Contacts of the helix formed by residues 795 - 807 (chain C) in PDB entry 3QNF
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 SER 795 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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792C SER 5.5 0.4 + - - -
794C SER* 1.3 79.5 - - - +
796C THR* 1.3 57.7 + - - -
797C GLU 3.4 1.3 - - - +
798C LYS* 3.9 16.4 - - - +
799C SER* 2.8 28.1 + - - -
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Residues in contact with THR 796 (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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338C LYS 4.7 8.7 - - - -
340C SER* 3.6 34.5 - - - -
794C SER* 2.8 15.4 + - - -
795C SER* 1.3 72.4 - - - +
797C GLU* 1.3 60.8 + - - +
799C SER* 2.8 18.3 + - - -
800C GLN* 3.2 22.6 - - - +
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Residues in contact with GLU 797 (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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772C PHE* 4.2 11.2 - - + -
792C SER* 5.2 7.2 - - - -
794C SER* 3.8 21.0 - - - -
795C SER 3.4 0.2 - - - -
796C THR* 1.3 79.3 - - - +
798C LYS* 1.3 59.1 + - - +
800C GLN* 3.5 11.1 + - - +
801C ILE* 3.0 28.8 + - - +
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Residues in contact with LYS 798 (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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789C TYR* 3.8 22.6 - - + +
792C SER* 4.2 24.3 - - - +
795C SER* 3.8 17.4 + - - +
796C THR 3.4 0.6 - - - -
797C GLU* 1.3 79.2 - - - +
799C SER* 1.3 57.2 - - - +
801C ILE* 3.6 5.1 + - - +
802C GLU* 2.9 30.4 + - - +
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Residues in contact with SER 799 (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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769C LEU* 5.5 0.2 - - - +
795C SER 2.8 15.1 + - - -
796C THR* 2.8 21.8 + - - -
798C LYS* 1.3 75.1 - - - +
800C GLN* 1.3 66.1 + - - +
802C GLU* 3.1 29.6 - - - +
803C PHE* 3.1 10.6 + - - +
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Residues in contact with GLN 800 (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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340C SER* 5.4 2.4 - - - -
765C VAL* 3.3 35.3 + - - +
768C THR* 2.9 27.8 + - + +
769C LEU* 3.8 41.3 - - + +
772C PHE* 3.8 17.2 - - + +
796C THR* 3.2 25.2 + - - +
797C GLU* 3.8 8.3 - - - +
798C LYS 3.4 0.2 - - - -
799C SER* 1.3 81.7 + - - +
801C ILE* 1.3 64.4 + - - +
803C PHE* 3.6 4.0 + - - +
804C ALA* 3.4 18.7 + - - +
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Residues in contact with ILE 801 (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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772C PHE* 3.7 15.3 - - + -
785C LEU* 4.6 17.0 - - + +
788C LYS* 6.0 2.2 - - + -
789C TYR* 4.6 20.0 - - + +
797C GLU 3.0 18.2 + - - +
798C LYS* 3.8 7.2 - - - +
800C GLN* 1.3 72.3 - - - +
802C GLU* 1.3 67.5 + - - +
804C ALA* 3.0 16.2 + - - +
805C LEU* 3.2 17.5 + - + +
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Residues in contact with GLU 802 (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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789C TYR* 3.2 40.8 + - + +
798C LYS* 2.9 16.8 + - - +
799C SER* 3.1 18.8 - - - +
801C ILE* 1.3 77.6 - - - +
803C PHE* 1.3 64.3 + - - +
804C ALA 3.2 0.2 + - - -
805C LEU* 3.3 7.7 + - - +
806C CYS* 3.2 25.0 - - - -
834C GLN* 5.3 11.2 - - - +
835C ILE* 5.9 6.7 - - + -
838C LEU* 4.4 11.7 - - + +
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Residues in contact with PHE 803 (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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733C LEU* 4.2 36.8 - - + -
737C VAL* 4.9 8.3 - - + -
769C LEU* 4.7 15.7 - - + -
773C ALA* 5.2 2.2 - - + -
799C SER 3.1 11.5 + - - +
800C GLN 4.0 5.6 - - - +
801C ILE 3.3 0.4 - - - -
802C GLU* 1.3 78.3 - - - +
804C ALA* 1.3 63.9 + - - +
806C CYS* 3.5 2.6 + - - +
807C ARG* 3.1 36.6 + - + +
838C LEU* 3.8 37.8 - - + +
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Residues in contact with ALA 804 (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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769C LEU 5.7 0.2 - - - +
772C PHE* 3.2 41.5 - - + +
773C ALA* 3.9 9.2 - - - +
776C ALA* 3.2 15.7 - - - +
785C LEU* 3.7 15.5 - - + -
800C GLN 3.4 4.2 + - - +
801C ILE 3.0 10.6 + - - +
803C PHE* 1.3 80.1 - - - +
805C LEU* 1.3 60.6 + - - +
807C ARG* 3.3 18.2 + - - +
808C THR 4.1 0.2 + - - -
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Residues in contact with LEU 805 (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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776C ALA* 4.6 0.2 - - + -
782C TRP* 3.0 80.4 + - + +
785C LEU* 4.2 14.6 - - + -
786C TYR* 4.1 21.5 - - + +
789C TYR* 3.8 34.5 - - + -
801C ILE 3.2 14.2 + - - +
802C GLU* 3.3 5.4 + - - +
804C ALA* 1.3 75.7 - - - +
806C CYS* 1.3 63.3 + - - +
808C THR* 3.4 11.1 - - - +
814C LEU* 3.8 4.0 - - - +
817C LEU* 5.6 2.9 - - + -
839C ILE* 5.5 0.2 - - - +
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Residues in contact with CYS 806 (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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802C GLU* 3.2 20.2 + - - -
803C PHE* 3.9 5.4 - - + +
804C ALA 3.3 0.6 - - - -
805C LEU* 1.3 80.9 - - - +
807C ARG* 1.3 55.6 + - - +
808C THR 3.2 7.8 + - - -
814C LEU* 3.4 10.6 - - - +
835C ILE* 3.9 24.0 - - - -
838C LEU* 3.5 39.7 - - + -
839C ILE* 3.8 18.5 - - + +
842C ASN* 3.2 18.4 + - - +
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Residues in contact with ARG 807 (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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737C VAL* 5.7 9.9 - - + -
773C ALA* 4.4 10.8 - - + +
776C ALA* 5.2 0.5 - - - +
777C GLN* 2.9 17.2 + - - -
803C PHE* 3.1 38.4 + - + +
804C ALA* 3.3 11.1 + - - +
806C CYS* 1.3 75.6 - - - +
808C THR* 1.3 56.4 + - - +
809C GLN* 4.4 1.6 + - - +
842C ASN* 3.4 13.0 - - - +
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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