Contacts of the helix formed by residues 630 - 648 (chain B) in PDB entry 2XBB
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 ASP 630 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628B ASN* 3.1 3.9 - - + +
629B GLU* 1.3 88.2 - - - +
631B HIS* 1.3 64.6 + - - +
632B LEU 3.2 3.3 + - - -
633B SER* 2.9 23.7 + - - +
634B TYR* 3.0 27.1 - - + -
42D ARG* 5.1 2.4 + - - -
73D LEU* 4.1 9.5 - - + +
75D GLY* 3.8 24.7 + - - +
76D GLY 4.2 13.5 + - - +
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Residues in contact with HIS 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B LEU* 3.5 28.3 - - + -
624B SER* 3.2 23.5 - - - +
625B GLY* 3.3 24.4 - - - -
628B ASN* 3.2 22.8 + - + +
629B GLU 3.6 11.4 + - - -
630B ASP* 1.3 77.4 - - - +
632B LEU* 1.3 94.1 + - + +
634B TYR* 3.0 6.1 + - - +
635B PHE* 2.8 37.8 + - + -
747B LYS* 6.1 0.4 - - + -
748B GLN* 4.0 10.5 - - + +
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Residues in contact with LEU 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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629B GLU 5.9 0.4 - - - +
630B ASP 3.2 1.0 + - - -
631B HIS* 1.3 109.9 - - + +
633B SER* 1.3 61.2 + - - +
635B PHE* 4.1 1.8 - - - -
636B LYS* 3.2 17.8 + - - +
747B LYS* 3.9 49.6 - - + +
748B GLN* 3.9 16.6 - - + +
751B ALA* 3.2 15.0 - - + +
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Residues in contact with SER 633 (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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557B TYR* 2.7 29.1 + - - -
561B MET* 3.7 9.1 - - - +
630B ASP* 2.9 23.4 + - - +
632B LEU* 1.3 78.1 - - - +
634B TYR* 1.3 59.1 + - - +
636B LYS* 3.4 8.5 + - - +
637B PHE* 3.0 25.3 + - - +
76D GLY 5.2 1.0 + - - -
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Residues in contact with TYR 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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553B LEU* 4.9 9.6 - - + -
554B GLU* 2.8 29.1 + - - -
557B TYR* 3.4 34.6 - + + -
607B LEU* 3.8 19.1 - - + -
630B ASP* 3.0 26.6 + - + -
631B HIS 3.0 7.9 + - - +
633B SER* 1.3 81.4 + - - +
635B PHE* 1.3 61.3 + - - +
637B PHE* 3.3 13.9 - + - +
638B ILE* 2.9 35.0 + - - +
73D LEU* 3.7 40.4 - - + -
74D ARG 3.1 18.4 + - - -
75D GLY* 3.4 20.3 - - - -
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Residues in contact with PHE 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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607B LEU* 3.4 36.6 - - + -
608B PHE* 3.8 29.2 - + - -
620B ILE* 3.8 19.3 - - + -
624B SER* 3.3 29.4 - - - -
631B HIS* 2.8 29.6 + - + +
632B LEU* 4.1 1.6 - - - -
633B SER 3.2 0.2 - - - -
634B TYR* 1.3 75.4 - - - +
636B LYS* 1.3 59.8 + - - +
637B PHE 3.2 0.2 - - - -
638B ILE* 3.5 5.9 + - + +
639B GLY 3.0 21.3 + - - -
748B GLN* 3.4 38.4 - - + +
751B ALA* 3.6 18.4 - - + -
752B PHE* 3.2 19.2 - + + +
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Residues in contact with LYS 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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561B MET* 4.5 10.1 - - - -
632B LEU 3.2 12.9 + - - +
633B SER* 3.6 11.0 - - - +
634B TYR 3.4 0.2 - - - -
635B PHE* 1.3 76.7 - - - +
637B PHE* 1.3 57.0 + - - +
639B GLY 3.3 0.3 + - - -
640B ARG* 2.9 39.5 + - - +
751B ALA* 3.1 23.5 + - + +
754B GLU* 3.0 30.1 + - + +
755B GLY* 3.5 10.3 - - - +
758B GLU* 3.4 32.6 + - - +
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Residues in contact with PHE 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 LEU* 4.0 23.3 - - + -
556B SER* 3.5 31.9 - - - -
557B TYR* 3.6 32.5 - + + -
560B ILE* 3.8 21.3 - - + -
561B MET* 3.7 20.4 - - + -
596B ILE* 4.1 4.7 - - + -
600B MET* 4.1 9.2 - - + -
633B SER 3.0 15.2 + - - +
634B TYR* 3.3 18.8 - + - +
636B LYS* 1.3 73.8 - - - +
638B ILE* 1.3 68.4 + - + +
640B ARG* 3.0 4.5 + - - +
641B VAL* 2.8 54.5 + - + +
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Residues in contact with ILE 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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600B MET* 3.7 51.5 - - + +
601B PHE* 3.9 23.3 - - + -
607B LEU* 4.1 15.3 - - + -
608B PHE* 3.6 26.0 - - + -
634B TYR* 2.9 24.5 + - + +
635B PHE* 3.9 7.6 - - + +
636B LYS 3.4 0.2 - - - -
637B PHE* 1.3 77.3 - - + +
639B GLY* 1.3 57.9 + - - +
641B VAL* 3.4 1.9 + - - +
642B ALA* 2.9 28.2 + - + +
752B PHE* 3.8 17.5 - - + -
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Residues in contact with GLY 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 PHE 3.0 10.5 + - - -
636B LYS 3.6 3.1 - - - -
637B PHE 3.1 0.2 - - - -
638B ILE* 1.3 74.9 - - - +
640B ARG* 1.3 58.9 + - - +
642B ALA* 3.3 1.6 + - - +
643B GLY 2.9 23.6 + - - -
752B PHE* 3.3 37.6 - - - -
756B PHE* 3.1 19.4 - - - +
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Residues in contact with ARG 640 (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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560B ILE* 3.0 32.9 + - + -
561B MET* 3.3 23.7 - - - +
563B VAL* 3.0 30.7 + - - +
564B LYS 3.8 10.7 + - - -
566B ALA* 4.1 10.4 - - - +
569B LEU* 3.9 13.6 - - + +
636B LYS* 2.9 25.1 + - - +
637B PHE 3.4 8.1 - - - +
639B GLY* 1.3 76.0 - - - +
641B VAL* 1.3 52.2 + - - +
643B GLY* 3.1 1.4 + - - -
644B MET* 2.7 39.9 + - - +
755B GLY* 3.5 19.4 - - - +
758B GLU* 2.6 37.0 + - - +
759B LEU* 3.7 10.3 - - + +
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Residues in contact with VAL 641 (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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560B ILE* 4.2 11.4 - - + -
592B TRP* 4.3 6.1 - - + -
593B PHE* 3.6 12.1 - - + -
596B ILE* 4.0 15.7 - - + -
600B MET* 3.9 28.9 - - + -
637B PHE* 2.8 48.6 + - + +
638B ILE 3.6 7.4 - - - +
640B ARG* 1.3 76.3 - - - +
642B ALA* 1.3 56.8 + - - +
644B MET* 3.1 9.9 + - - +
645B ALA* 2.9 25.5 + - - +
652B LEU* 4.0 9.2 - - + -
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Residues in contact with ALA 642 (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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638B ILE* 2.9 18.3 + - + +
639B GLY 3.6 4.5 - - - +
641B VAL* 1.3 76.8 - - - +
643B GLY* 1.3 61.2 + - - +
645B ALA* 3.4 3.8 + - - +
646B VAL* 3.2 27.0 + - - +
652B LEU* 3.6 32.8 - - + +
752B PHE* 3.9 16.6 - - + -
756B PHE* 3.7 13.5 - - + -
777B MET* 4.3 5.2 - - + +
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Residues in contact with GLY 643 (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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639B GLY 2.9 12.1 + - - -
640B ARG 3.1 4.2 + - - -
642B ALA* 1.3 74.8 - - - +
644B MET* 1.3 58.1 + - - +
646B VAL* 3.3 2.4 + - - +
647B TYR* 2.9 29.3 + - - +
756B PHE* 3.4 23.5 - - - -
759B LEU* 3.8 18.2 - - - -
760B ILE* 3.9 5.8 - - - +
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Residues in contact with MET 644 (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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543B PHE* 5.3 0.2 - - + -
545B MET* 5.1 4.0 - - - -
560B ILE* 3.8 26.5 - - + -
569B LEU* 4.2 29.4 - - + +
573B LEU* 3.8 28.0 - - + -
592B TRP* 3.7 28.3 - - + -
593B PHE* 3.9 7.0 - - + -
640B ARG 2.7 27.4 + - - +
641B VAL 3.5 4.5 - - - +
643B GLY* 1.3 69.4 - - - +
645B ALA* 1.3 66.2 + - - +
647B TYR* 3.2 0.7 + - - -
648B HIS* 2.9 34.7 + - + +
759B LEU* 3.3 24.2 - - + +
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Residues in contact with ALA 645 (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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593B PHE* 3.5 29.5 - - + -
641B VAL 2.9 9.1 + - - +
642B ALA 3.5 9.6 - - - +
644B MET* 1.3 77.5 - - - +
646B VAL* 1.3 56.9 + - + +
649B GLY 3.0 6.6 + - - -
650B LYS 2.7 47.4 + - - +
651B LEU* 4.4 1.8 - - - +
652B LEU* 4.2 17.3 - - + -
777B MET 4.8 2.2 - - - +
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Residues in contact with VAL 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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526B TYR* 5.1 0.5 + - - -
529B PHE* 3.6 24.5 - - + -
530B ARG* 4.3 9.5 + - - -
533B LEU* 4.6 2.3 - - - +
642B ALA 3.2 14.9 + - - +
643B GLY 3.7 6.3 - - - +
644B MET 3.2 0.2 - - - -
645B ALA* 1.3 73.0 - - + +
647B TYR* 1.3 66.7 + - - +
649B GLY* 3.3 12.1 + - - -
650B LYS 4.5 2.0 - - - -
756B PHE* 3.9 10.3 - - + -
760B ILE* 3.6 23.1 - - + -
765B ILE* 5.5 0.2 - - + -
776B LEU* 3.9 29.6 - - + +
777B MET* 3.8 29.2 - - + -
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Residues in contact with TYR 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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530B ARG* 3.4 23.1 + - - -
533B LEU* 4.0 31.3 + - + -
534B LYS 3.2 21.6 + - - -
535B LYS* 3.6 13.7 - - - +
536B GLN 4.3 0.3 + - - -
570B LYS* 3.3 64.1 + - + +
643B GLY 2.9 17.7 + - - +
644B MET* 3.7 7.6 - - - +
646B VAL* 1.3 78.4 - - - +
648B HIS* 1.3 73.7 + + + +
759B LEU* 4.2 16.6 - - + -
760B ILE* 3.9 6.3 - - + +
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Residues in contact with HIS 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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530B ARG* 3.9 7.6 + - - +
569B LEU 2.9 22.4 + - - -
570B LYS* 3.1 29.3 - - - -
571B ALA 3.3 13.5 - - - -
572B ARG* 4.6 2.3 - - - -
573B LEU* 3.6 35.4 + - + +
593B PHE* 5.1 0.2 - - + -
644B MET* 2.9 32.8 + - + +
647B TYR* 1.3 87.9 - + - +
649B GLY* 1.3 63.7 + - - +
650B LYS* 3.2 32.2 + - + +
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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