Contacts of the helix formed by residues 595 - 606 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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593C SER 3.7 3.1 + - - +
594C ASN* 1.3 78.7 - - - +
596C LEU* 1.3 64.8 + - - +
597C GLN* 3.3 2.7 - - + +
598C ILE* 3.2 36.5 + - + +
599C VAL 4.2 1.2 + - - -
629C PRO 3.8 6.5 - - - +
630C ASN* 3.1 35.2 - - - +
631C LYS 3.4 6.3 - - - -
632C SER* 4.3 0.9 - - - +
633C LEU* 4.3 2.3 - - - +
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Residues in contact with LEU 596 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594C ASN 3.7 0.2 + - - -
595C LYS* 1.3 69.9 - - - +
597C GLN* 1.3 64.9 + - - +
599C VAL* 3.0 19.7 + - + +
600C PHE* 3.1 38.0 + - + -
624C VAL* 3.7 28.7 - - + +
627C LEU* 3.8 13.2 - - + -
628C ASP 3.5 18.2 - - - +
629C PRO 3.0 8.6 + - - +
631C LYS* 2.7 20.4 + - + +
632C SER 5.2 0.2 - - - -
633C LEU* 3.7 23.8 - - + -
636C VAL* 4.1 22.2 - - + -
638C LEU* 4.3 4.0 - - + -
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Residues in contact with GLN 597 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B ARG* 4.3 18.6 - - - -
595C LYS* 3.3 2.4 - - + -
596C LEU* 1.3 76.3 - - - +
598C ILE* 1.3 58.1 + - + +
600C PHE* 2.9 18.1 + - + +
601C ASP* 2.7 51.8 + - - +
610C TRP* 6.1 2.2 - - + -
629C PRO* 3.0 26.8 + - + +
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Residues in contact with ILE 598 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588A ARG* 4.1 47.7 + - - +
588C ARG* 5.6 1.1 - - - +
590C PHE* 3.4 29.6 - - + -
594C ASN* 4.7 17.9 - - + +
595C LYS* 3.3 35.7 - - + +
596C LEU 3.1 0.8 - - - -
597C GLN* 1.3 78.0 - - + +
599C VAL* 1.3 60.2 + - - +
601C ASP* 3.3 10.4 + - - +
602C PHE* 2.9 26.2 + - + +
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Residues in contact with VAL 599 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576C LEU* 3.9 28.3 - - + -
578C ILE* 4.8 8.5 - - + -
590C PHE* 4.1 17.5 - - + -
595C LYS 4.8 1.3 - - - +
596C LEU* 3.0 12.9 + - + +
598C ILE* 1.3 75.7 - - - +
600C PHE* 1.3 64.9 + - + +
602C PHE* 2.9 14.7 + - + +
603C VAL* 3.1 15.0 + - + +
615C LEU* 4.3 22.7 - - + -
624C VAL* 6.1 1.1 - - + -
633C LEU* 3.3 38.1 - - + -
638C LEU* 6.2 1.3 - - + -
644C LEU* 5.1 2.0 - - + -
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Residues in contact with PHE 600 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596C LEU* 3.1 24.4 + - + -
597C GLN* 2.9 25.3 + - + +
599C VAL* 1.3 80.3 - - + +
601C ASP* 1.3 61.9 + - - +
603C VAL* 3.3 7.9 - - + +
604C ALA* 3.2 23.8 + - - +
610C TRP* 3.4 45.0 - + + +
615C LEU* 5.2 6.5 - - + -
624C VAL* 3.3 37.7 - - + -
625C THR* 3.5 34.8 - - + -
627C LEU 4.0 1.1 - - - -
629C PRO* 3.8 31.2 - - + -
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Residues in contact with ASP 601 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A ARG* 5.0 10.2 + - - +
605A SER* 5.7 4.7 - - - +
606A LYS* 4.9 8.0 + - - -
620B PRO* 4.5 9.8 - - + +
621B ARG* 3.9 33.6 + - - +
597C GLN* 2.7 38.6 + - - +
598C ILE* 3.6 9.9 - - - +
599C VAL 3.1 0.2 - - - -
600C PHE* 1.3 73.6 - - - +
602C PHE* 1.3 56.1 + - - +
604C ALA* 3.0 6.5 + - - +
605C SER* 2.7 37.8 + - - -
610C TRP* 5.2 2.4 + - - -
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Residues in contact with PHE 602 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576C LEU* 5.9 0.4 - - + -
578C ILE* 4.1 23.6 - - + -
586C LEU* 4.2 20.2 - - + -
587C GLU 4.3 9.6 - - - -
588C ARG* 3.4 54.3 - - + +
590C PHE* 3.8 29.6 - + + -
598C ILE 2.9 14.8 + - - +
599C VAL* 2.9 10.3 + - + +
601C ASP* 1.3 75.9 - - - +
603C VAL* 1.3 74.0 + - + +
605C SER* 3.0 23.1 + - - -
606C LYS* 3.2 32.2 + - + +
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Residues in contact with VAL 603 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578C ILE* 3.9 41.5 - - + -
586C LEU* 4.5 5.2 - - + -
599C VAL* 3.1 13.0 + - + +
600C PHE* 3.3 18.2 - - + +
602C PHE* 1.3 84.1 - - + +
604C ALA* 1.3 66.5 + - - +
606C LYS* 3.3 12.9 + - - +
607C GLY 3.3 0.9 + - - -
608C PHE* 2.8 40.9 + - + +
610C TRP* 4.9 6.7 - - + -
615C LEU* 4.6 17.7 - - + -
646C LEU* 4.5 5.6 - - + -
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Residues in contact with ALA 604 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619B PHE* 4.1 31.1 - - + +
620B PRO* 4.3 13.2 - - + +
600C PHE 3.2 19.6 + - - +
601C ASP* 3.0 8.0 + - - +
603C VAL* 1.3 78.4 - - - +
605C SER* 1.3 53.1 + - - +
607C GLY* 2.8 26.3 + - - -
608C PHE 3.3 12.4 + - - +
609C PRO* 4.1 9.0 - - + +
610C TRP* 4.8 0.7 - - + +
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Residues in contact with SER 605 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A ASP* 5.7 3.3 - - - +
605A SER* 4.4 17.7 - - - -
620B PRO* 4.8 12.0 - - - +
601C ASP 2.7 19.2 + - - -
602C PHE* 3.0 13.4 + - - -
604C ALA* 1.3 68.3 - - - +
606C LYS* 1.3 70.5 + - - +
607C GLY 3.0 8.6 + - - -
620D PRO* 3.8 30.2 - - - +
622D ARG* 3.7 17.2 + - - +
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Residues in contact with LYS 606 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A ASP* 4.2 17.4 + - - -
586C LEU* 3.6 40.7 - - + +
588C ARG* 5.0 0.9 - - - +
602C PHE* 3.2 38.4 + - + +
603C VAL 3.6 8.7 - - - +
604C ALA 3.2 0.6 - - - -
605C SER* 1.3 84.9 + - - +
607C GLY* 1.3 55.4 + - - +
608C PHE* 3.5 6.3 - - - -
620D PRO* 6.1 1.1 - - - -
621D ARG* 2.9 49.7 + - - +
622D ARG* 4.1 17.1 - - + +
623D ASP 5.0 3.3 + - - +
626D GLN* 5.5 0.2 - - - +
627D LEU* 3.0 20.7 - - - +
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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