Contacts of the helix formed by residues 622 - 641 (chain B) in PDB entry 6RKU
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 ASP 622 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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619B ASP 3.4 8.8 + - - +
621B SER* 1.3 77.2 - - - +
623B GLU* 1.3 62.6 + - - +
624B GLN* 2.7 41.9 + - - +
625B THR* 2.8 48.3 + - + +
626B VAL* 3.7 6.4 + - - +
660B PHE* 4.0 1.6 - - - -
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Residues in contact with GLU 623 (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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621B SER 3.5 0.4 + - - -
622B ASP* 1.3 76.0 + - - +
624B GLN* 1.3 54.6 + - - +
626B VAL* 3.4 5.5 + - + +
627B THR* 2.7 45.9 + - - +
651B VAL* 4.1 22.3 - - + +
660B PHE* 3.5 35.0 - - + -
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Residues in contact with GLN 624 (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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622B ASP* 2.7 27.0 + - - +
623B GLU* 1.3 71.1 - - - +
625B THR* 1.3 57.9 + - - +
627B THR* 4.1 6.7 - - - -
628B ARG* 2.8 33.0 + - + +
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Residues in contact with THR 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619B ASP* 3.3 27.6 + - - +
622B ASP* 2.8 45.0 + - + +
624B GLN* 1.3 78.3 - - - +
626B VAL* 1.3 62.3 + - - +
628B ARG* 3.3 4.4 + - - +
629B TRP* 2.9 25.0 + - - +
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Residues in contact with VAL 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615B LEU* 6.0 4.0 - - + -
619B ASP* 3.6 29.4 - - + +
620B LEU* 4.9 2.2 - - + -
622B ASP 3.8 5.8 - - - +
623B GLU* 3.4 8.7 + - + +
624B GLN 3.4 0.2 - - - -
625B THR* 1.3 81.2 + - - +
627B THR* 1.3 57.9 + - - +
629B TRP* 3.3 8.9 + - + +
630B VAL* 2.9 31.6 + - + +
651B VAL* 5.3 13.7 - - + -
660B PHE* 4.5 21.1 - - + +
661B GLU 5.4 0.7 - - - -
662B PRO* 3.6 37.7 - - + -
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Residues in contact with THR 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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623B GLU* 2.7 33.9 + - - +
624B GLN* 3.6 9.6 - - + -
625B THR 3.2 0.2 - - - -
626B VAL* 1.3 77.2 - - - +
628B ARG* 1.3 57.4 + - - +
630B VAL* 3.2 11.8 - - + +
631B ASN* 2.9 36.5 + - + +
649B PHE* 5.8 7.2 - - + -
651B VAL* 4.4 14.6 - - + +
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Residues in contact with ARG 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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624B GLN* 2.8 21.4 + - + +
625B THR* 3.8 5.8 - - - +
627B THR* 1.3 77.2 - - - +
629B TRP* 1.3 63.4 + - - +
631B ASN* 3.7 9.9 - - - +
632B ALA* 2.9 57.2 + - - +
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Residues in contact with TRP 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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605B MET* 6.5 0.7 - - - -
609B LEU* 4.2 23.1 - - + -
612B GLN* 4.7 8.5 + - - +
613B PRO* 4.0 35.3 + - + +
614B THR 4.1 10.2 + - - -
615B LEU* 3.6 44.2 - - + -
625B THR 2.9 18.1 + - - +
626B VAL* 3.6 9.0 - - + +
628B ARG* 1.3 77.5 - - - +
630B VAL* 1.3 71.0 + - + +
632B ALA* 3.3 5.3 + - + +
633B LEU* 3.0 42.1 + - + +
662B PRO* 3.9 32.1 - - + -
677B LEU* 3.9 17.5 - - + -
687B TYR* 4.8 4.3 - + - -
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Residues in contact with VAL 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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626B VAL* 2.9 18.5 + - + +
627B THR* 3.2 21.3 - - + +
629B TRP* 1.3 87.0 - - + +
631B ASN* 1.3 57.5 + - + +
633B LEU* 3.3 8.8 + - + +
634B VAL* 2.9 40.3 + - + +
649B PHE* 3.7 37.2 - - + -
650B ASP 4.9 1.8 - - - +
651B VAL* 4.8 9.2 - - + -
662B PRO* 5.0 13.5 - - + -
663B ILE 4.7 8.7 - - - +
664B VAL* 4.9 10.5 - - + -
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Residues in contact with ASN 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627B THR* 2.9 25.0 + - + +
628B ARG* 3.7 12.8 - - - +
630B VAL* 1.3 76.3 - - + +
632B ALA* 1.3 60.2 + - - +
634B VAL* 3.4 4.8 + - - +
635B SER* 2.9 33.6 + - - -
649B PHE* 5.6 11.8 - - + -
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Residues in contact with ALA 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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612B GLN* 4.2 12.2 + - - +
613B PRO* 6.0 2.2 - - + -
628B ARG* 2.9 38.3 + - - +
629B TRP* 3.7 5.6 - - + +
631B ASN* 1.3 75.9 - - - +
633B LEU* 1.3 61.8 + - - +
635B SER* 3.8 4.9 - - - -
636B GLU* 3.0 26.7 + - - +
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Residues in contact with LEU 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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605B MET* 4.6 20.6 - - + -
608B GLU* 3.8 16.4 - - + -
609B LEU* 4.8 7.9 - - + -
612B GLN* 3.7 33.3 + - + +
629B TRP* 3.0 38.4 + - + +
630B VAL* 3.6 12.1 - - + +
631B ASN 3.2 0.2 - - - -
632B ALA* 1.3 78.7 - - - +
634B VAL* 1.3 59.5 + - + +
636B GLU* 3.8 1.4 - - - +
637B LEU* 2.9 47.1 + - + +
664B VAL* 4.5 21.3 - - + -
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Residues in contact with VAL 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630B VAL* 2.9 26.6 + - + +
631B ASN* 4.0 5.2 - - - +
633B LEU* 1.3 78.9 - - + +
635B SER* 1.3 58.1 + - - +
637B LEU* 3.3 8.8 + - + +
638B ASN* 2.9 34.9 + - - +
647B TRP* 3.4 33.7 - - + +
648B LYS* 4.0 13.5 - - - +
649B PHE* 3.8 30.3 - - + +
664B VAL* 5.2 7.9 - - + -
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Residues in contact with SER 635 (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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631B ASN* 2.9 25.5 + - - -
632B ALA* 3.8 5.8 - - - -
634B VAL* 1.3 77.4 - - - +
636B GLU* 1.3 56.7 + - - +
638B ASN* 3.3 7.5 + - - +
639B ASP* 2.9 28.5 + - - +
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Residues in contact with GLU 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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608B GLU* 3.1 31.2 - - - +
612B GLN* 3.8 11.2 - - - +
632B ALA 3.0 17.6 + - - +
633B LEU 3.9 1.1 - - - +
635B SER* 1.3 76.9 - - - +
637B LEU* 1.3 59.1 + - - +
639B ASP* 3.3 15.4 + - - +
640B LYS* 2.9 53.6 + - - +
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Residues in contact with LEU 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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604B ALA* 4.0 25.4 - - + +
605B MET* 4.8 6.5 - - + -
608B GLU* 4.0 27.8 - - + +
633B LEU* 2.9 42.8 + - + +
634B VAL* 3.7 7.9 - - + +
636B GLU* 1.3 76.6 - - - +
638B ASN* 1.3 57.9 + - - +
640B LYS* 3.3 5.4 + - + +
641B GLU* 2.9 30.3 + - - +
647B TRP* 3.6 45.3 + - + -
664B VAL* 5.3 4.5 - - + -
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Residues in contact with ASN 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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634B VAL* 2.9 29.5 + - - +
635B SER* 3.9 5.9 - - - +
637B LEU* 1.3 75.5 - - - +
639B ASP* 1.3 62.7 + - - +
641B GLU* 3.6 15.9 + - - +
645B SER 5.1 0.3 - - - +
646B GLN* 3.5 7.8 - - - +
647B TRP* 2.9 51.0 + - - +
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Residues in contact with ASP 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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635B SER 2.9 17.9 + - - +
636B GLU* 3.5 22.4 - - - +
637B LEU 3.2 0.2 - - - -
638B ASN* 1.3 79.0 - - - +
640B LYS* 1.3 65.4 + - - +
641B GLU 3.3 4.7 + - - +
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Residues in contact with LYS 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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608B GLU* 4.5 8.1 - - - +
636B GLU* 2.9 43.0 + - + +
637B LEU* 4.1 6.1 - - + +
639B ASP* 1.3 78.8 - - - +
641B GLU* 1.3 59.8 + - - +
642B GLN* 3.0 17.5 + - - +
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Residues in contact with GLU 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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637B LEU 2.9 17.8 + - - +
638B ASN* 3.8 17.0 - - - +
639B ASP 3.2 4.6 - - - +
640B LYS* 1.3 73.3 - - - +
642B GLN* 1.3 57.4 + - - +
643B HIS* 3.1 39.6 - - - +
645B SER* 3.2 46.5 - - - +
647B TRP* 3.6 19.1 + - + +
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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
------------------------------------------------------------
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