Contacts of the strand formed by residues 716 - 723 (chain C) 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 ILE 716 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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706C LEU* 3.8 1.1 - - - -
707C TRP* 2.7 60.5 + - + +
709C PRO* 3.6 17.5 - - + -
714C VAL* 3.3 35.0 - - + -
715C LYS* 1.3 70.6 - - - +
717C PRO* 1.3 81.2 - - + +
718C VAL* 3.4 3.1 - - + +
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Residues in contact with PRO 717 (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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704C LYS* 5.3 4.5 - - + -
705C GLY 3.4 10.8 - - - +
706C LEU* 3.8 5.6 - - + -
715C LYS 3.6 8.9 - - - +
716C ILE* 1.3 95.0 - - + +
718C VAL* 1.3 65.3 + - - +
767C GLN* 5.6 0.5 - - - -
768C LEU* 3.8 29.4 + - + +
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Residues in contact with VAL 718 (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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681C ARG* 5.4 3.4 - - - +
688C PHE* 5.3 3.1 - - + -
704C LYS* 3.7 4.9 - - - -
705C GLY 2.9 35.7 + - - -
706C LEU 4.1 8.1 - - - +
707C TRP* 3.6 18.4 - - + +
716C ILE* 3.4 14.4 - - + +
717C PRO* 1.3 82.3 - - - +
719C ALA* 1.3 60.4 + - - +
720C ILE* 3.7 24.0 - - + -
765C ILE* 3.7 26.5 - - + -
766C THR 3.8 7.2 - - - +
767C GLN* 5.3 1.1 - - - +
768C LEU* 3.7 14.4 - - - +
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Residues in contact with ALA 719 (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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1C ITI 3.0 49.4 - - + +
702C VAL* 5.1 0.7 - - + -
703C TYR 3.5 7.4 - - - +
718C VAL* 1.3 73.1 - - - +
720C ILE* 1.3 59.5 + - - +
764C LEU 3.6 0.3 - - - +
765C ILE* 3.2 8.0 - - - +
766C THR* 2.9 41.5 + - - +
768C LEU* 3.8 7.6 - - + +
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Residues in contact with ILE 720 (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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1C ITI 4.2 1.8 - - - -
688C PHE* 4.4 10.1 - - + -
689C LYS 4.2 5.8 - - - +
690C LYS* 4.3 17.9 - - + -
701C THR 3.7 0.9 - - - +
702C VAL* 3.4 2.9 - - - +
703C TYR* 2.7 43.7 + - + +
704C LYS 4.3 1.8 - - - -
705C GLY* 3.1 40.8 - - - +
706C LEU 4.4 0.2 - - - +
718C VAL* 3.7 10.5 - - + -
719C ALA* 1.3 75.4 - - - +
721C LYS* 1.3 65.8 + - - +
722C GLU 4.4 1.1 - - - +
763C GLN* 3.9 33.2 - - + +
764C LEU 3.3 2.5 - - - +
765C ILE* 3.2 30.7 - - + -
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Residues in contact with LYS 721 (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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1C ITI 2.6 62.1 + - + -
699C PHE* 6.4 0.7 - - + -
700C GLY* 4.9 5.8 - - - +
701C THR 3.3 15.7 - - - +
702C VAL* 3.7 10.5 - - + -
720C ILE* 1.3 73.5 - - - +
722C GLU* 1.3 59.9 + - - +
723C LEU* 3.7 22.6 + - + +
762C VAL 3.6 1.6 - - - +
763C GLN* 3.4 1.9 - - - -
764C LEU* 2.7 49.5 + - + +
830C THR* 4.2 0.6 + - - +
831C ASP* 2.7 41.7 + - - +
834C LEU* 5.5 1.8 - - + -
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Residues in contact with GLU 722 (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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690C LYS* 3.8 23.2 + - - -
700C GLY* 3.2 3.1 - - - -
701C THR* 2.8 37.0 + - - -
703C TYR* 3.9 31.6 + - + -
720C ILE* 4.0 2.2 - - + -
721C LYS* 1.3 71.6 - - - +
723C LEU* 1.3 64.8 + - - +
761C THR* 2.6 42.9 + - - +
762C VAL 3.6 2.0 - - - -
763C GLN* 3.6 15.1 + - + +
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Residues in contact with LEU 723 (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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699C PHE* 3.6 15.0 - - + +
721C LYS* 4.1 23.8 - - + +
722C GLU* 1.3 78.2 - - - +
724C ARG* 1.3 63.1 + - - +
725C GLU 3.3 6.8 + - - -
761C THR* 4.1 18.9 - - - +
762C VAL* 2.9 45.9 + - + +
764C LEU* 4.2 19.5 - - + -
834C LEU* 3.8 32.8 - - + -
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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