Contacts of the helix formed by residues 626 - 641 (chain A) in PDB entry 2XPH
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 HIS 626 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420A PHE* 3.8 29.1 - + - -
621A ASN 4.8 1.8 - - - -
622A PHE* 3.4 14.6 - - + -
623A THR* 2.7 47.6 + - + +
624A GLN 3.0 1.4 - - - -
625A GLN* 1.3 82.6 - - + +
627A MET* 1.3 58.4 + - - +
628A PRO* 3.3 2.2 - - - -
629A TYR* 3.0 15.9 + + + +
630A PHE* 3.0 44.3 + - + -
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Residues in contact with MET 627 (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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602A ASP* 3.6 21.5 - - - +
605A MET* 3.4 31.2 - - - -
606A PHE* 3.8 40.4 - - + -
609A LYS* 4.6 2.5 - - + -
622A PHE* 3.5 38.4 - - + -
623A THR 4.0 3.6 - - - +
624A GLN* 3.2 15.7 + - - +
626A HIS* 1.3 79.3 - - - +
628A PRO* 1.3 62.4 - - + +
630A PHE* 3.7 19.8 - - + +
631A ARG* 2.9 35.8 + - + +
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Residues in contact with PRO 628 (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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463A LEU* 6.3 3.4 - - + -
624A GLN* 4.0 7.6 - - - +
625A GLN* 3.5 14.1 - - - +
626A HIS 3.5 3.8 - - - -
627A MET* 1.3 90.7 - - + +
629A TYR* 1.3 65.7 + - - +
631A ARG* 3.6 10.4 + - + +
632A LYS* 3.4 25.3 + - - +
1647A GOL 4.2 13.0 + - - +
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Residues in contact with TYR 629 (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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420A PHE* 3.3 31.2 - + + +
421A PRO 2.8 29.9 + - - -
422A GLU* 5.1 0.9 - - - -
423A ILE* 4.0 20.6 - - + +
625A GLN 5.2 0.9 + - - +
626A HIS* 3.0 18.9 + + + +
628A PRO* 1.3 78.9 - - - +
630A PHE* 1.4 89.5 + + - +
632A LYS* 3.2 7.5 + - - +
633A ARG* 2.9 57.3 + - - +
1647A GOL 3.7 40.6 - - - -
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Residues in contact with PHE 630 (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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420A PHE* 3.7 7.2 - + - -
605A MET* 3.6 17.5 - - + -
609A LYS* 3.6 32.7 - - + +
622A PHE* 3.5 44.0 - + + -
626A HIS* 3.0 24.4 + - + +
627A MET* 3.7 16.8 - - + +
629A TYR* 1.4 102.3 - + - +
631A ARG* 1.3 56.0 + - - +
633A ARG* 3.6 10.1 - - - +
634A MET* 2.7 36.2 + - - +
1649A GOL 3.7 28.5 - - - -
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Residues in contact with ARG 631 (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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435A PHE* 5.6 0.7 - - + -
459A THR 3.9 0.8 + - - -
460A LEU* 3.0 39.2 + - + +
461A ASN 3.4 5.7 + - - -
462A HIS 2.9 28.5 + - - -
463A LEU* 3.8 8.8 - - - +
464A ASN 2.6 29.3 + - - -
466A LEU* 4.3 10.8 - - - +
601A SER 3.7 11.1 + - - -
602A ASP* 2.6 33.7 + - - +
605A MET* 3.9 18.9 - - + +
627A MET 2.9 29.1 + - - +
628A PRO* 4.0 9.4 - - - +
629A TYR 3.2 0.2 - - - -
630A PHE* 1.3 77.4 - - - +
632A LYS* 1.3 58.3 + - + +
634A MET* 2.8 8.5 + - - +
635A VAL* 2.8 33.3 + - - +
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Residues in contact with LYS 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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423A ILE* 4.2 6.3 - - + -
428A GLU* 3.0 29.3 + - - +
431A ILE* 3.4 27.4 - - + +
435A PHE* 4.5 16.6 - - + -
628A PRO 3.4 9.8 + - - +
629A TYR* 3.2 5.9 + - - +
631A ARG* 1.3 79.1 - - + +
633A ARG* 1.3 64.3 + - - +
635A VAL* 2.8 22.2 + - - +
636A TRP 3.0 9.4 + - - -
1647A GOL 3.4 39.6 + - - -
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Residues in contact with ARG 633 (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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421A PRO* 3.8 7.3 - - - +
423A ILE* 3.7 17.4 - - + +
609A LYS* 3.7 14.8 - - - +
612A ASP* 4.3 3.2 + - - -
616A LYS* 5.1 0.4 - - - +
629A TYR* 2.9 57.3 + - + +
630A PHE* 3.7 11.1 - - - +
632A LYS* 1.3 75.5 - - - +
634A MET* 1.4 63.1 + - - +
636A TRP* 3.0 7.2 + - - +
637A GLU* 2.7 56.3 + - - +
643A LEU* 6.1 0.2 - - - +
644A LEU* 3.3 43.3 + - + +
1649A GOL 3.3 40.6 + - - -
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Residues in contact with MET 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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460A LEU* 3.9 21.3 - - + -
466A LEU* 4.3 2.2 - - - -
470A ILE* 3.9 17.9 - - - -
474A TYR* 3.7 40.2 - - + -
477A MET* 5.5 0.2 - - + -
605A MET* 3.4 29.6 - - + +
608A CYS* 3.8 17.7 - - + -
609A LYS* 4.7 4.0 - - + -
630A PHE 2.7 22.3 + - - +
631A ARG* 2.8 6.8 + - - +
633A ARG* 1.4 72.5 - - - +
635A VAL* 1.3 66.2 + - - +
637A GLU* 3.4 10.6 + - - +
638A ILE* 3.2 33.2 + - + +
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Residues in contact with VAL 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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431A ILE* 4.1 12.3 - - + -
434A VAL* 3.6 31.0 - - + -
435A PHE* 3.3 35.4 - - + -
457A ILE* 3.9 18.2 - - + +
460A LEU* 3.9 17.5 - - + -
631A ARG 2.8 17.1 + - - +
632A LYS* 2.8 8.9 + - - +
634A MET* 1.3 79.4 - - - +
636A TRP* 1.3 62.4 + - - +
638A ILE* 3.1 2.3 + - - +
639A LEU* 3.1 26.7 + - + +
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Residues in contact with TRP 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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423A ILE* 5.9 0.7 - - + -
427A MET* 3.5 52.4 - - + +
430A GLU* 3.0 25.4 + - + -
431A ILE* 4.0 13.4 - - + +
632A LYS 3.0 9.7 + - - +
633A ARG* 3.0 11.0 + - - +
635A VAL* 1.3 75.8 - - - +
637A GLU* 1.3 70.9 - - - +
638A ILE 3.1 0.2 + - - -
639A LEU* 3.2 7.1 + - + +
640A HIS* 3.0 63.4 + + + -
642A LYS* 3.6 28.7 - - + -
644A LEU* 3.7 37.5 - - + -
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Residues in contact with GLU 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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474A TYR* 3.9 14.6 + - - -
477A MET* 3.7 11.5 - - + +
609A LYS* 4.8 2.1 + - - -
633A ARG* 2.7 56.4 + - + +
634A MET* 3.8 10.2 - - - +
636A TRP* 1.3 84.3 - - + +
638A ILE* 1.3 53.9 + - - +
641A ARG* 2.7 28.4 + - - -
642A LYS 2.7 34.8 + - - +
643A LEU* 3.7 17.3 - - - +
644A LEU* 2.9 21.7 + - + +
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Residues in contact with ILE 638 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445A SER* 2.8 30.2 + - - -
452A ILE* 4.0 24.7 - - + -
457A ILE* 4.5 7.2 - - + -
460A LEU* 4.1 5.6 - - + -
470A ILE* 4.0 34.5 - - + +
473A PHE* 3.9 26.6 - - + -
474A TYR* 5.3 0.9 - - + -
477A MET* 3.7 22.9 - - + -
634A MET* 3.2 33.6 + - + +
635A VAL 3.1 3.9 + - - +
636A TRP 3.1 0.6 - - - -
637A GLU* 1.3 76.5 - - - +
639A LEU* 1.3 63.1 + - + +
641A ARG* 3.2 8.9 + - - +
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Residues in contact with LEU 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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430A GLU* 4.2 15.5 - - + +
431A ILE* 5.0 0.4 - - - -
434A VAL* 3.4 37.9 - - + -
444A LEU* 3.6 52.5 - - + +
445A SER* 4.1 7.2 + - - -
457A ILE* 4.9 7.0 - - + -
635A VAL* 3.1 22.5 + - + +
636A TRP* 3.4 11.0 - - - +
638A ILE* 1.3 78.1 - - + +
640A HIS* 1.3 68.7 + - + +
641A ARG* 5.3 0.2 - - - +
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Residues in contact with HIS 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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430A GLU* 3.0 33.6 + - + -
636A TRP* 3.0 68.6 + + + +
639A LEU* 1.3 83.6 - - + +
641A ARG* 1.4 71.1 + - - +
642A LYS* 3.1 19.7 + - + +
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Residues in contact with ARG 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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445A SER* 4.9 4.5 - - - +
446A GLU 4.9 2.2 + - - -
447A ALA* 3.4 32.1 - - - +
448A PHE* 3.9 11.6 - - + -
473A PHE* 4.4 10.3 - - + -
477A MET* 3.9 13.3 - - - +
480A GLU* 2.4 58.9 + - - +
637A GLU 2.7 9.4 + - - -
638A ILE 3.2 10.3 + - - +
639A LEU 5.3 0.2 - - - +
640A HIS* 1.4 79.2 - - - +
642A LYS* 1.3 59.7 + - - +
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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