Contacts of the helix formed by residues 609 - 624 (chain B) in PDB entry 2XTA
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 VAL 609 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536B ALA* 4.1 16.4 - - + -
537B MET* 4.8 9.2 - - - +
600B THR* 3.7 21.8 - - + -
601B ALA 3.5 24.0 - - - +
602B ASN* 3.7 24.9 - - + -
603B PRO* 4.9 3.3 - - + +
605B HIS 4.8 2.1 + - - +
607B GLU* 4.8 4.9 - - - +
608B ALA* 1.3 76.8 - - - +
610B ASP* 1.3 74.7 + - - +
611B PRO* 3.5 0.7 - - - -
612B VAL* 3.1 19.0 + - + -
613B LEU* 2.9 22.9 + - - +
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Residues in contact with ASP 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B GLU* 2.6 54.4 + - - +
609B VAL* 1.3 84.4 - - - +
611B PRO* 1.4 64.1 - - + +
613B LEU* 3.4 11.7 + - - +
614B GLU* 3.4 15.6 + - - +
641B MET* 3.4 43.6 - - + +
642B LEU 5.1 1.9 - - - +
643B HIS* 3.7 1.2 - - - -
653B VAL 4.9 1.3 - - - +
654B VAL* 3.8 12.0 - - - +
657B THR* 3.8 15.8 - - + +
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Residues in contact with PRO 611 (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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608B ALA 3.3 17.5 - - - +
610B ASP* 1.4 91.2 - - + +
612B VAL* 1.3 61.7 + - + +
614B GLU* 3.4 5.7 + - + +
615B GLY* 3.1 24.3 + - - -
653B VAL* 3.7 19.5 - - + -
657B THR* 3.6 21.9 - - + +
660B LEU* 4.6 13.9 - - + +
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Residues in contact with VAL 612 (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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600B THR* 4.8 9.9 - - - +
601B ALA 5.3 2.5 - - - +
608B ALA 4.0 15.3 - - - +
609B VAL* 3.1 22.4 + - + +
611B PRO* 1.3 76.9 - - + +
613B LEU* 1.4 60.3 + - - +
615B GLY* 3.3 1.7 + - - -
616B LEU* 2.9 33.2 + - + +
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Residues in contact with LEU 613 (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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534B VAL* 3.5 45.3 - - + +
535B ILE 4.1 2.0 - - - +
536B ALA* 3.5 29.8 - - + -
600B THR* 4.5 7.4 - - + -
609B VAL* 2.9 11.3 + - - +
610B ASP* 3.7 8.3 - - - +
612B VAL* 1.4 74.7 - - - +
614B GLU* 1.3 58.8 + - - +
616B LEU* 3.3 5.7 + - + +
617B VAL* 2.9 36.7 + - + +
639B PRO* 3.8 22.7 - - + -
640B LEU 4.0 13.5 - - - +
641B MET* 4.0 20.6 - - + -
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Residues in contact with GLU 614 (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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610B ASP 3.4 12.7 + - - +
611B PRO* 3.6 9.2 - - + +
612B VAL 3.3 0.2 - - - -
613B LEU* 1.3 75.8 - - - +
615B GLY* 1.3 56.8 + - - +
617B VAL* 3.3 2.7 + - - -
618B ARG* 2.9 26.7 + - - +
639B PRO* 3.8 7.5 - - - +
641B MET* 4.5 6.6 - - - +
657B THR* 3.6 23.6 - - + +
660B LEU* 5.0 11.2 - - + -
661B ALA* 6.6 0.7 - - - -
666B TYR 5.0 6.5 - - - +
668B THR* 2.7 42.2 + - + +
671B THR* 2.6 31.6 + - - +
673B HIS* 5.2 1.0 - - - -
734B ASP* 5.4 0.3 - - - +
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Residues in contact with GLY 615 (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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611B PRO 3.1 14.0 + - - -
612B VAL* 3.8 2.7 - - - -
614B GLU* 1.3 73.3 - - - +
616B LEU* 1.3 65.3 + - - +
618B ARG* 3.5 5.7 + - - +
619B ALA* 3.1 24.8 + - - +
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Residues in contact with LEU 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B VAL* 4.2 15.0 - - + -
600B THR* 3.4 31.0 - - + +
612B VAL* 2.9 21.9 + - + +
613B LEU* 3.5 6.5 - - - +
615B GLY* 1.3 77.5 - - - +
617B VAL* 1.4 61.1 + - + +
619B ALA* 3.4 6.6 + - - +
620B LYS* 3.2 49.8 + - + +
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Residues in contact with VAL 617 (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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534B VAL* 3.8 34.1 - - + -
613B LEU* 2.9 21.2 + - + +
614B GLU 3.8 3.1 - - - +
616B LEU* 1.4 73.8 - - - +
618B ARG* 1.4 53.2 + - - +
620B LYS* 3.1 8.8 + - - +
621B GLN* 2.8 43.3 + - - +
637B VAL* 3.4 30.3 - - + +
639B PRO* 3.9 34.1 - - + -
668B THR* 3.9 3.8 - - + -
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Residues in contact with ARG 618 (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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614B GLU 2.9 17.6 + - - +
615B GLY* 3.9 7.4 - - - +
616B LEU 3.4 0.2 - - - -
617B VAL* 1.4 74.5 - - - +
619B ALA* 1.3 52.1 - - - +
621B GLN* 3.2 13.0 + - - +
622B ASP* 2.8 61.5 + - - +
628B GLU* 3.6 19.4 - - - +
629B GLU* 3.5 27.1 + - - +
664B ARG 2.9 29.3 + - - -
665B GLY* 3.5 15.8 + - - +
666B TYR* 3.5 9.3 - - - +
667B ARG 3.0 36.6 + - - +
668B THR* 3.8 10.7 - - + +
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Residues in contact with ALA 619 (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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615B GLY 3.1 18.8 + - - +
616B LEU* 3.6 8.1 - - - +
617B VAL 3.3 0.2 - - - -
618B ARG* 1.3 74.6 - - - +
620B LYS* 1.4 58.3 + - + +
622B ASP* 3.5 10.1 + - - +
623B LEU* 3.1 35.2 + - + +
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Residues in contact with LYS 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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532B GLU* 2.7 39.7 + - - +
534B VAL* 4.0 12.8 - - + -
583B THR* 6.3 0.4 - - - +
598B SER* 4.7 2.0 - - - -
616B LEU* 3.2 37.5 + - + +
617B VAL 3.1 8.3 + - - +
619B ALA* 1.4 72.2 - - + +
621B GLN* 1.3 65.2 + - - +
623B LEU* 3.3 13.3 + - + +
624B LEU* 3.0 29.2 + - + +
637B VAL* 4.0 16.2 - - + -
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Residues in contact with GLN 621 (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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617B VAL* 2.8 26.0 + - - +
618B ARG* 3.2 14.5 + - - +
620B LYS* 1.3 73.8 - - - +
622B ASP* 1.4 58.5 + - - +
624B LEU 3.4 0.7 + - - -
625B ASP 3.2 3.3 + - - -
626B THR* 2.9 57.4 + - + +
628B GLU 5.5 0.3 + - - -
635B PHE* 3.5 25.0 + - - +
637B VAL* 2.7 38.2 + - + +
667B ARG 4.1 3.5 - - - +
668B THR* 2.7 40.5 + - - +
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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
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618B ARG* 2.8 51.4 + - - +
619B ALA* 3.7 9.2 - - - +
620B LYS 3.3 0.2 - - - -
621B GLN* 1.4 72.6 - - - +
623B LEU* 1.4 60.6 + - - +
625B ASP* 3.1 15.6 + - - +
626B THR 4.7 2.6 - - - +
629B GLU* 3.4 32.2 + - + +
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Residues in contact with LEU 623 (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 ALA* 3.1 21.6 + - + +
620B LYS* 3.3 16.1 + - + +
622B ASP* 1.4 74.6 - - - +
624B LEU* 1.3 61.2 + - + +
625B ASP* 3.2 2.4 + - - +
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Residues in contact with LEU 624 (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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531B ASP* 3.6 32.5 - - + +
532B GLU* 6.0 1.1 - - + +
620B LYS* 3.0 15.6 + - + +
621B GLN 3.9 4.0 - - - +
622B ASP 3.3 0.2 - - - -
623B LEU* 1.3 77.5 - - + +
625B ASP* 1.4 67.6 + - - +
626B THR* 3.4 11.7 + - + -
632B ASP* 5.2 1.7 - - - +
636B SER* 4.3 0.9 - - - +
637B VAL* 3.6 31.0 - - + -
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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