Contacts of the helix formed by residues 627 - 639 (chain A) in PDB entry 5XOU
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 PRO 627 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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625A ASP 3.4 7.4 - - - +
626A THR* 1.3 92.0 - - + +
628A LEU* 1.3 66.9 + - + +
629A GLU* 4.5 5.8 - - + +
630A ALA* 2.9 24.5 + - + +
631A LEU* 3.3 8.5 + - - +
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Residues in contact with LEU 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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593A TYR* 3.4 17.5 - - + +
595A PRO* 5.9 0.4 - - + -
598A ASP* 4.9 6.3 - - - +
599A LYS* 3.8 38.6 - - + +
600A THR 4.6 0.7 - - - +
601A PHE* 3.4 35.7 - - + -
621A HIS* 3.7 31.4 - - + +
626A THR 3.4 1.7 + - - +
627A PRO* 1.3 71.6 - - - +
629A GLU* 1.3 62.8 + - - +
631A LEU* 3.2 8.6 + - + +
632A ALA* 2.9 23.0 + - - +
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Residues in contact with GLU 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.6 25.8 - - - +
314A TYR* 4.6 10.7 - - - +
316A LEU* 4.6 9.7 - - + +
593A TYR* 3.7 33.4 + - + +
627A PRO* 3.2 4.9 - - + +
628A LEU* 1.3 77.9 - - - +
630A ALA* 1.3 58.2 + - - +
632A ALA* 3.3 2.8 + - - +
633A HIS* 2.9 28.2 + - + +
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Residues in contact with ALA 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A PRO* 4.4 16.4 - - + +
626A THR* 3.7 16.6 - - + -
627A PRO* 2.9 20.0 + - + +
629A GLU* 1.3 77.1 + - - +
631A LEU* 1.3 64.7 + - - +
633A HIS* 3.2 8.5 + - - +
634A GLN* 3.0 24.8 + - - +
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Residues in contact with LEU 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A PRO* 5.5 4.5 - - + -
542A LEU* 3.8 24.0 - - + +
569A ASP* 3.8 24.7 - - + +
571A VAL* 4.1 7.4 - - + -
601A PHE* 4.7 6.1 - - + -
621A HIS* 3.3 49.8 - - + +
626A THR* 3.8 19.1 - - + +
627A PRO 3.3 1.9 + - - +
628A LEU* 3.2 14.3 + - + +
630A ALA* 1.3 77.0 - - - +
632A ALA* 1.3 58.2 + - - +
634A GLN* 3.4 3.7 + - - +
635A ILE* 2.9 44.8 + - + +
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Residues in contact with ALA 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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316A LEU* 3.9 4.8 - - + +
593A TYR* 3.7 33.2 - - + -
601A PHE* 3.7 19.0 - - + -
603A LEU* 4.0 9.1 - - + +
628A LEU 2.9 13.2 + - - +
629A GLU 3.5 8.3 - - - +
631A LEU* 1.3 78.0 - - - +
633A HIS* 1.3 56.6 + - - +
635A ILE* 4.0 3.5 - - - +
636A PHE* 2.9 33.4 + - - +
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Residues in contact with HIS 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A LEU* 4.3 13.1 - - + +
317A SER* 3.1 25.8 + - - -
467A GLY* 6.2 0.7 - - - -
468A ALA 4.0 11.0 + - - -
469A TYR* 3.3 34.3 - + - -
470A PRO* 5.5 2.4 - - - +
629A GLU* 2.9 14.7 + - + +
630A ALA* 3.4 13.1 + - - +
632A ALA* 1.3 76.8 - - - +
634A GLN* 1.3 65.0 + - - +
636A PHE* 3.8 1.7 - - - +
637A HIS* 2.9 58.2 + + - +
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Residues in contact with GLN 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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469A TYR* 3.3 37.0 - - + +
470A PRO* 3.4 12.6 - - + +
471A ALA* 2.8 50.7 + - - +
474A ALA* 4.8 6.1 - - - +
496A GLY 5.5 0.6 + - - -
542A LEU* 3.7 16.8 - - + +
630A ALA 3.0 14.9 + - - +
631A LEU* 4.0 4.2 - - - +
633A HIS* 1.3 76.9 - - - +
635A ILE* 1.3 57.8 + - - +
637A HIS* 3.7 1.6 - - - +
638A LEU* 2.8 53.7 + - + +
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Residues in contact with ILE 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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542A LEU* 4.1 10.1 - - + -
544A LEU* 4.0 30.5 - - + -
571A VAL* 4.1 13.5 - - + -
573A VAL* 5.5 0.7 - - + -
601A PHE* 4.7 1.6 - - + -
603A LEU* 3.7 17.9 - - + -
605A THR* 5.3 2.0 - - + -
617A LEU* 5.4 1.6 - - + -
619A LEU* 3.6 28.7 - - + -
631A LEU* 2.9 29.8 + - + +
632A ALA 4.0 2.2 - - - +
634A GLN* 1.3 72.4 - - - +
636A PHE* 1.3 67.6 + - - +
638A LEU* 3.0 17.9 + - - +
639A THR* 3.1 13.5 + - - +
653A PRO* 3.8 24.1 - - + +
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Residues in contact with PHE 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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316A LEU* 3.7 32.8 - - + -
317A SER 3.6 17.3 - - - -
318A ILE* 5.0 0.7 - - - -
319A PRO* 3.9 11.4 - - + -
590A ASP* 4.3 4.0 - - - -
591A GLY* 3.3 28.5 - - - -
603A LEU* 4.0 9.8 - - + +
604A LEU 4.5 0.2 - - - -
605A THR* 3.2 24.5 - - + -
632A ALA 2.9 22.2 + - - +
633A HIS 3.8 1.3 - - - +
635A ILE* 1.3 73.3 - - - +
637A HIS* 1.3 71.6 + + - +
639A THR* 2.8 30.7 + - - -
640A ARG* 3.0 38.9 + - - +
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Residues in contact with HIS 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A SER* 3.0 32.1 + - - -
318A ILE 4.3 1.1 - - - -
319A PRO* 3.5 33.9 - - + +
320A LYS 4.9 0.9 - - - -
465A LEU* 3.6 15.2 - - + +
466A SER 5.5 2.0 - - - -
469A TYR* 2.5 38.8 + + + +
633A HIS* 2.9 49.7 + + - +
634A GLN 3.7 3.6 - - - +
636A PHE* 1.3 85.6 - + - +
638A LEU* 1.3 58.1 + - - +
640A ARG* 2.8 26.9 + - - +
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Residues in contact with LEU 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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465A LEU* 4.1 15.0 - - + +
474A ALA* 3.9 25.6 - - + -
493A ALA* 4.6 10.8 - - + -
498A GLY* 5.9 2.0 - - - -
542A LEU* 4.0 9.6 - - + -
544A LEU* 4.6 9.2 - - + -
634A GLN* 2.8 47.6 + - + +
635A ILE* 3.0 8.9 + - - +
637A HIS* 1.3 74.5 - - - +
639A THR* 1.3 62.7 + - - +
640A ARG 3.1 0.5 + - - -
641A LEU* 3.3 17.6 + - + +
653A PRO* 3.5 12.1 - - + -
654A ALA* 2.9 22.2 + - - +
655A PRO* 4.1 16.2 - - + -
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Residues in contact with THR 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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605A THR* 3.8 20.8 + - + -
606A VAL* 4.9 0.4 - - - +
635A ILE 3.1 10.3 + - - +
636A PHE 2.8 19.0 + - - +
637A HIS 3.0 1.2 + - - -
638A LEU* 1.3 78.1 - - - +
640A ARG* 1.3 78.9 + - - +
641A LEU 3.4 0.4 + - - -
642A TYR* 4.4 1.7 + - - +
649A PHE* 3.8 3.1 - - - +
650A PRO* 3.3 38.8 - - - +
651A ARG 3.4 24.5 - - - +
652A LEU 3.8 7.4 - - - +
653A PRO* 3.8 12.1 - - + -
654A ALA 4.3 0.7 - - - +
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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