Contacts of the strand formed by residues 716 - 723 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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706A LEU* 4.0 1.6 - - - -
707A TRP* 2.5 61.1 + - + -
709A PRO* 3.5 21.3 - - + -
714A VAL* 3.5 29.2 - - + -
715A LYS* 1.3 71.8 - - - +
717A PRO* 1.3 80.5 - - + +
718A VAL* 3.4 6.1 - - + +
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Residues in contact with PRO 717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704A LYS* 5.3 4.5 - - + -
705A GLY 3.3 10.8 - - - +
706A LEU* 3.8 9.6 - - + -
715A LYS 3.7 7.6 - - - +
716A ILE* 1.3 95.2 - - + +
718A VAL* 1.3 65.2 + - - +
767A GLN* 5.7 0.5 - - - -
768A LEU* 3.8 27.8 + - + +
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Residues in contact with VAL 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681A ARG* 5.2 6.3 - - - +
688A PHE* 5.4 4.0 - - + -
704A LYS* 3.7 4.5 - - - -
705A GLY 2.9 32.3 + - - +
706A LEU 3.9 6.5 - - - +
707A TRP* 3.9 15.9 - - + +
716A ILE* 3.4 13.9 - - + +
717A PRO* 1.3 81.9 - - - +
719A ALA* 1.3 59.3 + - - +
720A ILE* 3.7 24.0 - - + -
765A ILE* 3.7 26.5 - - + -
766A THR 3.8 6.3 - - - +
767A GLN* 6.1 0.4 - - - -
768A LEU* 3.7 14.4 - - - +
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Residues in contact with ALA 719 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ITI 2.9 51.6 - - + +
702A VAL* 5.2 1.3 - - + -
703A TYR 3.5 6.3 - - - +
718A VAL* 1.3 73.7 - - - +
720A ILE* 1.3 59.9 + - - +
721A LYS 4.2 0.2 - - - -
764A LEU 3.6 0.5 - - - +
765A ILE* 3.2 8.3 - - - +
766A THR* 2.9 38.7 + - + +
768A LEU* 3.8 8.0 - - + +
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Residues in contact with ILE 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ITI 4.3 2.2 - - - -
688A PHE* 4.4 10.8 - - + -
689A LYS 4.2 5.8 - - - +
690A LYS* 4.3 16.8 - - + -
701A THR 3.7 0.9 - - - +
702A VAL* 3.5 2.4 - - - +
703A TYR* 2.8 45.1 + - + +
704A LYS 4.2 1.8 - - - -
705A GLY* 3.1 40.2 - - - +
706A LEU 4.5 0.2 - - - +
718A VAL* 3.7 10.8 - - + -
719A ALA* 1.3 75.6 - - - +
721A LYS* 1.3 65.7 + - - +
722A GLU 4.5 0.9 - - - +
763A GLN* 3.9 32.8 - - + +
764A LEU 3.2 2.2 - - - -
765A ILE* 3.1 31.6 - - + -
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Residues in contact with LYS 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ITI 2.7 67.7 + - + -
699A PHE* 5.2 7.2 - - + -
700A GLY 4.9 3.8 - - - +
701A THR 3.3 15.0 - - - +
702A VAL* 4.0 8.3 - - + -
720A ILE* 1.3 72.7 - - - +
722A GLU* 1.3 63.5 + - - +
723A LEU* 3.6 22.3 + - + +
762A VAL 3.6 1.4 - - - +
763A GLN* 3.4 1.2 - - - -
764A LEU* 2.7 48.2 + - + +
830A THR* 4.1 1.0 + - - +
831A ASP* 2.7 43.6 + - - +
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Residues in contact with GLU 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690A LYS* 3.6 23.3 + - - -
700A GLY* 3.1 3.6 - - - -
701A THR* 2.9 37.1 + - - +
703A TYR* 3.8 26.0 + - + -
720A ILE 4.0 1.8 + - - -
721A LYS* 1.3 71.4 - - - +
723A LEU* 1.3 65.2 + - - +
761A THR* 2.5 43.6 + - - +
762A VAL 3.6 2.5 - - - -
763A GLN* 3.5 20.1 + - + +
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Residues in contact with LEU 723 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699A PHE 3.1 16.6 - - - +
721A LYS* 4.1 23.3 - - + +
722A GLU* 1.3 77.2 - - - +
724A ARG* 1.3 62.4 - - - +
725A GLU* 3.3 6.1 + - - +
761A THR* 4.1 19.2 - - - +
762A VAL* 2.8 47.4 + - + +
764A LEU* 4.2 22.7 - - + -
834A LEU* 4.0 29.8 - - + -
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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