Contacts of the helix formed by residues 831 - 842 (chain B) 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 GLU 831 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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789B TYR* 3.9 22.1 + - - +
829B THR* 3.4 3.3 - - - +
830B GLN* 1.3 76.6 - - - +
832B PHE* 1.3 63.7 + - - +
833B PRO* 3.6 2.9 - - - -
834B GLN* 3.6 12.7 - - + +
835B ILE* 3.4 14.7 + - - +
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Residues in contact with PHE 832 (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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817B LEU 5.2 3.1 - - - -
818B LEU* 4.1 26.9 - - + -
820B GLU 6.1 0.7 - - - -
829B THR* 3.4 24.7 - - - +
831B GLU* 1.3 73.0 - - - +
833B PRO* 1.4 87.3 - - + +
834B GLN 3.0 4.5 - - - -
835B ILE* 2.7 31.0 + - + +
836B LEU* 2.9 35.9 + - + -
852B PHE* 3.8 31.2 - + - -
853B LEU* 6.2 0.7 - - - -
874B MET* 5.9 1.8 - - + -
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Residues in contact with PRO 833 (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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829B THR 4.8 1.1 - - - +
830B GLN* 4.0 12.6 - - - +
831B GLU 3.6 1.8 - - - -
832B PHE* 1.4 111.9 - - + +
834B GLN* 1.3 58.7 + - - +
836B LEU* 4.1 6.0 - - + +
837B THR* 3.2 25.6 + - - -
874B MET* 3.9 25.5 - - + +
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Residues in contact with GLN 834 (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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802B GLU* 6.1 3.8 - - + -
831B GLU* 3.6 13.5 - - + +
832B PHE 3.0 0.6 - - - -
833B PRO* 1.3 78.9 - - - +
835B ILE* 1.3 66.7 + - - +
837B THR* 3.2 4.5 + - - -
838B LEU* 2.8 37.8 + - + +
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Residues in contact with ILE 835 (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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802B GLU* 6.4 0.9 - - - +
806B CYS* 4.2 16.2 - - - -
817B LEU* 5.0 19.1 - - + +
818B LEU* 5.5 0.7 - - + -
831B GLU 3.4 7.5 + - - +
832B PHE* 2.7 21.8 + - + +
834B GLN* 1.3 74.0 - - - +
836B LEU* 1.3 63.4 + - - +
838B LEU* 3.2 4.6 + - - +
839B ILE* 2.9 36.9 + - + +
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Residues in contact with LEU 836 (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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818B LEU* 3.4 25.9 - - + +
832B PHE* 2.9 37.3 + - + +
833B PRO* 4.4 4.7 - - + -
835B ILE* 1.3 72.0 - - - +
837B THR* 1.3 53.4 + - - +
839B ILE* 2.9 9.9 + - - +
840B GLY* 2.7 32.9 + - - -
849B ALA* 3.2 34.8 - - + +
852B PHE* 4.9 5.8 - - + -
853B LEU* 3.9 24.9 - - + -
874B MET* 4.0 12.8 - - + +
878B THR* 3.4 21.1 - - + -
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Residues in contact with THR 837 (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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833B PRO 3.2 18.8 + - - -
834B GLN* 3.2 5.7 + - - -
836B LEU* 1.3 79.3 - - - +
838B LEU* 1.3 67.2 + - + +
840B GLY* 3.1 2.9 + - - +
841B ARG* 3.1 24.2 + - + +
873B HIS 4.0 15.8 + - - -
874B MET* 4.4 6.4 + - - -
877B GLY* 4.2 20.3 - - - +
878B THR* 4.8 5.8 - - - +
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Residues in contact with LEU 838 (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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799B SER 5.7 0.2 - - - +
802B GLU* 3.6 37.7 - - + +
803B PHE* 3.6 34.3 - - + +
806B CYS* 3.6 19.1 - - + +
807B ARG* 5.8 2.3 - - - -
834B GLN* 2.8 31.7 + - + +
835B ILE* 3.3 8.1 - - - +
837B THR* 1.3 74.9 - - + +
839B ILE* 1.3 62.4 + - - +
841B ARG* 3.2 8.6 + - + +
842B ASN* 3.2 18.5 + - - +
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Residues in contact with ILE 839 (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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806B CYS* 3.9 17.9 - - + -
814B LEU* 4.0 34.8 - - + +
817B LEU* 4.8 5.2 - - + -
818B LEU* 3.5 38.4 - - + -
835B ILE* 2.9 37.3 + - + +
836B LEU 2.9 2.9 + - - +
838B LEU* 1.3 71.5 - - - +
840B GLY* 1.3 57.9 + - - +
841B ARG 3.0 4.5 - - - -
842B ASN* 3.0 24.6 + - + +
845B GLY* 3.4 32.2 - - - +
848B LEU* 4.8 1.3 - - + -
849B ALA* 4.0 6.7 - - + +
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Residues in contact with GLY 840 (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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689B LYS* 3.4 22.7 - - - -
836B LEU 2.7 16.2 + - - -
837B THR 3.1 5.8 + - - -
839B ILE* 1.3 72.4 - - - +
841B ARG* 1.3 56.2 + - - +
846B TYR* 3.8 10.6 - - - +
849B ALA* 3.3 21.2 - - - +
877B GLY 4.5 9.9 - - - +
878B THR* 4.7 15.4 - - - +
881B GLN* 4.5 1.0 - - - +
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Residues in contact with ARG 841 (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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685B LYS* 3.2 30.7 + - - -
688B GLU* 3.8 2.8 - - - +
689B LYS* 4.0 3.9 + - - -
807B ARG* 5.9 0.7 - - - -
837B THR* 3.1 12.0 + - + +
838B LEU* 3.6 11.0 - - + +
839B ILE 3.0 0.6 - - - -
840B GLY* 1.3 76.3 - - - +
842B ASN* 1.3 64.0 + - - +
843B PRO 3.5 0.7 - - - -
877B GLY 5.9 0.9 - - - +
881B GLN* 4.3 17.3 - - - +
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Residues in contact with ASN 842 (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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689B LYS* 5.3 0.2 - - - -
806B CYS 2.8 29.6 + - - +
807B ARG* 3.3 32.4 + - - +
808B THR 3.4 13.8 + - - -
809B GLN* 4.0 2.0 + - - -
814B LEU* 4.6 2.9 - - - -
838B LEU 3.2 8.2 + - - +
839B ILE* 3.0 14.4 + - + +
841B ARG* 1.3 76.8 - - - +
843B PRO* 1.3 71.9 - - - +
844B VAL* 2.8 25.0 + - - +
845B GLY* 3.0 20.4 + - - +
846B TYR* 3.2 14.0 + - - +
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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