Contacts of the strand formed by residues 716 - 723 (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 ILE 716 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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706B LEU* 3.2 2.4 - - - -
707B TRP* 2.6 59.8 + - + +
709B PRO* 3.6 15.5 - - + -
714B VAL* 3.4 39.5 - - + -
715B LYS* 1.3 69.1 - - - +
717B PRO* 1.3 83.7 - - + +
718B VAL* 3.4 6.5 - - + +
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Residues in contact with PRO 717 (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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704B LYS* 5.3 2.5 - - + -
705B GLY 3.4 9.2 - - - +
706B LEU* 4.3 9.8 - - + -
715B LYS 3.8 7.2 - - - +
716B ILE* 1.3 96.7 - - + +
718B VAL* 1.3 64.9 + - - +
767B GLN* 5.6 0.5 - - - -
768B LEU* 3.6 29.1 + - + +
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Residues in contact with VAL 718 (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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681B ARG* 5.1 5.4 - - - +
688B PHE* 5.4 2.9 - - + -
704B LYS* 3.7 4.5 - - - -
705B GLY 2.8 43.4 + - - +
706B LEU 4.0 7.6 - - - +
707B TRP* 3.9 17.0 - - + -
716B ILE* 3.4 14.4 - - + +
717B PRO* 1.3 81.7 - - - +
719B ALA* 1.3 60.3 + - - +
720B ILE* 3.7 17.0 - - + -
765B ILE* 3.7 25.6 - - + -
766B THR 3.8 7.4 - - - +
767B GLN* 5.2 1.1 - - - +
768B LEU* 3.7 14.1 - - - +
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Residues in contact with ALA 719 (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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1B ITI 2.9 52.2 - - + +
702B VAL* 5.1 1.1 - - + -
703B TYR 3.5 7.6 - - - +
718B VAL* 1.3 73.6 - - - +
720B ILE* 1.3 60.1 + - - +
721B LYS 4.2 0.2 - - - -
764B LEU 3.6 0.5 - - - +
765B ILE* 3.2 7.6 - - - +
766B THR* 2.9 38.4 + - + +
768B LEU* 3.9 7.4 - - + +
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Residues in contact with ILE 720 (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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1B ITI 4.3 2.2 - - - -
688B PHE* 4.4 11.9 - - + -
689B LYS 4.2 6.3 - - - +
690B LYS* 4.3 16.6 - - + -
701B THR 3.7 1.0 - - - +
702B VAL* 3.4 3.1 - - - +
703B TYR* 2.8 44.6 + - + +
704B LYS 4.3 1.6 - - - -
705B GLY* 3.1 40.2 - - - +
706B LEU 4.5 0.4 - - - +
718B VAL* 3.7 10.1 - - + -
719B ALA* 1.3 74.5 - - - +
721B LYS* 1.3 64.0 + - - +
722B GLU 4.5 1.1 - - - +
763B GLN* 3.9 33.0 - - + +
764B LEU 3.3 2.0 - - - -
765B ILE* 3.1 30.7 - - + -
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Residues in contact with LYS 721 (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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1B ITI 2.8 60.1 + - + -
699B PHE 6.1 0.2 - - - -
700B GLY* 4.9 4.5 - - - +
701B THR 3.3 14.4 - - - +
702B VAL* 3.8 11.0 - - + +
720B ILE* 1.3 75.0 - - - +
722B GLU* 1.3 60.8 + - - +
723B LEU* 3.7 23.0 + - + +
762B VAL 3.6 1.4 - - - +
763B GLN* 3.4 1.9 - - - -
764B LEU* 2.7 49.7 + - + +
830B THR* 4.1 1.0 + - - +
831B ASP* 2.7 43.1 + - - +
834B LEU* 5.3 2.0 - - + -
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Residues in contact with GLU 722 (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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690B LYS* 3.9 21.3 + - - -
700B GLY* 3.1 3.4 - - - -
701B THR* 2.8 36.9 + - - +
703B TYR* 3.9 31.2 + - + -
720B ILE* 4.0 2.0 + - + -
721B LYS* 1.3 72.5 - - - +
723B LEU* 1.3 64.6 + - - +
761B THR* 2.6 41.5 + - - +
762B VAL 3.6 2.2 - - - -
763B GLN* 3.5 15.4 + - + +
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Residues in contact with LEU 723 (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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699B PHE* 3.6 14.4 - - + +
721B LYS* 4.1 24.5 - - + +
722B GLU* 1.3 76.8 - - - +
724B ARG* 1.3 64.8 - - - +
725B GLU 3.4 3.6 + - - -
761B THR* 4.1 19.6 - - - +
762B VAL* 2.9 49.1 + - + +
764B LEU* 4.2 14.8 - - + -
834B LEU* 4.1 35.7 - - + -
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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