Contacts of the helix formed by residues 595 - 606 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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593D SER 3.6 3.9 + - - +
594D ASN* 1.3 78.6 - - - +
596D LEU* 1.3 66.2 + - - +
597D GLN* 3.2 3.8 - - + +
598D ILE* 3.2 36.3 + - + +
599D VAL 4.2 0.5 + - - -
629D PRO 3.8 5.4 - - - +
630D ASN* 3.2 35.7 - - - +
631D LYS 3.4 6.3 - - - -
632D SER* 4.4 0.7 - - - +
633D LEU* 4.4 2.1 - - - +
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Residues in contact with LEU 596 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594D ASN 3.7 0.2 + - - -
595D LYS* 1.3 67.0 - - - +
597D GLN* 1.3 59.6 + - - +
598D ILE 3.0 2.7 - - - -
599D VAL* 2.9 26.8 + - + +
600D PHE* 3.2 37.6 + - + -
624D VAL* 3.6 31.9 - - + +
627D LEU* 3.7 16.2 - - + -
628D ASP 3.5 16.2 - - - +
629D PRO 2.9 11.9 + - - +
631D LYS 2.8 16.5 + - - +
632D SER 5.4 0.4 - - - -
633D LEU* 3.8 23.8 - - + -
636D VAL* 4.3 11.4 - - + -
638D LEU* 4.1 9.6 - - + -
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Residues in contact with GLN 597 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595D LYS* 4.9 2.5 - - + -
596D LEU* 1.3 76.0 - - - +
598D ILE* 1.3 58.3 + - + +
600D PHE* 3.0 17.2 + - + +
601D ASP* 2.7 51.5 + - - +
629D PRO* 2.9 27.2 + - + +
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Residues in contact with ILE 598 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588D ARG* 5.7 2.2 - - - +
590D PHE* 3.3 31.4 - - + -
594D ASN* 4.5 21.3 - - + +
595D LYS* 3.2 37.9 - - + +
596D LEU 3.0 0.2 - - - -
597D GLN* 1.3 81.8 - - + +
599D VAL* 1.3 57.4 + - + +
601D ASP* 3.3 9.8 + - - +
602D PHE* 2.9 25.8 + - - +
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Residues in contact with VAL 599 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576D LEU* 3.8 29.6 - - + -
578D ILE* 4.7 8.5 - - + -
590D PHE* 4.0 22.0 - - + -
595D LYS 4.8 0.9 - - - +
596D LEU* 2.9 12.2 + - + +
598D ILE* 1.3 72.8 - - + +
600D PHE* 1.3 70.0 + - + +
602D PHE* 3.1 5.6 + - + +
603D VAL* 3.0 23.8 + - + +
615D LEU* 4.1 23.8 - - + -
624D VAL* 6.1 0.2 - - + -
633D LEU* 3.5 32.3 - - + -
638D LEU* 5.9 1.6 - - + -
644D LEU* 5.0 0.7 - - + -
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Residues in contact with PHE 600 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596D LEU* 3.5 25.6 - - + -
597D GLN* 3.1 22.4 - - + +
599D VAL* 1.3 81.9 - - + +
601D ASP* 1.3 60.5 + - - +
603D VAL* 3.2 10.7 - - + +
604D ALA* 3.1 28.3 + - - +
610D TRP* 3.7 36.7 + + + +
615D LEU* 5.2 6.1 - - + -
624D VAL* 3.3 28.0 - - + -
625D THR* 3.5 32.1 - - + -
627D LEU 3.9 1.1 - - - -
629D PRO* 3.7 34.3 - - + -
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Residues in contact with ASP 601 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597D GLN* 2.7 37.5 + - - +
598D ILE* 3.6 10.0 - - - +
600D PHE* 1.3 72.4 - - - +
602D PHE* 1.3 66.8 + - - +
604D ALA* 3.0 8.5 + - - +
605D SER* 2.8 27.4 + - - -
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Residues in contact with PHE 602 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576D LEU 5.8 0.2 - - - -
578D ILE* 4.1 23.6 - - + -
586D LEU* 4.2 20.9 - - + -
587D GLU 4.2 17.9 - - - -
588D ARG* 3.3 46.2 - - + +
590D PHE* 3.9 27.8 - + + -
598D ILE* 2.9 17.1 + - + +
599D VAL* 3.4 9.9 - - + +
601D ASP* 1.3 71.8 - - - +
603D VAL* 1.3 73.9 + - + +
605D SER* 3.0 23.5 + - - -
606D LYS* 3.2 35.4 + - + +
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Residues in contact with VAL 603 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578D ILE* 3.9 41.5 - - + -
586D LEU* 4.5 2.9 - - + -
599D VAL* 3.0 13.1 + - + +
600D PHE* 3.2 21.8 - - + +
602D PHE* 1.3 84.0 - - + +
604D ALA* 1.3 63.1 + - - +
606D LYS* 3.3 8.3 + - - +
607D GLY 3.3 5.0 + - - -
608D PHE* 2.8 42.9 + - + +
610D TRP* 5.3 4.0 - - - +
615D LEU* 4.8 13.7 - - + -
646D LEU* 4.5 11.9 - - + -
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Residues in contact with ALA 604 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600D PHE 3.1 18.7 + - - +
601D ASP* 3.0 9.8 + - - +
603D VAL* 1.3 78.4 - - - +
605D SER* 1.3 57.2 + - - +
607D GLY* 2.8 21.8 + - - -
608D PHE 3.5 11.7 + - - -
609D PRO* 3.8 21.6 - - + +
610D TRP* 4.4 3.6 - - + +
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Residues in contact with SER 605 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588D ARG* 5.8 0.2 + - - -
601D ASP* 2.8 17.8 + - - -
602D PHE* 3.0 18.1 + - - -
604D ALA* 1.3 69.1 - - - +
606D LYS* 1.3 67.4 + - - +
607D GLY* 3.0 9.1 + - - -
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Residues in contact with LYS 606 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586D LEU* 3.7 40.1 - - + +
588D ARG* 4.9 5.9 - - - +
602D PHE* 3.2 41.2 + - + +
603D VAL 3.8 5.2 - - - +
604D ALA 3.2 0.6 - - - -
605D SER* 1.3 80.3 + - - +
607D GLY* 1.3 56.8 + - - +
608D PHE* 3.3 18.9 - - - -
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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