Contacts of the strand formed by residues 826 - 829 (chain B) in PDB entry 3LZB
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 HIS 826 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748B PRO* 2.5 41.1 + - + +
749B HIS* 3.7 16.8 + + - -
796B GLN* 3.3 2.7 - - - -
822B LYS* 2.7 61.1 + - + +
823B THR* 3.0 21.5 + - + +
824B PRO 3.5 0.8 - - - -
825B GLN* 1.3 83.1 - - + +
827B VAL* 1.3 61.5 + - - +
828B LYS* 4.1 13.8 - - + -
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Residues in contact with VAL 827 (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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749B HIS* 3.2 28.1 + - - +
774B LEU* 4.3 16.6 - - + -
793B TRP* 3.9 30.5 - - + +
796B GLN* 2.7 32.9 + - + +
797B ILE* 4.3 10.8 - - + +
819B VAL* 3.7 18.2 - - + -
820B LEU 3.2 16.8 - - - +
821B VAL* 4.0 10.8 - - + -
823B THR 4.5 3.1 - - - +
826B HIS* 1.3 78.6 - - - +
828B LYS* 1.3 61.2 + - - +
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Residues in contact with LYS 828 (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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747B ASN 4.1 5.7 + - - -
748B PRO* 3.7 23.8 + - - +
749B HIS* 3.6 4.7 - - - -
750B VAL 3.6 19.6 + - - +
751B CYS* 3.8 23.7 - - + +
752B ARG* 5.3 2.8 - - - +
767B GLN* 5.7 2.0 - - - -
769B MET* 4.5 15.5 - - + -
819B VAL* 4.4 2.9 - - - -
820B LEU* 2.8 45.2 + - + +
822B LYS* 4.7 20.4 - - + +
826B HIS* 4.1 16.6 - - + +
827B VAL* 1.3 77.9 - - - +
829B ILE* 1.3 62.7 + - - +
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Residues in contact with ILE 829 (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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749B HIS 3.0 24.5 + - - +
750B VAL* 3.8 10.7 - - + +
751B CYS* 2.8 25.3 + - - +
796B GLN 4.7 0.2 - - - +
797B ILE* 3.3 41.5 - - + +
800B GLY* 4.1 1.8 - - - -
801B MET* 4.0 18.4 - - - +
804B LEU* 4.5 8.7 - - + -
811B HIS* 3.5 33.2 - - + +
814B LEU* 4.0 14.1 - - + -
818B ASN 3.6 5.6 - - - +
819B VAL* 4.1 13.0 - - + +
828B LYS* 1.3 72.2 - - - +
830B THR* 1.3 66.7 + - - +
832B PHE* 4.0 2.1 - - + -
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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