Contacts of the helix formed by residues 622 - 637 (chain B) in PDB entry 4RG7
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 GLU 622 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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617B PHE* 2.9 22.3 + - + +
620B THR* 4.1 12.3 - - - +
621B GLU* 1.3 71.1 - - - +
623B LEU* 1.3 58.5 + - - +
624B ASP* 3.3 2.9 - - - -
625B LYS* 3.1 24.5 + - + +
626B ALA* 3.0 23.6 + - - +
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Residues in contact with LEU 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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618B VAL* 5.7 3.8 - - + +
621B GLU* 3.5 5.7 + - - -
622B GLU* 1.3 72.0 - - - +
624B ASP* 1.3 58.1 + - - +
626B ALA* 3.6 9.8 - - + +
627B LEU* 2.7 51.0 + - + +
650B ILE* 5.7 5.6 - - + -
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Residues in contact with ASP 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 GLU 3.3 1.3 - - - -
623B LEU* 1.3 78.8 - - - +
625B LYS* 1.3 64.0 + - + +
627B LEU* 3.7 6.6 + - - +
628B ALA* 3.5 18.5 + - - +
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Residues in contact with LYS 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617B PHE* 4.7 5.8 - - + -
622B GLU* 3.1 23.8 + - + +
624B ASP* 1.3 79.0 - - + +
626B ALA* 1.3 63.6 + - - +
628B ALA* 3.3 7.5 + - - +
629B CYS* 3.2 30.7 + - - -
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Residues in contact with ALA 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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614B GLY* 3.8 7.4 - - - +
617B PHE* 3.7 19.7 - - + +
618B VAL* 3.7 26.7 - - + +
622B GLU 3.0 13.1 + - - +
623B LEU* 3.2 12.1 + - + +
625B LYS* 1.3 75.8 - - - +
627B LEU* 1.3 64.9 + - + +
629B CYS* 3.5 3.3 + - - +
630B PHE* 3.1 31.7 + - + -
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Residues in contact with LEU 627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623B LEU* 2.7 41.2 + - + +
624B ASP* 4.0 6.7 - - - +
626B ALA* 1.3 73.9 - - + +
628B ALA* 1.3 52.8 + - - +
630B PHE* 3.4 8.7 + - + +
631B ARG* 2.7 37.9 + - - +
647B LEU* 5.8 9.0 - - + -
650B ILE* 4.5 20.4 - - + -
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Residues in contact with ALA 628 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624B ASP 3.5 11.2 + - - +
625B LYS* 3.3 12.7 + - - +
626B ALA 3.2 0.4 - - - -
627B LEU* 1.3 76.8 - - - +
629B CYS* 1.3 55.7 + - - +
631B ARG* 3.4 6.0 - - - +
632B ASN* 2.5 50.3 + - - +
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Residues in contact with CYS 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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610B TYR* 3.2 31.4 - - + +
613B LEU* 4.0 21.1 - - - -
614B GLY* 4.0 9.9 - - - +
617B PHE* 5.5 1.8 - - - -
625B LYS* 3.2 19.0 + - - -
626B ALA 3.8 5.6 - - - +
628B ALA* 1.3 77.7 - - - +
630B PHE* 1.3 52.4 + - - +
632B ASN* 3.0 9.2 + - - +
633B ALA* 2.5 36.2 + - - +
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Residues in contact with PHE 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611B THR* 3.4 37.5 - - + -
614B GLY* 3.6 23.3 - - - -
615B HIS* 3.6 6.1 - - + -
618B VAL* 4.2 18.4 - - + -
626B ALA* 3.1 22.4 + - + +
627B LEU* 3.8 6.5 - - - +
629B CYS* 1.3 78.8 - - - +
631B ARG* 1.3 62.8 + - - +
633B ALA* 3.1 7.2 + - - +
634B ILE* 3.0 24.6 + - - +
642B ASN 4.9 1.3 - - - -
643B ALA* 3.6 28.9 - - + +
646B GLY* 3.7 35.7 - - - -
647B LEU* 3.9 11.7 - - + +
650B ILE* 5.6 3.8 - - + -
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Residues in contact with ARG 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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627B LEU 2.7 23.5 + - - +
628B ALA* 3.4 8.5 - - - +
630B PHE* 1.3 75.2 - - - +
632B ASN* 1.3 62.4 + - - +
634B ILE* 3.0 31.6 - - + +
635B ARG* 3.5 6.4 + - - +
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Residues in contact with ASN 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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610B TYR* 4.3 24.3 - - + -
628B ALA* 2.5 37.6 + - - +
629B CYS* 3.3 8.8 - - - +
631B ARG* 1.3 73.4 - - - +
633B ALA* 1.3 61.4 + - - +
634B ILE 3.3 0.2 + - - -
635B ARG* 3.4 8.6 + - - +
636B VAL* 3.2 22.9 + - - +
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Residues in contact with ALA 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B ALA* 4.0 5.4 - - + +
610B TYR* 3.8 19.4 - - + +
611B THR* 3.7 19.1 - - + -
629B CYS 2.5 17.0 + - - +
630B PHE* 3.1 13.9 + - - +
632B ASN* 1.3 73.3 - - - +
634B ILE* 1.3 49.2 + - - +
636B VAL* 3.3 2.8 - - - +
637B ASN* 2.6 37.8 + - - +
640B HIS* 5.8 1.3 - - + -
643B ALA* 3.7 17.5 - - + -
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Residues in contact with ILE 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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630B PHE 3.0 9.7 + - - +
631B ARG* 3.0 27.8 - - + +
633B ALA* 1.3 69.0 - - - +
635B ARG* 1.3 77.6 + - + +
636B VAL 3.1 1.3 - - - -
637B ASN 2.9 25.8 - - - +
638B PRO* 3.3 6.1 - - + +
640B HIS* 4.8 0.7 - - + +
643B ALA* 3.8 23.1 - - + -
644B TRP* 3.5 51.1 - - + +
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Residues in contact with ARG 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 ARG 3.5 6.7 + - - +
632B ASN* 3.4 12.7 + - - +
634B ILE* 1.3 87.5 - - + +
636B VAL* 1.3 61.1 + - - +
637B ASN* 4.6 0.2 - - - -
638B PRO* 4.7 2.8 - - - +
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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
----------------------------------------------------------
604B PRO 5.0 4.5 - - - +
605B ASN* 5.4 5.4 - - - -
607B ALA* 4.2 12.5 - - + +
610B TYR* 4.2 22.0 - - + -
632B ASN 3.2 12.0 + - - +
633B ALA 3.3 9.6 - - - +
635B ARG* 1.3 80.7 - - - +
637B ASN* 1.3 58.3 + - - +
638B PRO 4.1 1.1 - - - -
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Residues in contact with ASN 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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607B ALA* 3.5 18.2 - - + -
633B ALA 2.6 15.6 + - - +
634B ILE* 2.9 24.1 - - - +
636B VAL* 1.3 75.0 - - - +
638B PRO* 1.3 65.3 - - - +
639B ARG 3.5 1.1 - - - +
640B HIS* 3.4 31.6 + - + +
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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