Contacts of the helix formed by residues 629 - 649 (chain A) in PDB entry 5UO5
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 LEU 629 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626A THR 2.9 21.3 + - - +
627A SER* 3.9 5.6 - - - +
628A SER* 1.3 81.2 + - - +
630A TRP* 1.3 59.0 + - - +
631A LYS 3.1 2.2 - - - -
632A ASP* 3.1 19.6 + - + +
633A GLN* 2.9 27.6 + - - +
636B VAL* 4.1 8.1 - - + +
639B ASN* 3.6 34.1 - - + +
640B ILE* 3.8 21.3 - - + +
643B LEU* 3.6 20.6 - - + -
655B ASP* 4.5 1.6 - - + -
656B HIS* 3.7 29.4 - - + +
657B HIS* 4.2 5.6 - - + -
688B MET* 4.9 2.0 - - - -
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Residues in contact with TRP 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A LEU* 4.1 13.0 - - + -
613A GLU* 4.3 8.7 - - + -
616A ALA* 3.4 24.5 - - + -
621A LEU* 3.4 27.3 - - + +
622A ASP 3.5 21.3 - - - +
623A MET* 3.6 50.4 + - + -
625A LYS 3.6 12.2 + - - -
626A THR* 4.4 12.9 - - + +
628A SER* 3.2 17.7 - - - +
629A LEU* 1.3 77.0 - - - +
631A LYS* 1.3 104.5 + - + +
633A GLN* 4.3 3.6 - - - +
634A ALA* 3.0 26.2 + - + +
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Residues in contact with LYS 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A ASN* 5.2 10.5 + - - +
612A LEU* 3.7 26.6 - - + +
626A THR* 6.4 2.4 - - - +
629A LEU* 3.1 0.6 - - - +
630A TRP* 1.3 125.1 - - + +
632A ASP* 1.3 61.6 + - - +
634A ALA* 3.4 2.0 + - - -
635A LEU* 2.9 30.0 + - - +
657B HIS* 4.4 18.8 + - + +
692B ILE* 3.9 26.3 + - + +
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Residues in contact with ASP 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A LEU* 3.1 25.1 + - - +
631A LYS* 1.3 71.2 - - - +
633A GLN* 1.3 65.6 + - - +
635A LEU* 3.4 4.4 + - - +
636A VAL* 3.2 27.7 + - - +
636B VAL* 3.9 22.2 - - + +
656B HIS* 2.9 24.5 + - - -
657B HIS* 2.8 24.9 + - - -
688B MET* 4.1 2.9 - - + +
689B SER* 2.4 33.1 + - - +
692B ILE* 4.2 4.3 - - - -
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Residues in contact with GLN 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A MET* 4.7 7.0 - - + -
621A LEU* 3.4 32.0 - - + +
628A SER 4.3 2.4 - - - +
629A LEU 2.9 12.8 + - - +
630A TRP* 3.8 7.2 - - - +
632A ASP* 1.3 80.0 - - - +
634A ALA* 1.3 61.5 + - - +
636A VAL* 3.3 11.3 + - - +
637A GLU* 3.4 21.8 + - - +
553B HIS* 6.0 0.4 - - - -
636B VAL* 3.9 13.9 - - + -
637B GLU* 2.7 32.4 + - - +
640B ILE* 3.5 22.8 - - - +
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Residues in contact with ALA 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A LEU* 3.9 27.1 - - + +
615A VAL* 4.2 12.9 - - + +
616A ALA* 4.3 10.1 - - + +
619A MET* 4.1 12.3 - - - -
621A LEU* 4.3 0.8 - - + +
630A TRP 3.0 18.8 + - - +
631A LYS* 3.8 3.8 - - - +
633A GLN* 1.3 73.8 - - - +
635A LEU* 1.3 65.7 + - - +
637A GLU* 3.3 3.5 + - - +
638A ILE* 3.1 29.1 + - - +
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Residues in contact with LEU 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599A GLY 3.8 3.1 - - - +
600A VAL* 3.8 16.8 - - + -
604A CYS* 3.7 25.6 - - + -
612A LEU* 3.9 7.6 - - + +
631A LYS 2.9 18.6 + - - +
632A ASP 3.6 5.6 - - - +
634A ALA* 1.3 76.8 - - - +
636A VAL* 1.3 61.1 + - + +
638A ILE* 3.6 2.7 + - - +
639A ASN* 2.7 53.4 + - - +
687A PRO 5.2 0.4 - - - +
688A MET* 3.8 32.5 - - + -
689B SER* 4.5 9.4 - - - +
692B ILE* 4.1 28.9 - - + -
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Residues in contact with VAL 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A ASP 3.2 14.7 + - - +
633A GLN* 3.7 7.4 - - - +
634A ALA 3.2 0.8 - - - -
635A LEU* 1.3 75.0 - - - +
637A GLU* 1.3 60.5 + - + +
639A ASN* 3.2 3.5 + - - +
640A ILE* 2.9 37.3 + - + +
688A MET* 3.8 22.7 - - + -
689A SER* 5.6 0.2 - - - +
629B LEU* 4.0 3.8 - - + +
632B ASP* 4.0 16.6 - - + +
633B GLN* 3.6 37.5 - - + +
636B VAL* 3.9 20.6 - - + -
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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
----------------------------------------------------------
553A HIS* 3.0 38.5 + - + +
556A PHE* 3.8 15.3 - - + -
559A PHE* 4.7 2.2 - - + -
615A VAL* 5.1 3.6 - - + -
619A MET* 3.5 37.0 - - + +
633A GLN* 3.4 10.4 + - - +
634A ALA 3.3 6.8 + - - +
636A VAL* 1.3 77.5 - - - +
638A ILE* 1.3 57.7 + - - +
640A ILE* 3.2 8.1 + - - +
641A ALA* 2.9 23.9 + - - +
633B GLN* 3.0 34.7 + - - +
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Residues in contact with ILE 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A ILE* 6.3 0.2 - - + -
559A PHE* 4.0 15.7 - - + -
599A GLY* 3.6 21.1 - - - +
603A TYR* 4.0 24.0 - - + -
604A CYS* 3.6 23.3 - - - -
611A ILE* 3.7 11.2 - - + -
612A LEU* 4.1 7.6 - - + -
615A VAL* 3.6 38.6 - - + -
634A ALA 3.1 18.5 + - - +
635A LEU 3.8 4.0 - - - +
637A GLU* 1.3 75.4 - - - +
639A ASN* 1.3 64.4 + - - +
641A ALA* 3.2 4.7 + - - +
642A VAL* 3.1 22.5 + - + +
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Residues in contact with ASN 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A GLY* 3.8 3.9 - - - +
596A THR* 3.5 15.8 + - + +
599A GLY* 3.1 39.1 + - - -
600A VAL* 3.3 22.8 - - - +
635A LEU* 2.7 29.3 + - - +
636A VAL 3.7 0.4 - - - +
638A ILE* 1.3 77.2 - - - +
640A ILE* 1.3 65.6 + - - +
642A VAL* 3.5 5.6 + - - +
643A LEU* 3.2 29.5 + - + +
688A MET* 3.7 9.8 - - - -
629B LEU* 3.6 20.9 - - + -
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Residues in contact with ILE 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A HIS* 4.1 6.7 - - + +
554A PRO* 4.0 24.9 - - + -
636A VAL* 2.9 24.3 + - + +
637A GLU* 3.4 17.5 - - - +
639A ASN* 1.3 78.0 - - - +
641A ALA* 1.3 57.3 + - - +
643A LEU* 3.4 4.2 + - - +
644A TYR* 3.0 27.7 + - + +
627B SER 5.1 3.6 - - - +
628B SER* 3.7 24.9 - - - +
629B LEU* 3.8 14.1 - - + -
633B GLN* 3.4 36.8 - - - +
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Residues in contact with ALA 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A ILE* 3.8 13.0 - - + -
552A ARG 3.2 21.6 - - - +
553A HIS* 4.0 11.9 - - + +
559A PHE* 3.9 15.9 - - + -
637A GLU 2.9 12.6 + - - +
638A ILE 3.2 9.6 + - - +
640A ILE* 1.3 75.1 - - - +
642A VAL* 1.3 57.9 + - - +
644A TYR* 3.7 2.9 - - - +
645A SER* 2.6 38.3 + - - -
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Residues in contact with VAL 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A ILE* 4.2 14.6 - - + -
595A GLY* 4.1 17.9 - - - +
598A ILE* 4.2 17.9 - - + -
599A GLY* 4.1 18.2 - - - -
603A TYR* 4.1 22.2 - - + -
638A ILE* 3.1 21.1 + - + +
639A ASN* 3.8 7.2 - - - +
640A ILE 3.3 0.2 - - - -
641A ALA* 1.3 76.6 - - - +
643A LEU* 1.3 65.1 + - - +
645A SER* 3.9 0.2 - - - -
646A PHE* 3.1 30.4 + - + -
653A ILE* 4.0 20.6 - - + -
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Residues in contact with LEU 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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595A GLY* 4.2 11.2 - - - -
639A ASN* 3.2 18.2 + - + +
640A ILE* 3.9 3.4 - - - +
642A VAL* 1.3 80.0 - - - +
644A TYR* 1.3 62.2 + - - +
646A PHE* 4.0 0.9 - - - +
647A GLN* 3.0 42.3 + - - +
653A ILE* 4.0 29.1 - - + +
654A VAL* 4.1 3.1 - - - +
655A ASP* 3.6 44.0 - - + +
656A HIS* 5.4 2.0 - - - +
627B SER* 3.6 24.5 - - - +
629B LEU* 3.9 17.3 - - + -
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Residues in contact with TYR 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A ARG* 3.8 32.5 - - + -
553A HIS 4.0 1.8 - - - -
554A PRO* 3.5 53.2 - - + +
640A ILE* 3.0 18.7 + - + +
641A ALA 3.7 2.2 - - - +
643A LEU* 1.3 77.6 - - - +
645A SER* 1.3 56.5 + - - +
647A GLN* 4.0 9.4 - - + +
648A SER* 2.8 53.6 + - - -
627B SER 5.6 0.2 + - - -
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Residues in contact with SER 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A VAL* 3.4 17.9 - - - +
550A PRO 3.4 20.9 - - - -
551A ILE* 3.4 8.2 - - - -
552A ARG* 2.8 39.9 + - - +
641A ALA 2.6 22.4 + - - -
642A VAL 3.9 2.9 - - - -
644A TYR* 1.3 75.9 - - - +
646A PHE* 1.3 63.5 + - - +
648A SER* 3.5 0.5 + - - -
649A ASP* 3.2 21.1 + - - +
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Residues in contact with PHE 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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549A VAL* 3.8 32.5 - - + -
551A ILE* 4.4 13.5 - - + -
566A TRP* 4.7 4.7 - - + -
567A TYR 3.9 13.5 - - - -
568A GLY* 4.1 12.1 - - - -
593A TYR* 4.6 3.6 - + + -
598A ILE* 3.6 28.5 - - + -
642A VAL* 3.1 22.6 + - + +
643A LEU 4.0 0.2 - - - +
645A SER* 1.3 75.2 - - - +
647A GLN* 1.3 65.1 + - - +
649A ASP* 3.2 2.5 + - - +
650A LYS 3.0 4.3 + - - -
651A VAL* 2.9 59.8 + - + +
652A THR 4.0 3.4 - - - -
653A ILE* 3.5 38.4 - - + -
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Residues in contact with GLN 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A LEU* 3.0 32.8 + - - +
644A TYR* 4.0 8.6 - - + +
646A PHE* 1.3 75.9 - - - +
648A SER* 1.3 62.8 + - - +
650A LYS* 3.1 18.2 + - - +
651A VAL 4.8 1.3 - - - -
653A ILE* 4.4 13.9 + - + +
655A ASP 6.0 0.2 - - - +
625B LYS* 5.8 3.4 - - - +
627B SER* 2.9 38.2 + - - +
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Residues in contact with SER 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A ARG* 3.6 22.8 + - - -
644A TYR* 2.8 50.5 + - - -
645A SER 3.8 0.9 - - - -
646A PHE 3.2 0.2 - - - -
647A GLN* 1.3 78.9 - - - +
649A ASP* 1.3 61.2 + - - +
650A LYS* 3.2 11.4 + - - +
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Residues in contact with ASP 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A LYS 5.6 0.9 - - - +
548A GLU 4.8 2.0 - - - +
549A VAL* 3.5 15.5 - - + +
550A PRO* 3.6 11.8 - - - +
552A ARG* 2.5 45.8 + - - -
645A SER 3.2 9.9 + - - +
646A PHE 3.2 2.0 + - - +
648A SER* 1.3 77.1 - - - +
650A LYS* 1.3 71.3 + - - +
651A VAL* 3.2 17.4 + - + +
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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
------------------------------------------------------------
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