Contacts of the helix formed by residues 617 - 634 (chain B) in PDB entry 3S95
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 617 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577B PRO* 3.9 37.0 - - + +
578B SER* 4.4 6.7 - - - +
606B THR* 3.4 18.6 - - - +
607B LEU* 3.8 24.5 - - + -
610B HIS* 3.6 41.4 + - + +
616B PRO* 1.3 72.5 - - - +
618B GLY* 1.3 64.4 + - - +
620B GLN* 6.0 0.2 - - - +
621B LEU* 3.7 32.9 + - + +
622B GLU* 5.1 8.7 + - + +
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Residues in contact with GLY 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616B PRO* 3.5 9.2 - - - +
617B LEU* 1.3 80.6 - - - +
619B PRO* 1.3 77.2 - - - +
620B GLN 3.4 2.4 + - - -
621B LEU 3.5 0.2 + - - -
622B GLU* 3.0 33.7 + - - +
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Residues in contact with PRO 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618B GLY* 1.3 85.7 - - - +
620B GLN* 1.3 63.6 + - + +
622B GLU* 3.7 14.7 - - + +
623B GLN* 3.0 29.5 + - - +
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Residues in contact with GLN 620 (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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599B LYS* 3.9 14.2 - - - +
602B HIS* 4.0 11.3 - - - -
603B TRP* 2.9 36.5 + - + +
618B GLY 3.4 0.8 - - - -
619B PRO* 1.3 81.1 - - + +
621B LEU* 1.3 60.0 + - + +
623B GLN* 3.2 6.5 + - - +
624B LEU* 2.9 29.0 + - - +
639B MRD 3.3 31.1 + - - +
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Residues in contact with LEU 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B SER* 3.9 25.1 - - - +
582B ILE* 4.0 8.5 - - + -
603B TRP* 3.6 62.8 - - + +
606B THR* 4.0 7.2 - - + -
607B LEU* 4.5 1.6 - - + +
617B LEU* 3.7 49.8 + - + +
618B GLY 3.5 2.2 + - - +
619B PRO 3.4 0.2 - - - -
620B GLN* 1.3 75.6 - - - +
622B GLU* 1.3 67.2 + - - +
624B LEU* 3.6 12.5 - - + +
625B ASP* 2.9 25.8 + - - +
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Residues in contact with GLU 622 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617B LEU* 5.1 7.4 + - + +
618B GLY* 3.0 29.0 + - - +
619B PRO* 3.7 17.0 - - - +
621B LEU* 1.3 77.1 - - - +
623B GLN* 1.3 56.1 + - - +
625B ASP* 3.4 4.4 + - - +
626B ARG* 3.0 38.9 + - - +
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Residues in contact with GLN 623 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619B PRO 3.0 18.8 + - - +
620B GLN* 3.2 5.6 + - - +
622B GLU* 1.3 74.1 - - - +
624B LEU* 1.3 59.9 + - - +
626B ARG* 3.4 25.0 + - - +
627B GLY* 2.7 41.4 + - - -
630B GLU* 5.4 3.0 + - - -
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Residues in contact with LEU 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B SER* 4.3 2.7 - - - +
581B PRO* 3.8 9.3 - - + +
582B ILE* 3.5 45.3 - - + +
585B ARG* 4.3 28.3 - - + +
603B TRP* 3.9 26.0 - - + -
620B GLN 2.9 16.7 + - - +
621B LEU* 3.6 13.5 - - + +
623B GLN* 1.3 77.8 - - - +
625B ASP* 1.3 61.8 + - - +
627B GLY* 4.0 0.4 - - - -
628B PHE* 3.1 25.5 + - - +
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Residues in contact with ASP 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577B PRO* 4.1 11.4 - - + +
578B SER* 2.8 34.2 + - - -
581B PRO* 3.4 17.5 - - - +
621B LEU 2.9 18.2 + - - +
622B GLU* 3.9 4.5 - - - +
624B LEU* 1.3 77.2 - - - +
626B ARG* 1.3 63.0 + - - +
628B PHE* 3.5 0.9 + - - +
629B TRP* 3.1 44.5 + - - -
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Residues in contact with ARG 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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622B GLU* 3.0 27.0 + - - +
623B GLN* 3.4 32.1 + - - +
625B ASP* 1.3 76.5 - - - +
627B GLY* 1.3 60.9 + - - +
629B TRP* 3.3 5.6 + - - +
630B GLU* 2.9 54.2 + - + +
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Residues in contact with GLY 627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623B GLN* 2.7 33.1 + - - -
624B LEU* 4.0 0.4 - - - -
626B ARG* 1.3 72.5 - - - +
628B PHE* 1.3 63.3 + - - +
630B GLU* 3.4 9.9 + - - +
631B THR* 2.8 31.4 + - - -
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Residues in contact with PHE 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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563B VAL* 3.8 20.0 - - + -
567B LEU* 4.4 1.1 - - + -
580B PHE* 3.9 14.1 - + - -
581B PRO* 3.8 20.2 - - + -
584B VAL* 3.9 34.5 - - + -
624B LEU* 3.1 18.6 + - + +
625B ASP 3.7 2.7 - - - +
627B GLY* 1.3 76.6 - - - +
629B TRP* 1.3 106.1 + + - +
631B THR* 3.6 5.4 - - + -
632B TYR* 2.8 38.4 + + + +
637B SER* 4.0 18.4 - - - -
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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
----------------------------------------------------------
567B LEU* 3.9 27.4 - - + -
580B PHE* 4.9 5.4 - + + -
581B PRO* 4.3 5.1 - - + +
625B ASP* 3.1 47.0 + - - +
626B ARG* 4.0 4.3 - - - +
628B PHE* 1.3 105.2 - + - +
630B GLU* 1.3 57.4 + - - +
632B TYR* 3.8 31.1 - + + +
633B ARG* 3.0 36.5 + - - +
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Residues in contact with GLU 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623B GLN* 5.4 2.9 + - - -
626B ARG* 2.9 54.6 + - + +
627B GLY* 3.8 8.9 - - - +
628B PHE 3.2 0.2 - - - -
629B TRP* 1.3 74.8 - - - +
631B THR* 1.3 60.4 + - - +
633B ARG* 3.3 33.6 + - - +
634B ARG* 3.0 54.0 + - - +
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Residues in contact with THR 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 GLY 2.8 22.0 + - - -
628B PHE* 3.6 6.9 - - - -
630B GLU* 1.3 72.2 - - - +
632B TYR* 1.3 66.3 + - - +
634B ARG* 3.3 24.5 + - - +
635B GLY 3.3 0.2 + - - -
636B GLU* 3.1 60.3 + - + +
637B SER* 4.2 4.7 - - - +
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Residues in contact with TYR 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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563B VAL* 4.2 9.0 - - + -
564B ARG* 3.3 65.1 + - + +
567B LEU* 3.5 25.1 - - + +
568B ASP* 4.8 2.6 + - - -
628B PHE* 2.8 28.1 + + + +
629B TRP* 3.8 30.1 - + + +
631B THR* 1.3 77.2 - - - +
633B ARG* 1.3 58.5 + - - +
635B GLY* 2.8 21.8 + - - -
636B GLU 4.6 0.9 - - - +
637B SER* 3.3 27.5 + - - +
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Residues in contact with ARG 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629B TRP* 3.0 27.4 + - - +
630B GLU* 3.5 45.8 + - - +
632B TYR* 1.3 78.6 - - - +
634B ARG* 1.3 63.2 + - - +
635B GLY 3.2 1.3 + - - -
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Residues in contact with ARG 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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627B GLY 5.6 0.2 + - - -
630B GLU* 3.0 44.0 + - - +
631B THR* 3.8 20.0 + - - +
632B TYR 3.2 0.6 - - - -
633B ARG* 1.3 79.9 - - + +
635B GLY* 1.3 61.6 + - - +
636B GLU* 2.9 48.8 + - - +
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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