Contacts of the helix formed by residues 630 - 651 (chain B) in PDB entry 2XWU
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 ASN 630 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627B GLU* 5.2 4.6 + - - +
628B ILE* 3.2 19.3 + - - +
629B PRO* 1.3 85.8 - - - +
631B PRO* 1.3 72.6 - - + +
632B SER* 4.1 3.4 - - - +
633B ASN* 3.2 22.3 + - + +
634B LYS* 2.8 29.3 + - - +
695B TRP* 3.7 1.7 - - - -
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Residues in contact with PRO 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630B ASN* 1.3 91.5 - - + +
632B SER* 1.3 72.2 + - - +
634B LYS* 3.5 6.4 + - + +
635B LEU* 3.3 25.2 + - - +
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Residues in contact with SER 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630B ASN* 3.2 3.3 - - - -
631B PRO* 1.3 81.9 - - - +
633B ASN* 1.3 65.0 + - - +
634B LYS 3.2 0.4 - - - -
635B LEU* 3.5 9.6 + - - +
636B ALA* 3.3 22.7 + - - +
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Residues in contact with ASN 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624B LEU* 3.7 25.2 - - - +
627B GLU* 3.5 32.3 + - - +
628B ILE 3.2 21.2 - - - +
629B PRO 4.0 0.2 - - - -
630B ASN* 3.0 32.0 + - + +
632B SER* 1.3 79.6 - - - +
634B LYS* 1.3 55.3 + - - +
636B ALA* 3.6 5.6 + - - +
637B ILE* 3.1 27.4 + - - +
695B TRP* 3.8 13.3 - - + -
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Residues in contact with LYS 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 ASN 2.8 11.9 + - - +
631B PRO* 3.7 8.5 - - + +
632B SER 3.2 0.2 - - - -
633B ASN* 1.3 75.2 - - - +
635B LEU* 1.3 67.2 + - + +
637B ILE* 3.3 3.0 + - - +
638B VAL* 2.9 30.2 + - + +
695B TRP* 3.3 30.5 - - + -
698B ASP* 4.4 8.1 - - - +
700B GLN* 6.4 1.8 - - + -
701B VAL* 4.8 4.5 - - + -
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Residues in contact with LEU 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631B PRO 3.3 12.7 + - - +
632B SER* 3.8 11.2 - - - +
633B ASN 3.5 0.2 - - - -
634B LYS* 1.3 78.0 - - + +
636B ALA* 1.3 57.1 + - - +
638B VAL* 3.6 8.8 + - + +
639B HIS* 3.0 29.3 + - - +
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Residues in contact with ALA 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624B LEU* 5.8 3.6 - - + -
632B SER 3.3 13.9 + - - +
633B ASN* 3.8 9.6 - - - +
634B LYS 3.2 0.6 - - - -
635B LEU* 1.3 78.6 - - - +
637B ILE* 1.3 64.8 + - - +
639B HIS* 3.4 5.8 + - - +
640B ILE* 3.2 35.0 + - + +
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Residues in contact with ILE 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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621B LEU* 4.7 10.0 - - + +
624B LEU* 5.2 11.4 - - + +
633B ASN* 3.1 19.6 + - - +
634B LYS* 3.8 5.2 - - - +
636B ALA* 1.3 76.9 - - - +
638B VAL* 1.3 62.2 + - - +
640B ILE* 3.5 8.8 + - - +
641B LEU* 3.2 30.2 + - + +
691B VAL* 5.2 13.0 - - + -
695B TRP* 5.0 12.8 - - + +
701B VAL* 5.3 6.1 - - + -
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Residues in contact with VAL 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B LYS* 2.9 20.9 + - + +
635B LEU* 3.8 9.0 - - + +
637B ILE* 1.3 75.3 - - - +
639B HIS* 1.3 62.0 + - - +
641B LEU* 3.2 8.4 + - - +
642B GLY* 2.8 27.4 + - - -
700B GLN* 4.1 23.1 - - + +
701B VAL* 3.9 26.5 - - + -
704B ALA* 4.3 10.2 - - + +
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Residues in contact with HIS 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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584B THR* 2.8 31.1 + - + +
587B CYS* 3.6 36.3 - - + -
588B MET* 3.5 17.0 - - + +
617B TYR* 5.2 7.6 + + - -
635B LEU 3.0 18.8 + - - +
636B ALA* 3.4 5.8 + - - +
638B VAL* 1.3 79.0 - - - +
640B ILE* 1.3 73.9 + - + +
642B GLY* 3.3 1.6 + - - +
643B LEU* 3.1 37.4 + - + +
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Residues in contact with ILE 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617B TYR* 4.1 35.2 - - + +
620B GLN* 4.1 31.6 - - + +
621B LEU* 4.3 28.9 - - + +
624B LEU* 5.7 2.7 - - + -
636B ALA* 3.2 24.9 + - + +
637B ILE* 3.8 6.5 - - - +
639B HIS* 1.3 84.7 - - + +
641B LEU* 1.3 68.1 + - - +
643B LEU* 3.3 16.1 + - + +
644B LEU* 3.4 19.6 + - + +
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Residues in contact with LEU 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B LEU* 4.5 19.7 - - + -
637B ILE* 3.2 20.1 + - + +
638B VAL* 3.6 5.8 - - - +
640B ILE* 1.3 76.5 - - + +
642B GLY* 1.3 64.8 + - - +
644B LEU* 3.0 21.3 + - + +
645B SER* 3.1 11.7 + - - -
684B VAL* 6.3 1.8 - - + -
688B ILE* 6.1 6.1 - - + -
691B VAL* 5.3 9.9 - - + -
701B VAL* 4.5 10.8 - - + +
704B ALA* 3.8 22.4 - - + +
705B VAL* 3.7 30.5 - - + +
708B ILE* 3.4 29.6 - - + +
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Residues in contact with GLY 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B MET* 3.4 15.3 - - - -
638B VAL 2.8 14.5 + - - -
639B HIS* 3.3 4.9 + - - -
640B ILE 3.2 0.4 - - - -
641B LEU* 1.3 76.4 - - - +
643B LEU* 1.3 60.6 + - - +
645B SER* 3.1 8.4 + - - -
646B ASN* 2.8 30.3 + - - -
704B ALA* 5.4 2.6 - - - +
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Residues in contact with LEU 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577B LEU* 5.3 4.5 - - + -
587B CYS* 3.9 16.4 - - + +
588B MET* 3.1 27.9 - - + -
591B MET* 3.6 35.8 - - + +
617B TYR* 3.8 43.7 - - + +
639B HIS* 3.1 30.1 + - - +
640B ILE* 3.5 14.8 - - + +
641B LEU 3.2 0.2 - - - -
642B GLY* 1.3 75.4 - - - +
644B LEU* 1.3 61.4 + - + +
646B ASN* 3.3 2.6 + - - +
647B LEU* 2.8 30.0 + - - +
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Residues in contact with LEU 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591B MET* 6.2 0.9 - - + -
614B ILE* 3.4 45.1 - - + -
617B TYR* 6.5 0.4 - - + -
621B LEU* 6.3 3.4 - - + -
640B ILE* 3.4 18.4 + - + +
641B LEU* 3.0 13.2 + - + +
643B LEU* 1.3 78.6 - - + +
645B SER* 1.3 65.8 + - - +
647B LEU* 3.0 9.6 + - + +
648B PHE* 3.0 44.7 + - + -
680B VAL* 5.6 0.2 - - + -
684B VAL* 4.5 25.1 - - + -
708B ILE* 4.1 20.9 - - + -
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Residues in contact with SER 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B LEU 3.1 4.6 + - - -
642B GLY* 3.1 17.0 + - - -
644B LEU* 1.3 75.7 - - - +
646B ASN* 1.3 60.3 + - - +
648B PHE* 3.5 3.3 + - - -
649B THR* 2.7 32.8 + - - -
704B ALA 5.0 0.5 + - - -
707B ALA* 3.7 19.0 - - - +
708B ILE* 3.6 38.1 - - - +
711B LYS* 3.5 10.5 - - - +
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Residues in contact with ASN 646 (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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588B MET* 3.1 48.7 - - + +
591B MET* 4.1 4.5 - - + -
592B GLN* 2.7 48.2 + - + +
642B GLY* 2.8 27.8 + - - +
643B LEU 3.7 3.4 - - - +
645B SER* 1.3 79.9 + - - +
647B LEU* 1.3 65.8 + - - +
649B THR* 3.6 12.2 + - - -
650B THR* 3.7 1.7 + - - -
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Residues in contact with LEU 647 (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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591B MET* 3.5 45.3 - - + +
594B LEU* 4.2 8.5 - - + +
595B GLY* 3.8 13.2 - - - +
598B LEU* 5.4 2.2 - - + -
610B LEU* 3.6 29.8 - - + -
613B LEU* 4.4 9.2 - - + -
614B ILE* 4.4 13.7 - - + -
643B LEU 2.8 14.8 + - - +
644B LEU* 3.0 10.7 + - + +
646B ASN* 1.3 78.5 - - - +
648B PHE* 1.3 71.3 + - + +
649B THR 3.2 1.0 + - - -
650B THR* 3.4 6.8 + - - -
651B LEU* 3.2 27.7 + - + +
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Residues in contact with PHE 648 (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 LEU* 4.7 4.5 - - + -
614B ILE* 4.4 8.5 - - + -
644B LEU* 3.0 40.1 + - + +
645B SER* 3.9 5.4 - - - +
646B ASN 3.4 0.2 - - - -
647B LEU* 1.3 91.3 - - + +
649B THR* 1.3 56.0 + - - +
651B LEU* 3.8 14.0 + - + +
677B VAL* 3.8 38.6 - - + -
680B VAL* 4.2 24.9 - - + -
681B LEU* 4.6 10.5 - - + -
708B ILE* 4.7 6.5 - - + -
711B LYS* 3.4 11.0 - - + +
712B SER* 3.7 28.3 - - - +
715B THR* 2.5 33.0 + - + +
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Residues in contact with THR 649 (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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592B GLN* 5.3 7.2 - - - +
645B SER 2.7 22.9 + - - -
646B ASN* 3.8 11.1 + - - -
647B LEU 3.2 1.0 - - - -
648B PHE* 1.3 80.3 - - - +
650B THR* 1.3 69.0 + - + +
652B ASP* 5.1 3.3 + - - +
711B LYS* 3.3 37.1 - - + +
715B THR* 3.9 7.1 + - - -
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Residues in contact with THR 650 (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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552B LYS* 5.6 0.2 - - - -
559B LYS* 5.7 0.2 + - - -
592B GLN* 2.8 55.4 + - + +
595B GLY* 3.0 18.7 - - - +
596B PHE* 3.5 45.3 + - + -
599B SER* 4.4 1.2 - - - -
647B LEU 3.4 4.2 + - - -
649B THR* 1.3 84.2 - - + +
651B LEU* 1.3 57.8 + - - +
652B ASP* 3.1 15.0 + - - +
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Residues in contact with LEU 651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595B GLY* 3.6 10.5 - - - +
598B LEU* 3.9 11.9 - - + +
599B SER* 3.5 33.7 - - - +
606B ILE* 4.4 6.7 - - + -
610B LEU* 4.1 29.6 - - + -
647B LEU* 3.2 23.2 + - + +
648B PHE* 3.8 12.7 - - + +
649B THR 3.4 1.8 - - - -
650B THR* 1.3 75.6 - - - +
652B ASP* 1.3 56.5 + - - +
653B ILE* 3.6 13.7 + - + -
677B VAL* 4.0 26.7 - - + +
715B THR* 2.8 19.5 - - - +
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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