Contacts of the helix formed by residues 595 - 606 (chain B) in PDB entry 3QCA
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 LYS 595 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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593B SER 3.7 3.6 + - - +
594B ASN* 1.3 78.7 - - - +
596B LEU* 1.3 67.5 - - - +
597B GLN* 3.3 3.6 - - + +
598B ILE* 3.3 35.2 + - + +
629B PRO 3.9 6.5 - - - +
630B ASN* 3.5 31.4 - - - +
631B LYS 3.5 6.1 - - - +
632B SER* 4.4 2.2 - - - +
633B LEU* 4.1 3.1 - - - +
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Residues in contact with LEU 596 (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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594B ASN 3.7 0.4 + - - -
595B LYS* 1.3 68.2 - - - +
597B GLN* 1.3 56.9 + - - +
598B ILE 3.0 2.5 - - - -
599B VAL* 2.8 30.7 + - + +
600B PHE* 3.1 37.2 + - + -
624B VAL* 3.7 30.1 - - + +
627B LEU* 3.9 16.4 - - + -
628B ASP 3.6 16.2 - - - +
629B PRO* 3.2 8.0 + - + +
631B LYS 2.8 20.0 + - - +
632B SER 5.2 0.4 - - - -
633B LEU* 3.7 24.0 - - + -
636B VAL* 4.2 11.2 - - + -
638B LEU* 3.8 12.6 - - + -
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Residues in contact with GLN 597 (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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595B LYS* 4.9 2.2 - - + -
596B LEU* 1.3 75.5 - - - +
598B ILE* 1.3 59.4 + - + +
600B PHE* 2.9 18.1 + - + +
601B ASP* 2.6 51.9 + - - +
629B PRO* 3.0 27.9 + - + +
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Residues in contact with ILE 598 (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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588B ARG* 5.6 2.0 - - - +
590B PHE* 3.4 31.0 - - + -
594B ASN* 4.6 20.6 - - + +
595B LYS* 3.3 39.0 - - + +
597B GLN* 1.3 81.4 - - + +
599B VAL* 1.3 62.9 + - - +
601B ASP* 3.1 10.2 + - - +
602B PHE* 2.8 21.2 + - + +
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Residues in contact with VAL 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B LEU* 3.8 30.7 - - + -
578B ILE* 4.8 6.1 - - + -
590B PHE* 4.0 21.1 - - + -
595B LYS 4.8 0.4 - - - +
596B LEU* 2.8 16.4 + - + +
598B ILE* 1.3 71.6 - - - +
600B PHE* 1.3 66.9 + - + +
602B PHE* 3.0 5.5 + - + +
603B VAL* 3.0 23.7 + - + +
615B LEU* 4.0 24.0 - - + -
633B LEU* 3.6 33.9 - - + -
638B LEU* 5.5 2.0 - - + -
644B LEU* 4.8 2.5 - - + -
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Residues in contact with PHE 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B LEU* 3.1 23.6 + - + -
597B GLN* 2.9 24.4 + - + +
599B VAL* 1.3 81.8 - - + +
601B ASP* 1.3 64.4 + - - +
603B VAL* 3.2 11.1 - - + +
604B ALA* 3.1 23.1 + - - +
610B TRP* 4.9 22.1 + + + +
615B LEU* 4.9 5.8 - - + -
624B VAL* 3.3 36.6 - - + -
625B THR* 3.6 38.8 - - + -
627B LEU 4.1 1.6 - - - -
629B PRO* 3.6 33.9 - - + -
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Residues in contact with ASP 601 (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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597B GLN* 2.6 37.1 + - - +
598B ILE* 3.5 10.7 - - - +
600B PHE* 1.3 74.5 - - - +
602B PHE* 1.3 67.6 + - - +
604B ALA* 3.0 7.8 + - - +
605B SER* 2.7 28.6 + - - -
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Residues in contact with PHE 602 (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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576B LEU* 5.9 0.7 - - + -
578B ILE* 4.1 24.5 - - + -
586B LEU* 4.2 17.7 - - + -
587B GLU 4.2 19.1 - - - -
588B ARG* 3.2 45.1 - - + +
590B PHE* 3.8 29.4 - + + -
598B ILE 2.8 16.5 + - - +
599B VAL* 3.0 9.4 + - + +
601B ASP* 1.3 72.5 - - - +
603B VAL* 1.3 72.5 + - + +
605B SER* 3.1 22.9 + - - -
606B LYS* 3.2 34.4 + - + +
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Residues in contact with VAL 603 (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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578B ILE* 4.0 40.6 - - + -
586B LEU* 4.5 2.9 - - + -
599B VAL* 3.0 12.0 + - + +
600B PHE* 3.2 21.3 - - + +
602B PHE* 1.3 83.0 - - + +
604B ALA* 1.3 57.0 + - - +
606B LYS* 3.3 14.3 + - - +
607B GLY 3.3 0.5 + - - -
608B PHE* 2.8 42.9 + - - +
610B TRP* 5.6 2.5 - - - +
615B LEU* 4.7 17.0 - - + -
625B THR* 6.2 1.8 - - + -
646B LEU* 4.2 16.4 - - + -
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Residues in contact with ALA 604 (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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600B PHE 3.1 17.9 + - - +
601B ASP* 3.0 9.8 + - - +
603B VAL* 1.3 78.3 - - - +
605B SER* 1.3 54.3 + - - +
607B GLY* 2.7 28.4 + - - -
608B PHE 3.3 11.7 + - - -
609B PRO* 3.7 23.5 - - + +
610B TRP 4.7 1.6 - - - +
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Residues in contact with SER 605 (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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601B ASP* 2.7 18.6 + - - -
602B PHE* 3.1 13.1 + - - -
604B ALA* 1.3 72.9 - - - +
606B LYS* 1.3 70.5 + - - +
607B GLY* 3.1 4.5 + - - -
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Residues in contact with LYS 606 (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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586B LEU* 3.7 40.3 - - + +
588B ARG* 4.9 4.9 - - - +
602B PHE* 3.2 38.3 + - + +
603B VAL 3.6 9.4 - - - +
604B ALA 3.1 1.2 - - - -
605B SER* 1.3 84.5 + - - +
607B GLY* 1.3 57.4 + - - +
608B PHE* 3.3 16.6 - - - -
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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