Contacts of the helix formed by residues 623 - 640 (chain B) in PDB entry 4REA
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 ASN 623 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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618B ALA* 2.9 26.3 + - + +
621B ASN* 3.6 23.9 - - - +
622B GLY* 1.3 76.7 + - - +
624B TRP* 1.3 57.7 + - - +
625B GLU 3.2 3.7 + - - -
626B GLU* 3.3 14.4 + - + +
627B ALA* 2.8 26.5 + - - +
28C C 4.8 2.9 + - - -
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Residues in contact with TRP 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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619B MET* 3.7 40.2 - - + -
622B GLY* 3.1 33.1 + - - -
623B ASN* 1.3 71.2 - - - +
625B GLU* 1.3 61.2 + - + +
627B ALA* 3.6 6.5 - - - +
628B LYS* 2.9 28.9 + - - +
675B GLU* 4.0 9.2 - - + -
676B ILE* 3.8 35.6 - - + +
679B ARG* 3.3 74.4 - - + +
680B LEU* 4.1 19.6 - - + +
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Residues in contact with GLU 625 (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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441A LEU* 3.1 25.3 - - - +
623B ASN 3.2 1.0 - - - -
624B TRP* 1.3 77.3 - - + +
626B GLU* 1.3 63.6 + - - +
628B LYS* 3.2 17.8 + - - +
629B GLU* 2.8 34.7 + - - +
680B LEU* 3.0 33.7 - - - +
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Residues in contact with GLU 626 (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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618B ALA* 4.4 8.4 - - + +
623B ASN* 3.3 20.8 + - + +
625B GLU* 1.3 74.7 - - - +
627B ALA* 1.3 64.2 + - - +
628B LYS 3.2 0.2 + - - -
629B GLU* 3.3 13.2 + - + +
630B LEU* 3.1 46.4 + - - +
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Residues in contact with ALA 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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615B ILE* 4.0 8.5 - - + +
618B ALA* 3.9 16.1 - - + +
619B MET* 3.9 29.4 - - + +
623B ASN 2.8 18.9 + - - +
624B TRP* 3.6 9.6 - - - +
625B GLU 3.2 0.2 - - - -
626B GLU* 1.3 75.3 - - - +
628B LYS* 1.3 57.6 + - - +
630B LEU* 3.6 6.0 + - - +
631B ALA* 3.0 29.6 + - - +
676B ILE* 4.5 8.1 - - + +
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Residues in contact with LYS 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 TRP 2.9 14.4 + - - +
625B GLU* 3.5 13.6 - - + +
626B GLU 3.1 0.4 - - - -
627B ALA* 1.3 75.8 - - - +
629B GLU* 1.3 83.1 + - - +
631B ALA* 3.2 6.9 + - - +
632B GLN* 2.8 53.7 + - + +
673B PHE* 4.0 5.4 - - + -
676B ILE* 4.0 17.3 - - + -
677B LEU* 6.0 5.2 - - + -
680B LEU* 3.9 20.6 - - + -
682B MET* 4.9 15.0 - - - -
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Residues in contact with GLU 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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625B GLU* 2.8 30.7 - - - +
626B GLU* 3.3 17.7 + - + +
628B LYS* 1.3 93.8 + - - +
630B LEU* 1.3 67.5 + - - +
632B GLN* 3.1 23.8 + - - +
633B CYS* 2.9 33.3 + - - -
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Residues in contact with LEU 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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611B MET* 3.5 31.9 - - + +
614B ASP* 3.7 18.8 - - + +
615B ILE* 3.5 37.5 - - + +
618B ALA* 5.3 1.1 - - + -
626B GLU* 3.1 31.5 + - - +
627B ALA* 3.6 9.6 - - - +
629B GLU* 1.3 80.2 - - - +
631B ALA* 1.3 57.1 + - - +
633B CYS* 3.3 6.5 + - + +
634B ALA* 3.0 28.2 + - - +
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Residues in contact with ALA 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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615B ILE* 3.5 24.4 - - + +
627B ALA 3.0 12.7 + - - +
628B LYS 3.2 4.7 + - - +
630B LEU* 1.3 76.0 - - - +
632B GLN* 1.3 52.9 + - - +
634B ALA* 3.3 3.9 + - - +
635B LYS* 2.7 34.3 + - - +
669B ILE* 4.7 6.3 - - + +
673B PHE* 3.0 33.7 - - + -
676B ILE* 4.2 9.0 - - + -
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Residues in contact with GLN 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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628B LYS* 2.8 47.8 + - - +
629B GLU* 3.1 24.8 + - - +
631B ALA* 1.3 73.5 - - - +
633B CYS* 1.3 60.4 + - - +
635B LYS* 3.2 11.0 + - + +
636B ARG* 2.6 61.2 + - - +
673B PHE* 3.7 17.4 - - + -
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Residues in contact with CYS 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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611B MET* 5.2 5.6 - - + -
629B GLU* 2.9 23.9 + - - -
630B LEU* 3.7 9.2 - - + +
632B GLN* 1.3 75.4 - - - +
634B ALA* 1.3 59.6 + - - +
636B ARG* 2.8 19.2 + - - +
637B ASP* 2.8 39.8 + - - +
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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
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611B MET* 3.8 29.3 - - + +
630B LEU 3.0 17.2 + - - +
631B ALA* 3.6 5.6 - - - +
633B CYS* 1.3 76.2 - - - +
635B LYS* 1.3 63.6 + - - +
637B ASP* 3.2 6.9 + - - -
638B TRP 3.1 9.7 + - - -
666B TYR* 3.0 36.0 - - + -
669B ILE* 4.0 15.0 - - + -
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Residues in contact with LYS 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 ALA 2.7 21.6 + - - +
632B GLN* 3.4 10.5 - - + +
633B CYS 3.1 0.2 - - - -
634B ALA* 1.3 76.2 - - - +
636B ARG* 1.3 66.0 + - + +
638B TRP* 3.3 4.3 + - - +
639B ASN* 3.3 42.2 + - - +
670B LEU* 4.1 28.6 - - + +
673B PHE* 4.7 13.5 - - + -
688B ARG* 5.4 4.9 - - - +
689B GLU* 3.0 32.2 + - - +
692B SER* 6.4 0.6 - - - -
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Residues in contact with ARG 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632B GLN* 2.6 71.0 + - - +
633B CYS* 2.8 25.9 + - - +
635B LYS* 1.3 81.2 - - + +
637B ASP* 1.3 63.8 + - - +
639B ASN* 4.3 3.2 - - - +
640B ARG* 2.8 31.7 + - - +
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Residues in contact with ASP 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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611B MET* 5.3 4.5 - - - +
633B CYS* 2.8 32.9 + - - +
634B ALA* 3.2 4.1 + - - +
636B ARG* 1.3 76.1 - - - +
638B TRP* 1.3 60.5 + - - +
640B ARG* 3.5 15.4 - - + +
641B LEU* 3.4 21.7 + - - +
666B TYR* 3.4 22.9 + - - +
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Residues in contact with TRP 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 ALA 3.1 9.8 + - - +
635B LYS* 3.3 5.1 + - + +
636B ARG 3.2 0.4 - - - -
637B ASP* 1.3 75.0 - - - +
639B ASN* 1.3 78.8 + - - +
641B LEU* 3.1 41.6 + - + +
642B LYS* 3.3 29.4 + - + +
647B LEU* 3.9 27.4 - - + -
663B GLY* 3.5 31.6 - - - -
666B TYR* 3.3 48.5 - + + +
667B THR* 5.5 2.5 + - - +
670B LEU* 4.0 26.9 - - + +
699B TYR* 4.4 14.8 - + - -
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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
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635B LYS* 3.3 38.8 + - - +
636B ARG* 4.5 3.3 - - - +
638B TRP* 1.3 87.0 + - - +
640B ARG* 1.3 58.1 + - - +
641B LEU 2.9 9.8 + - - -
642B LYS* 3.1 39.3 + - - +
670B LEU* 5.6 0.9 - - - +
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Residues in contact with ARG 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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636B ARG* 2.8 22.4 + - - +
637B ASP* 3.5 18.2 - - - +
639B ASN* 1.3 76.0 - - - +
641B LEU* 1.3 56.4 + - + +
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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
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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