Contacts of the helix formed by residues 629 - 649 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636A VAL* 4.0 6.5 - - + +
639A ASN* 3.6 32.8 - - + +
640A ILE* 3.8 23.6 - - + +
643A LEU* 3.9 21.5 - - + -
655A ASP* 4.6 1.3 - - + -
656A HIS* 3.6 31.6 - - + -
657A HIS* 4.1 4.9 - - + -
688A MET* 4.9 2.7 - - - -
626B THR 2.9 19.1 + - - +
627B SER* 4.1 1.3 - - - +
628B SER* 1.3 80.6 - - - +
630B TRP* 1.3 64.9 + - - +
631B LYS 3.2 2.9 - - - -
632B ASP* 3.0 28.4 + - + +
633B GLN* 3.0 13.6 + - - +
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Residues in contact with TRP 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B LEU* 4.1 17.0 - - + -
613B GLU* 4.6 11.7 - - + -
616B ALA* 3.4 26.9 - - + -
621B LEU* 3.7 25.5 - - + +
622B ASP 3.8 7.2 - - - +
623B MET* 3.5 55.3 + - + -
625B LYS 3.6 10.6 + - - -
626B THR* 4.6 12.3 - - + +
628B SER* 3.1 26.8 + - - +
629B LEU* 1.3 76.5 - - - +
631B LYS* 1.3 115.7 + - + +
633B GLN* 3.4 6.1 + - - +
634B ALA* 3.0 24.8 + - + +
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Residues in contact with LYS 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A HIS* 4.2 20.4 + - + +
692A ILE* 4.0 26.0 + - + +
606B ASN* 5.1 12.5 + - - +
612B LEU* 3.7 25.0 - - + +
626B THR* 6.4 1.6 - - - -
629B LEU 3.2 0.2 - - - -
630B TRP* 1.3 126.9 - - + +
632B ASP* 1.3 60.7 + - - +
634B ALA* 3.4 1.6 + - - -
635B LEU* 2.9 30.1 + - - +
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Residues in contact with ASP 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A VAL* 4.1 16.8 - - + -
656A HIS* 2.8 24.5 + - - -
657A HIS* 2.7 25.8 + - - -
688A MET* 3.8 4.2 - - + +
689A SER* 2.7 30.9 + - - +
692A ILE* 4.3 4.0 - - - -
629B LEU* 3.0 29.2 + - + +
631B LYS* 1.3 71.2 - - - +
633B GLN* 1.3 67.3 + - - +
635B LEU* 3.4 4.2 + - - +
636B VAL* 3.2 28.2 + - - +
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Residues in contact with GLN 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A VAL* 3.6 22.0 - - + -
637A GLU* 3.0 27.9 + - - +
640A ILE* 3.4 22.0 - - - +
619B MET* 4.7 6.5 - - + -
621B LEU* 3.4 35.5 - - + +
628B SER 4.5 2.4 - - - +
629B LEU 3.0 7.4 + - - +
630B TRP* 3.7 12.1 - - - +
632B ASP* 1.3 77.4 - - - +
634B ALA* 1.3 61.0 + - - +
636B VAL* 3.3 6.7 + - - +
637B GLU* 3.2 27.6 + - + +
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Residues in contact with ALA 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B LEU* 3.7 21.5 - - + +
615B VAL* 4.4 6.1 - - + +
616B ALA* 4.2 30.3 - - + +
619B MET* 4.0 13.0 - - - -
621B LEU* 4.5 1.0 - - + +
630B TRP 3.0 17.2 + - - +
631B LYS* 4.4 0.7 - - - -
633B GLN* 1.3 74.8 - - - +
635B LEU* 1.3 63.1 + - - +
637B GLU* 3.3 2.4 + - - +
638B ILE* 3.1 27.4 + - - +
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Residues in contact with LEU 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A SER* 4.6 9.4 - - - +
692A ILE* 4.1 27.8 - - + -
600B VAL* 3.9 20.0 - - + -
604B CYS* 3.6 29.8 - - + -
612B LEU* 3.7 6.9 - - + +
631B LYS 2.9 17.4 + - - +
632B ASP* 3.7 6.1 - - - +
633B GLN 3.2 0.6 - - - -
634B ALA* 1.3 78.0 - - - +
636B VAL* 1.3 61.3 + - - +
638B ILE* 3.3 4.0 + - - +
639B ASN* 2.8 47.2 + - - +
687B PRO 5.0 0.7 - - - +
688B MET* 3.8 32.5 - - + -
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Residues in contact with VAL 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A LEU* 4.3 4.0 - - + +
632A ASP* 3.9 16.8 - - + +
633A GLN* 3.9 36.1 - - + +
636A VAL* 3.9 19.7 - - + -
632B ASP 3.2 14.8 + - - +
633B GLN* 3.8 6.7 - - - +
635B LEU* 1.3 76.4 - - - +
637B GLU* 1.3 59.5 + - - +
639B ASN* 3.3 2.8 + - - +
640B ILE* 3.0 37.2 + - + +
688B MET* 3.6 24.9 - - + -
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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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633A GLN* 2.7 38.7 + - - +
553B HIS* 2.8 49.5 + - + +
556B PHE* 3.6 14.9 - - + -
559B PHE* 5.1 2.5 - - + -
615B VAL* 5.1 3.8 - - + -
619B MET* 3.7 30.9 - - + +
633B GLN 3.2 14.8 + - - +
634B ALA 3.8 7.0 - - - +
635B LEU 3.3 0.2 - - - -
636B VAL* 1.3 77.1 - - - +
638B ILE* 1.3 62.1 + - - +
640B ILE* 3.5 4.4 + - - +
641B ALA* 3.1 17.5 + - - +
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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
----------------------------------------------------------
551B ILE* 6.2 0.4 - - + -
559B PHE* 4.2 16.1 - - + -
599B GLY* 3.6 22.9 - - - +
603B TYR* 4.1 21.8 - - + -
604B CYS* 3.7 16.6 - - - -
611B ILE* 3.7 29.6 - - + -
612B LEU* 3.9 9.0 - - + -
615B VAL* 3.7 24.2 - - + -
634B ALA 3.1 21.3 + - - +
635B LEU 3.6 4.3 - - - +
636B VAL 3.2 0.2 - - - -
637B GLU* 1.3 76.9 - - - +
639B ASN* 1.3 58.3 + - - +
641B ALA* 3.2 4.7 + - - +
642B VAL* 3.1 27.4 + - + +
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Residues in contact with ASN 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A LEU* 3.6 20.6 - - + -
595B GLY* 3.6 3.4 - - - +
596B THR* 3.5 15.3 + - + +
599B GLY* 3.3 29.0 + - - -
600B VAL* 3.3 31.6 + - - +
635B LEU* 2.8 29.8 + - - +
636B VAL 3.3 0.6 + - - +
638B ILE* 1.3 73.0 - - - +
640B ILE* 1.3 65.8 + - - +
642B VAL* 3.6 6.3 + - - +
643B LEU* 3.2 30.2 + - + +
656B HIS* 5.6 0.2 - - + -
688B MET* 3.6 11.3 - - - -
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Residues in contact with ILE 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627A SER 5.0 2.0 - - - +
628A SER* 3.4 30.5 - - - +
629A LEU* 3.9 13.9 - - + -
633A GLN* 3.5 32.8 - - - +
553B HIS* 3.8 15.9 - - + +
554B PRO* 3.9 20.4 - - + -
636B VAL* 3.0 24.6 + - + +
637B GLU* 3.5 14.4 - - - +
639B ASN* 1.3 77.5 - - - +
641B ALA* 1.3 57.3 + - - +
643B LEU* 3.4 3.8 + - - +
644B TYR* 2.9 28.4 + - + +
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Residues in contact with ALA 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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551B ILE* 3.8 2.7 - - + -
552B ARG 3.1 19.4 - - - +
553B HIS* 3.9 14.1 - - + +
559B PHE* 3.8 26.5 - - + -
637B GLU 3.1 10.5 + - - +
638B ILE 3.2 8.9 + - - +
640B ILE* 1.3 78.1 - - - +
642B VAL* 1.3 60.8 + - - +
644B TYR* 3.3 2.5 + - - +
645B SER* 2.8 35.4 + - - -
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Residues in contact with VAL 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B ILE* 4.1 20.0 - - + -
595B GLY* 4.1 15.9 - - - +
598B ILE* 4.1 24.5 - - + -
599B GLY* 4.1 18.6 - - - -
603B TYR* 4.2 9.9 - - + -
638B ILE* 3.1 19.7 + - + +
639B ASN* 3.9 6.5 - - - +
640B ILE 3.3 0.2 - - - -
641B ALA* 1.3 76.1 - - - +
643B LEU* 1.3 63.5 + - - +
645B SER* 3.3 1.9 + - - -
646B PHE* 3.1 31.9 + - + -
653B ILE* 4.0 20.0 - - + -
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Residues in contact with LEU 643 (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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627A SER* 3.5 25.4 - - - +
629A LEU* 3.6 24.7 - - + -
595B GLY* 4.1 12.6 - - - -
639B ASN* 3.2 19.3 + - + +
640B ILE 3.8 3.1 - - - +
642B VAL* 1.3 78.3 - - - +
644B TYR* 1.3 62.9 + - - +
646B PHE* 3.6 1.2 + - - +
647B GLN* 3.0 42.4 + - - +
653B ILE* 4.0 30.1 - - + -
655B ASP* 3.7 36.3 - - + +
656B HIS* 5.4 1.6 - - - +
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Residues in contact with TYR 644 (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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552B ARG* 3.7 29.2 - - + -
553B HIS 4.1 3.4 - - - -
554B PRO* 3.6 50.3 - - + +
640B ILE* 2.9 18.2 + - + +
641B ALA 3.7 2.5 - - - +
643B LEU* 1.3 77.6 - - - +
645B SER* 1.3 54.2 + - - +
647B GLN* 3.9 9.0 - - + +
648B SER* 2.7 56.2 + - - -
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Residues in contact with SER 645 (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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549B VAL* 3.6 11.0 - - - +
550B PRO 3.5 18.4 - - - -
551B ILE* 3.3 8.6 - - - -
552B ARG* 2.7 50.2 + - - +
641B ALA 2.8 20.7 + - - -
642B VAL 3.7 3.6 - - - -
644B TYR* 1.3 74.2 - - - +
646B PHE* 1.3 66.9 + - - +
648B SER 3.4 0.3 + - - -
649B ASP* 3.1 20.8 + - - +
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Residues in contact with PHE 646 (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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549B VAL* 3.8 29.8 - - + -
551B ILE* 4.6 7.9 - - + -
566B TRP* 4.9 4.5 - - + -
567B TYR 3.7 20.2 - - - -
568B GLY* 3.9 13.2 - - - -
593B TYR* 4.5 4.0 - + - -
598B ILE* 3.8 23.8 - - + -
642B VAL* 3.1 22.3 + - + +
645B SER* 1.3 79.6 - - - +
647B GLN* 1.3 62.0 + - - +
649B ASP* 3.1 3.5 + - - +
650B LYS 3.1 4.2 + - - -
651B VAL* 3.0 63.0 + - + +
652B THR 3.9 3.6 - - - -
653B ILE* 3.5 36.8 - - + -
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Residues in contact with GLN 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A LYS* 4.5 12.2 + - - +
627A SER* 3.1 37.6 + - - -
643B LEU* 3.0 30.0 + - - +
644B TYR* 3.9 7.8 - - + +
646B PHE* 1.3 77.2 - - - +
648B SER* 1.3 62.5 + - - +
650B LYS* 3.0 24.9 + - - +
651B VAL 4.7 2.7 - - - +
653B ILE* 4.2 19.1 + - + +
655B ASP 6.0 0.8 - - - +
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Residues in contact with SER 648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552B ARG* 3.5 21.1 - - - -
644B TYR* 2.7 48.4 + - - -
647B GLN* 1.3 77.2 - - - +
649B ASP* 1.3 61.0 + - - +
650B LYS* 3.3 19.6 + - - +
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Residues in contact with ASP 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B LYS 5.7 0.3 - - - +
547B LEU* 6.4 0.2 - - + -
548B GLU 4.6 2.3 - - - +
549B VAL* 3.7 13.9 - - + +
550B PRO* 3.8 10.9 - - - +
552B ARG* 2.6 41.0 + - - -
645B SER 3.1 9.8 + - - +
646B PHE 3.1 5.7 + - - +
648B SER* 1.3 78.0 - - - +
650B LYS* 1.3 73.9 + - - +
651B VAL* 3.2 17.9 + - + +
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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