Contacts of the helix formed by residues 630 - 648 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628A ASN* 3.1 2.4 - - - +
629A GLU* 1.3 88.8 + - - +
631A HIS* 1.3 63.4 + - - +
632A LEU 3.2 3.7 + - - -
633A SER* 3.1 24.7 + - - +
634A TYR* 3.1 28.5 - - + -
42C ARG* 5.4 1.9 + - - -
73C LEU* 3.9 13.3 - - + +
74C ARG 4.5 1.4 - - - +
75C GLY* 3.7 18.0 - - - -
76C GLY 4.0 10.2 + - - -
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Residues in contact with HIS 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A LEU* 3.6 25.1 - - + -
624A SER* 3.2 26.0 - - - +
625A GLY* 3.4 23.2 - - - -
628A ASN* 3.2 23.1 + - + +
629A GLU* 3.4 11.8 + - - -
630A ASP* 1.3 76.5 - - - +
632A LEU* 1.3 91.4 + - + +
634A TYR* 3.1 6.7 + - - +
635A PHE* 2.9 37.0 + - + -
748A GLN* 4.0 10.3 - - + +
73C LEU* 4.8 1.6 - - - -
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Residues in contact with LEU 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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629A GLU 5.6 1.3 - - - +
630A ASP 3.2 1.2 + - - -
631A HIS* 1.3 111.7 - - + +
633A SER* 1.3 63.5 - - - +
635A PHE* 3.2 3.6 + - - -
636A LYS* 3.1 18.5 + - - +
747A LYS* 3.8 58.1 - - + +
748A GLN* 4.0 8.1 - - + +
751A ALA* 3.3 14.2 - - + +
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Residues in contact with SER 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A TYR* 2.8 28.2 + - - -
561A MET* 3.8 9.5 - - - +
630A ASP* 3.1 19.3 + - - +
632A LEU* 1.3 79.1 - - - +
634A TYR* 1.3 56.0 + - - +
636A LYS* 3.4 10.1 + - - +
637A PHE* 2.9 26.0 + - - +
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Residues in contact with TYR 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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553A LEU* 4.9 9.9 - - + -
554A GLU* 2.8 29.0 + - - -
557A TYR* 3.3 38.4 - + + -
607A LEU* 3.8 20.0 - - + -
630A ASP* 3.1 29.4 + - + -
631A HIS 3.1 8.6 + - - +
633A SER* 1.3 79.8 + - - +
635A PHE* 1.3 60.6 + - - +
637A PHE* 3.3 13.1 + + - +
638A ILE* 2.9 35.8 + - + +
73C LEU* 3.8 34.3 - - + -
75C GLY* 2.8 39.0 + - - -
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Residues in contact with PHE 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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607A LEU* 3.3 31.4 - - + -
608A PHE* 3.9 28.9 - + - -
620A ILE* 3.9 17.3 - - + -
624A SER* 3.3 30.3 - - - -
631A HIS* 2.9 30.4 + - - -
632A LEU* 3.2 10.1 + - - +
634A TYR* 1.3 75.4 - - - +
636A LYS* 1.3 59.5 + - - +
638A ILE* 3.4 6.2 + - + +
639A GLY 3.0 22.3 + - - -
748A GLN* 3.3 51.6 - - + +
751A ALA* 3.8 2.5 - - + -
752A PHE* 3.3 17.3 - - + +
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Residues in contact with LYS 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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561A MET* 4.5 11.2 - - - -
564A LYS* 5.8 3.6 - - - +
632A LEU 3.1 11.8 + - - +
633A SER* 3.6 12.1 - - - +
634A TYR 3.3 0.2 - - - -
635A PHE* 1.3 76.7 - - - +
637A PHE* 1.3 57.0 + - - +
639A GLY 3.4 0.3 + - - -
640A ARG* 2.9 40.6 + - + +
751A ALA* 3.2 26.1 + - + +
754A GLU* 3.2 31.3 + - + +
755A GLY* 3.7 9.0 - - - +
758A GLU* 3.6 30.9 + - - +
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Residues in contact with PHE 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 LEU* 4.2 21.8 - - + -
556A SER* 3.5 32.1 - - - -
557A TYR* 3.6 33.9 - + + -
560A ILE* 4.0 10.3 - - + -
561A MET* 3.6 30.0 - - + -
596A ILE* 4.2 4.0 - - + -
600A MET* 4.2 15.3 - - + -
633A SER 2.9 14.3 + - - +
634A TYR* 3.3 18.6 - + - +
635A PHE 3.1 0.2 - - - -
636A LYS* 1.3 74.9 - - - +
638A ILE* 1.3 66.1 + - + +
640A ARG* 3.0 5.0 + - - +
641A VAL* 2.9 48.6 + - + +
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Residues in contact with ILE 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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600A MET* 3.8 44.1 - - + +
601A PHE* 3.9 24.9 - - + -
607A LEU* 3.9 22.2 - - + -
608A PHE* 3.5 28.0 - - + -
634A TYR* 2.9 25.9 + - + +
635A PHE* 3.8 7.2 - - + +
637A PHE* 1.3 75.4 - - + +
639A GLY* 1.3 56.4 + - - +
641A VAL* 3.3 1.4 + - - +
642A ALA* 2.9 28.6 + - + +
652A LEU* 5.4 0.4 - - + +
752A PHE* 4.1 15.0 - - + -
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Residues in contact with GLY 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 PHE 3.0 10.7 + - - -
636A LYS 3.7 2.2 - - - -
638A ILE* 1.3 74.7 - - - +
640A ARG* 1.3 57.5 + - - +
642A ALA* 3.3 2.3 + - - +
643A GLY 2.8 24.6 + - - -
752A PHE* 3.4 38.7 - - - -
756A PHE* 3.2 17.5 - - - -
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Residues in contact with ARG 640 (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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560A ILE* 3.0 26.4 + - + -
561A MET* 3.3 26.3 + - + +
563A VAL* 2.9 32.9 + - - +
564A LYS* 3.6 14.1 + - - +
566A ALA* 4.2 10.6 - - - +
569A LEU* 3.9 15.0 - - + +
636A LYS* 2.9 27.3 + - + +
637A PHE 3.0 7.8 + - - +
639A GLY* 1.3 76.1 - - - +
641A VAL* 1.3 57.8 + - - +
643A GLY* 3.2 1.0 + - - -
644A MET* 2.8 35.4 + - - +
755A GLY* 3.6 13.2 - - - +
758A GLU* 2.6 40.4 + - - +
759A LEU* 4.0 7.7 - - + +
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Residues in contact with VAL 641 (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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560A ILE* 4.2 4.0 - - + -
592A TRP* 4.0 17.3 - - + -
593A PHE* 3.5 12.7 - - + -
596A ILE* 4.0 20.6 - - + -
600A MET* 4.1 12.3 - - - -
637A PHE* 2.9 46.5 + - + +
638A ILE 3.7 7.0 - - - +
640A ARG* 1.3 75.4 - - - +
642A ALA* 1.3 57.8 + - - +
644A MET* 3.2 6.8 + - - -
645A ALA* 2.9 27.7 + - - +
652A LEU* 3.9 18.4 - - + -
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Residues in contact with ALA 642 (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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638A ILE 2.9 17.1 + - - +
639A GLY 3.5 5.2 - - - +
641A VAL* 1.3 77.2 - - - +
643A GLY* 1.3 60.0 + - - +
645A ALA* 3.3 4.2 + - - +
646A VAL* 3.2 26.2 + - - +
652A LEU* 3.6 31.2 - - + +
752A PHE* 3.9 17.0 - - + -
756A PHE* 3.8 14.5 - - + -
777A MET* 4.1 5.0 - - + +
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Residues in contact with GLY 643 (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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639A GLY 2.8 12.7 + - - -
640A ARG 3.6 3.6 - - - -
642A ALA* 1.3 74.2 - - - +
644A MET* 1.3 58.8 + - - +
646A VAL* 3.2 3.5 + - - +
647A TYR* 2.9 30.7 + - - +
756A PHE* 3.5 22.2 - - - -
759A LEU* 3.7 18.6 - - - -
760A ILE* 3.9 4.2 - - - +
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Residues in contact with MET 644 (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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543A PHE* 4.6 8.7 - - + -
545A MET* 5.0 0.9 - - - -
560A ILE* 3.7 25.4 - - + -
569A LEU* 4.0 29.2 - - + +
573A LEU* 3.6 30.7 - - + -
592A TRP* 4.0 23.3 - - + -
593A PHE* 3.8 7.1 - - + -
640A ARG 2.8 27.0 + - - +
641A VAL* 3.2 4.9 + - - +
643A GLY* 1.3 73.1 - - - +
645A ALA* 1.3 57.5 + - - +
647A TYR* 4.3 0.2 - - - -
648A HIS* 2.9 41.6 + - + +
759A LEU* 3.3 22.2 - - + -
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Residues in contact with ALA 645 (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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593A PHE* 3.4 25.9 - - + -
641A VAL 2.9 14.2 + - - +
642A ALA 3.3 9.9 - - - +
643A GLY 3.2 0.2 - - - -
644A MET* 1.3 76.6 - - - +
646A VAL* 1.3 62.0 + - + +
649A GLY 3.1 3.1 + - - -
650A LYS 2.7 45.1 + - - +
651A LEU* 4.5 1.3 - - - +
652A LEU* 4.0 17.5 - - + -
777A MET 5.0 2.0 - - - +
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Residues in contact with VAL 646 (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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526A TYR* 5.2 0.5 + - - -
529A PHE* 3.6 25.4 - - + -
530A ARG* 4.4 11.3 + - - -
642A ALA 3.2 13.0 + - - +
643A GLY 3.2 5.8 + - - +
645A ALA* 1.3 75.8 - - - +
647A TYR* 1.3 62.6 + - - +
649A GLY* 3.3 11.4 + - - -
650A LYS 4.5 2.0 - - - -
756A PHE* 3.9 13.7 - - + -
760A ILE* 3.6 23.3 - - + -
776A LEU* 4.0 27.9 - - + +
777A MET* 3.7 28.3 - - + -
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Residues in contact with TYR 647 (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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530A ARG* 3.4 23.7 + - - -
533A LEU* 4.2 23.9 + - + -
534A LYS 3.0 23.8 + - - -
535A LYS* 3.7 11.3 - - - +
536A GLN 4.3 0.3 + - - -
570A LYS* 3.1 59.2 - - + +
643A GLY 2.9 16.9 + - - +
644A MET* 3.8 7.2 - - - +
645A ALA 3.3 0.2 - - - -
646A VAL* 1.3 78.1 - - - +
648A HIS* 1.3 76.6 + + + +
649A GLY 3.3 0.2 - - - -
759A LEU* 3.8 23.3 - - + -
760A ILE* 3.8 11.4 - - + +
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Residues in contact with HIS 648 (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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530A ARG* 4.2 5.9 + - - +
569A LEU 2.8 21.2 + - - -
570A LYS* 3.1 28.9 - - - -
571A ALA 3.3 15.5 - - - -
572A ARG* 4.7 1.8 - - - -
573A LEU* 3.5 37.9 + - + +
593A PHE* 5.1 0.2 - - + -
644A MET* 2.9 34.5 + - + +
647A TYR* 1.3 86.2 - + - +
649A GLY* 1.3 63.2 + - - +
650A LYS* 3.3 26.4 + - + +
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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