS 3.3 0.2 - - - -
630B ILE* 1.3 74.4 - - - +
632B GLN* 1.3 57.8 + - - +
634B ALA* 3.2 8.7 + - - +
635B VAL* 2.9 32.9 + - + +
654B LEU* 3.8 22.0 - - + -
666B TRP* 4.6 1.1 - - + -
669B LEU* 3.8 28.0 - - + -
676B THR* 3.4 35.7 - - + +
679B LEU* 5.1 1.1 - - + -
680B TYR* 3.8 31.0 - - + +
684B LEU* 4.1 13.0 - - + -
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Residues in contact with GLN 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549B PRO* 3.9 23.3 - - + +
628B SER* 3.1 24.9 + - - +
629B LYS* 3.1 26.7 + - - +
631B ILE* 1.3 76.7 - - - +
633B VAL* 1.3 57.8 + - - +
635B VAL* 3.3 10.7 + - - +
636B GLU* 3.0 30.7 + - + +
676B THR* 4.3 18.5 + - + +
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Residues in contact with VAL 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B PRO* 3.8 27.8 - - + +
552B ILE* 4.0 33.2 - - + -
553B ALA* 4.4 6.7 - - + -
556B VAL* 5.6 2.2 - - + -
629B LYS* 3.0 20.6 + - + +
630B ILE* 3.2 9.2 + - - +
632B GLN* 1.3 73.4 - - - +
634B ALA* 1.3 55.0 + - - +
636B GLU* 2.9 6.3 + - - +
637B LEU* 2.7 46.3 + - + +
650B LEU* 3.8 16.4 - - + -
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Residues in contact with ALA 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630B ILE* 3.0 12.6 + - + +
631B ILE* 3.4 12.3 - - - +
633B VAL* 1.3 77.2 - - - +
635B VAL* 1.3 57.1 + - - +
637B LEU* 3.1 5.1 + - - -
638B LYS* 2.8 26.9 + - - +
647B PHE* 3.4 31.4 - - + -
650B LEU* 3.8 21.9 - - + +
651B MET* 4.8 7.2 - - - -
654B LEU* 6.1 2.0 - - + -
684B LEU* 4.7 6.1 - - + -
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Residues in contact with VAL 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631B ILE* 2.9 20.6 + - + +
632B GLN* 3.5 11.2 - - - +
633B VAL 3.3 0.2 - - - -
634B ALA* 1.3 74.8 - - - +
636B GLU* 1.3 64.1 + - - +
638B LYS* 3.8 4.4 - - - +
639B ASP* 2.8 46.0 + - + +
679B LEU* 3.6 36.1 - - + -
684B LEU* 3.8 21.1 - - + -
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Residues in contact with GLU 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549B PRO* 4.0 6.1 - - + +
550B LYS* 3.1 62.9 + - - +
553B ALA* 3.8 15.7 - - + -
632B GLN 3.0 16.7 + - - +
633B VAL 2.9 8.8 + - - +
635B VAL* 1.3 79.9 - - + +
637B LEU* 1.3 62.1 + - - +
640B SER* 2.9 38.4 + - - -
641B MET* 3.0 12.5 + - + +
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Residues in contact with LEU 637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553B ALA* 3.8 32.5 - - + +
556B VAL* 4.1 17.5 - - + -
633B VAL* 2.7 22.1 + - + +
634B ALA* 3.1 7.8 + - - +
636B GLU* 1.3 72.3 - - - +
638B LYS* 1.3 58.4 + - - +
641B MET* 3.6 4.2 - - + +
642B GLY 3.0 9.0 + - - -
643B ASP* 2.9 49.1 + - + +
646B SER* 3.9 23.1 - - - +
647B PHE* 4.0 12.8 - - + +
650B LEU* 3.8 31.0 - - + -
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Residues in contact with LYS 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634B ALA 2.8 16.1 + - - +
635B VAL* 3.8 3.6 - - - +
637B LEU* 1.3 80.6 - - - +
639B ASP* 1.3 94.9 + - - +
642B GLY* 3.4 13.7 + - - -
643B ASP 5.0 0.9 - - - +
644B LEU* 5.2 4.0 - - + -
647B PHE* 3.8 16.3 - - + -
683B GLN* 5.4 3.3 - - - +
684B LEU* 4.0 23.5 - - + +
687B PHE* 3.7 52.0 - - + -
701B PRO* 3.3 31.1 - - + +
702B PRO* 4.8 4.2 - - - +
704B ASN 4.8 0.2 - - - +
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Residues in contact with ASP 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635B VAL* 2.8 32.6 + - + +
638B LYS* 1.3 110.0 + - - +
640B SER* 1.3 61.6 + - - +
679B LEU* 6.0 2.1 - - - +
684B LEU* 6.1 0.5 - - - +
701B PRO* 4.2 4.0 - - - -
702B PRO* 3.7 26.4 - - + +
703B ASN* 3.3 24.7 + - - +
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Residues in contact with SER 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550B LYS* 3.2 23.6 + - - -
636B GLU* 2.9 23.3 + - - -
639B ASP* 1.3 86.0 + - - +
641B MET* 1.3 82.3 + - - +
642B GLY 3.5 0.4 - - - -
703B ASN* 2.8 28.7 + - - +
764B ILE* 3.4 8.3 - - - +
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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