Contacts of the helix formed by residues 815 - 824 (chain B) in PDB entry 3N56
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 ILE 815 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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811B PHE* 3.1 55.3 + - + +
812B ALA* 3.7 8.5 - - - +
814B ILE* 1.3 78.5 - - + +
816B SER* 1.3 66.2 + - - +
817B GLU 3.6 0.9 - - - -
818B PRO* 3.7 3.6 - - - -
819B ALA* 3.0 25.3 + - - +
835B SER* 4.3 10.5 - - - +
846B LEU* 4.1 13.2 - - + -
848B PHE* 4.0 28.7 - - + -
866B PHE* 4.4 5.4 - - + -
867B LEU* 5.2 1.3 - - + -
870B MET* 3.7 38.6 - - + -
874B ILE* 5.4 0.2 - - + -
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Residues in contact with SER 816 (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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132B SER* 4.7 5.7 + - - -
812B ALA 2.9 17.7 + - - -
813B GLN* 3.2 18.4 + - - -
814B ILE 3.4 0.2 - - - -
815B ILE* 1.3 80.4 - - - +
817B GLU* 1.3 64.4 + - - +
819B ALA* 3.9 2.6 - - - +
820B PHE* 3.6 15.6 + - - +
835B SER* 4.5 11.5 + - - -
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Residues in contact with GLU 817 (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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125B ASN* 3.1 27.3 - - - +
128B SER* 3.6 23.1 + - - +
129B GLN* 3.8 33.8 + - - +
132B SER* 3.4 25.0 + - - +
813B GLN 4.5 0.2 + - - -
816B SER* 1.3 76.9 + - - +
818B PRO* 1.4 79.9 - - + +
819B ALA 3.1 0.5 + - - -
820B PHE* 3.2 8.9 + - + +
821B ASN* 2.8 45.8 + - - +
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Residues in contact with PRO 818 (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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813B GLN 5.2 0.4 - - - +
814B ILE 3.4 25.6 - - - +
815B ILE 3.7 2.9 - - - +
817B GLU* 1.4 106.5 - - + +
819B ALA* 1.3 56.1 + - - +
821B ASN* 3.8 4.6 - - + +
822B THR* 2.9 36.5 + - - +
866B PHE* 3.5 3.8 - - + -
870B MET* 3.6 29.8 - - + -
873B SER* 5.7 1.1 - - - +
885B HIS* 5.9 2.9 - - + +
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Residues in contact with ALA 819 (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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815B ILE* 3.0 20.4 + - + +
816B SER 3.9 3.1 - - - +
817B GLU 3.2 0.2 - - - -
818B PRO* 1.3 73.6 - - - +
820B PHE* 1.3 61.6 + - - +
823B LEU* 2.9 48.8 + - + +
833B VAL* 4.5 3.1 - - + -
835B SER* 3.9 16.8 - - - +
848B PHE* 4.3 4.9 - - + -
866B PHE* 3.3 24.1 - - + -
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Residues in contact with PHE 820 (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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128B SER* 5.1 10.8 - - - -
816B SER 3.6 9.2 + - - +
817B GLU* 3.2 10.2 + - + +
819B ALA* 1.3 79.3 - - - +
821B ASN* 1.3 65.3 + - + +
824B ARG* 3.0 77.3 + - + +
825B THR* 3.3 17.2 + - - -
831B TYR 4.9 3.8 - - - -
833B VAL* 4.0 28.9 - - + +
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Residues in contact with ASN 821 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124B GLU* 5.0 2.0 + - - +
125B ASN* 3.4 34.6 + - - +
817B GLU* 2.8 36.0 + - - +
818B PRO* 3.8 5.8 - - + +
820B PHE* 1.3 75.8 - - + +
822B THR* 1.3 58.4 + - - +
825B THR* 3.3 26.4 + - - +
826B LYS* 2.9 56.3 + - - +
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Residues in contact with THR 822 (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 PRO* 2.9 24.5 + - - +
821B ASN* 1.3 78.9 + - - +
823B LEU* 1.3 63.2 + - + +
826B LYS* 3.5 17.0 + - + +
827B GLU* 2.9 54.8 + - + +
866B PHE* 3.6 32.2 - - + -
869B THR* 5.6 5.7 - - + +
981B SER* 5.5 5.2 - - - +
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Residues in contact with LEU 823 (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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819B ALA* 2.9 41.4 + - + +
822B THR* 1.3 79.7 - - + +
824B ARG* 1.3 57.7 + - - +
827B GLU* 4.4 4.9 - - - +
828B GLN 3.5 1.7 + - - -
829B LEU* 3.0 57.0 + - + +
833B VAL* 4.1 21.5 - - + +
848B PHE* 4.5 18.6 - - + -
850B ILE* 4.7 3.8 - - + -
862B ARG* 3.9 28.0 - - + +
863B VAL* 4.2 14.1 - - + -
866B PHE* 4.3 10.5 - - + -
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Residues in contact with ARG 824 (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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112B HIS* 4.3 6.7 + - - -
182B GLU* 3.3 27.2 + - - -
185B ALA* 4.2 10.6 - - + +
820B PHE* 3.0 51.2 + - + +
823B LEU* 1.3 79.3 - - - +
825B THR* 1.3 65.9 + - - +
826B LYS 3.3 1.1 - - - -
828B GLN* 2.7 39.5 + - - +
829B LEU 4.5 0.4 - - - +
830B GLY 3.2 21.5 + - - +
831B TYR* 3.1 58.0 + - - +
833B VAL* 4.2 11.9 - - + -
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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