Contacts of the helix formed by residues 626 - 641 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420B PHE* 3.4 34.3 - + - -
621B ASN 4.6 3.4 - - - -
622B PHE* 3.7 11.5 - - + -
623B THR* 2.8 40.9 + - + +
625B GLN* 1.3 106.2 + - + +
627B MET* 1.3 64.7 + - - +
628B PRO* 3.3 2.0 - - - -
629B TYR* 2.8 26.3 + + + +
630B PHE* 2.9 31.9 + - + -
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Residues in contact with MET 627 (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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602B ASP* 3.6 22.7 - - - +
605B MET* 3.4 27.4 - - - -
606B PHE* 3.6 44.9 - - + +
609B LYS* 4.1 2.7 - - + -
622B PHE* 3.8 25.4 - - + -
623B THR 4.7 1.3 - - - +
624B GLN* 3.3 30.7 + - - +
626B HIS* 1.3 76.5 - - - +
628B PRO* 1.3 67.3 - - + +
630B PHE* 3.7 20.2 - - + +
631B ARG* 2.9 30.8 + - - +
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Residues in contact with PRO 628 (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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462B HIS* 3.8 28.0 - - + +
624B GLN* 4.0 7.4 - - - +
625B GLN 3.5 12.6 - - - +
626B HIS 3.5 3.6 - - - -
627B MET* 1.3 92.2 - - + +
629B TYR* 1.3 59.9 + - - +
631B ARG* 3.3 6.8 + - - +
632B LYS* 3.2 27.3 + - + +
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Residues in contact with TYR 629 (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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420B PHE* 3.5 24.6 - + + +
421B PRO 2.6 41.8 + - - -
422B GLU* 5.2 0.9 - - - -
423B ILE* 3.9 26.5 - - + -
625B GLN 5.7 0.4 - - - +
626B HIS* 2.8 25.4 + + + +
628B PRO* 1.3 74.9 - - - +
630B PHE* 1.3 85.7 + + - -
632B LYS* 3.0 12.4 + - + +
633B ARG* 2.8 53.1 + - - +
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Residues in contact with PHE 630 (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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420B PHE* 4.5 13.0 - + - -
605B MET* 3.6 17.9 - - + +
609B LYS* 3.6 40.6 + - + +
612B ASP* 6.0 0.2 - - - -
622B PHE* 3.6 43.7 - + + -
626B HIS* 2.9 32.3 + - + -
627B MET* 3.2 19.3 + - + +
629B TYR* 1.3 99.5 - + - +
631B ARG* 1.3 58.2 + - - +
633B ARG* 3.7 16.2 - - - +
634B MET* 2.8 30.0 + - - +
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Residues in contact with ARG 631 (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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460B LEU* 3.2 36.5 + - + +
461B ASN 2.8 22.7 + - - -
462B HIS* 3.8 31.9 + - + +
464B ASN 2.9 24.8 + - - -
466B LEU* 3.9 11.7 - - - +
601B SER* 3.3 16.6 + - - -
602B ASP* 2.7 31.7 + - - +
605B MET* 4.2 19.8 - - + +
627B MET 2.9 17.9 + - - +
628B PRO* 3.6 7.9 - - - +
630B PHE* 1.3 76.0 - - - +
632B LYS* 1.3 60.4 + - - +
634B MET* 3.1 3.9 + - - +
635B VAL* 2.8 35.0 + - - +
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Residues in contact with LYS 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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423B ILE* 3.8 16.4 - - + -
428B GLU* 3.0 40.9 + - - +
431B ILE* 3.7 25.7 - - + +
462B HIS* 4.3 22.7 - - + -
628B PRO 3.2 12.7 + - - +
629B TYR* 3.0 13.8 + - + +
631B ARG* 1.3 78.5 - - - +
633B ARG* 1.3 65.1 + - - +
635B VAL* 3.2 6.2 + - - +
636B TRP 3.1 15.6 + - - -
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Residues in contact with ARG 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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420B PHE* 4.9 4.0 - - - -
421B PRO* 3.3 30.0 - - - +
423B ILE* 3.6 17.0 - - + +
474B TYR* 5.5 0.8 + - - -
481B ARG* 6.1 0.8 - - - +
609B LYS* 4.7 10.0 - - - +
612B ASP* 4.2 16.3 + - - -
629B TYR* 2.8 44.2 + - + +
630B PHE* 3.8 17.1 - - - +
632B LYS* 1.3 79.2 - - - +
634B MET* 1.3 51.2 + - - +
636B TRP* 3.0 6.1 + - + +
637B GLU* 2.5 72.6 + - + +
643B LEU* 5.6 2.2 - - - +
644B LEU* 3.7 32.4 + - + +
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Residues in contact with MET 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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460B LEU* 3.8 21.3 - - + -
466B LEU* 4.5 0.2 - - - -
470B ILE* 4.0 22.2 - - - -
474B TYR* 3.8 36.1 - - + -
605B MET* 3.3 32.1 - - + +
608B CYS* 4.0 21.8 - - + -
609B LYS* 4.2 8.1 - - + +
630B PHE 2.8 16.3 + - - +
631B ARG 3.1 3.8 + - - +
633B ARG* 1.3 73.5 - - - +
635B VAL* 1.3 69.7 + - - +
637B GLU* 3.9 8.0 - - - +
638B ILE* 3.0 32.1 + - + +
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Residues in contact with VAL 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B ILE* 4.3 15.3 - - + -
434B VAL* 3.6 28.0 - - + -
435B PHE* 4.3 19.5 - - + -
457B ILE* 3.8 26.2 - - + +
460B LEU* 3.9 16.7 - - + +
631B ARG 2.8 21.8 + - - +
632B LYS* 3.2 9.2 + - - +
634B MET* 1.3 77.8 - - - +
636B TRP* 1.3 63.7 + - - +
638B ILE* 3.7 1.7 - - - +
639B LEU* 3.0 37.6 + - + +
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Residues in contact with TRP 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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423B ILE* 5.6 1.1 - - + -
427B MET* 3.2 52.1 - - + +
430B GLU* 2.8 18.8 + - + -
431B ILE* 4.0 14.8 - - + -
632B LYS 3.1 9.6 + - - +
633B ARG* 3.0 12.2 + - + +
635B VAL* 1.3 78.5 - - - +
637B GLU* 1.3 71.6 + - + +
639B LEU* 3.2 12.9 + - + +
640B HIS* 2.8 69.9 + + + -
642B LYS* 3.7 26.0 - - + -
644B LEU* 3.7 34.5 - - + -
1646B CO 4.7 0.2 - - - -
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Residues in contact with GLU 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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474B TYR* 3.8 12.1 + - - -
477B MET* 4.0 5.2 - - + +
609B LYS* 4.9 2.8 + - - -
633B ARG* 2.5 64.9 + - + +
634B MET* 3.2 8.3 + - + +
636B TRP* 1.3 82.8 - - + +
638B ILE* 1.3 56.1 + - + +
640B HIS 3.4 0.2 + - - -
641B ARG* 3.0 9.7 + - - +
642B LYS 3.0 48.5 + - - +
643B LEU* 3.4 23.6 - - + +
644B LEU* 3.0 24.6 + - + +
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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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445B SER* 2.6 40.9 + - - -
452B ILE* 4.2 17.5 - - + -
457B ILE* 4.6 7.9 - - + -
460B LEU* 4.1 5.4 - - + -
470B ILE* 3.6 40.4 - - + +
473B PHE* 4.2 15.1 - - + -
477B MET* 3.6 26.2 - - + -
634B MET* 3.0 35.7 + - + +
635B VAL 3.7 3.1 - - - +
637B GLU* 1.3 76.3 - - - +
639B LEU* 1.3 57.6 + - + +
641B ARG* 3.1 8.9 + - - +
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Residues in contact with LEU 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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430B GLU* 4.1 17.5 - - + +
434B VAL* 3.4 31.9 - - + -
444B LEU* 4.1 37.2 - - + +
445B SER* 4.0 9.8 + - - -
457B ILE* 4.7 8.7 - - + -
635B VAL* 3.0 30.1 + - + +
636B TRP* 3.4 11.7 - - - +
638B ILE* 1.3 77.7 - - - +
640B HIS* 1.3 68.3 + - + +
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Residues in contact with HIS 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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430B GLU* 3.2 6.7 - - + -
445B SER* 5.2 0.2 - - - -
636B TRP* 2.8 74.1 + + + +
637B GLU 4.2 0.2 - - - +
638B ILE 3.2 0.6 - - - -
639B LEU* 1.3 84.0 - - + +
641B ARG* 1.3 69.4 + - - +
642B LYS* 3.9 21.4 - - + +
1646B CO 2.2 30.2 + - - -
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Residues in contact with ARG 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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445B SER* 4.5 4.0 + - - +
446B GLU 4.7 2.2 + - - -
447B ALA* 3.4 34.5 - - + +
448B PHE* 3.9 28.9 - - + +
473B PHE* 5.0 2.2 - - + -
477B MET* 3.5 18.3 - - + +
480B GLU* 2.8 40.7 + - - +
637B GLU 3.0 7.6 + - - -
638B ILE 3.1 11.7 + - - +
640B HIS* 1.3 83.2 - - - +
642B LYS* 1.1 57.7 + - - -
643B LEU 4.2 0.2 + - - -
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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