Contacts of the helix formed by residues 885 - 890 (chain N) in PDB entry 5LN3
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 MET 885 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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697N GLN* 3.2 38.8 - - - +
698N GLN* 3.8 11.0 - - - -
699N THR* 4.3 21.8 - - + +
702N THR* 4.5 9.2 - - + +
742N HIS* 6.0 1.8 - - - +
786N THR* 4.2 3.3 - - - +
810N THR 5.7 0.2 - - - +
811N PHE* 3.9 21.3 - - - -
812N ALA 4.8 0.7 - - - +
869N LYS* 6.1 0.7 - - - -
883N ARG* 4.1 17.0 - - + +
884N VAL* 1.4 77.7 - - - +
886N PRO* 1.4 68.3 - - + +
887N ALA* 3.7 18.8 - - + +
888N GLN* 3.6 22.6 - - - +
889N LEU* 3.0 25.3 + - - +
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Residues in contact with PRO 886 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662N GLY 4.9 11.7 - - - +
663N THR* 6.1 2.0 - - - +
697N GLN* 3.8 37.5 - - + +
745N THR* 5.5 5.2 - - + +
786N THR* 4.4 10.8 - - + +
869N LYS* 4.3 10.0 + - - +
885N MET* 1.4 87.9 - - + +
887N ALA* 1.3 57.4 + - - +
889N LEU* 3.2 28.0 + - + +
890N LYS* 3.4 16.3 + - - +
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Residues in contact with ALA 887 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702N THR* 5.1 3.6 - - + -
805N ASN* 3.2 16.8 + - - -
811N PHE* 3.6 23.1 - - + -
869N LYS* 3.8 38.0 - - + +
870N GLU 5.4 0.8 - - - +
871N PRO* 5.0 1.0 - - - +
885N MET* 3.2 16.9 - - + +
886N PRO* 1.3 76.2 - - - +
888N GLN* 1.3 63.0 + - - +
890N LYS* 3.3 15.3 - - - +
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Residues in contact with GLN 888 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804N SER* 4.9 3.0 + - - -
805N ASN* 3.1 14.0 - - - +
806N CYS* 3.8 22.4 - - + +
811N PHE* 3.4 21.0 - - + -
883N ARG* 3.1 51.5 + - - +
884N VAL* 3.3 27.7 - - + +
885N MET* 3.4 16.3 + - + +
886N PRO 3.3 0.2 - - - -
887N ALA* 1.3 80.5 - - - +
889N LEU* 1.4 60.5 - - - +
891N VAL 2.7 28.1 + - - +
892N LEU* 3.1 17.2 - - + +
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Residues in contact with LEU 889 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751N ARG* 3.5 34.3 - - - +
786N THR* 4.7 17.7 - - + -
787N CYS 4.9 5.6 - - - +
884N VAL* 4.5 2.9 - - + +
885N MET 3.0 13.7 + - - +
886N PRO* 3.2 18.6 - - + +
887N ALA 3.3 0.2 - - - -
888N GLN* 1.4 75.5 - - - +
890N LYS* 1.3 58.8 + - - +
892N LEU* 3.6 15.5 - - + +
908N ILE* 3.2 49.3 - - + +
909N GLY* 4.5 2.2 - - - -
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Residues in contact with LYS 890 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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805N ASN* 4.4 3.1 - - - +
869N LYS* 4.5 24.5 - - + +
871N PRO* 4.4 12.8 - - + -
886N PRO* 3.4 15.2 + - - +
887N ALA* 3.3 18.6 - - - +
888N GLN 3.1 0.2 - - - -
889N LEU* 1.3 75.9 - - - +
891N VAL* 1.3 64.0 + - + +
908N ILE* 4.3 5.2 - - - +
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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