Contacts of the strand formed by residues 716 - 723 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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706D LEU* 3.9 1.6 - - - -
707D TRP* 2.7 53.5 + - + +
709D PRO* 4.7 7.9 - - + -
714D VAL* 3.9 26.0 - - + -
715D LYS* 1.3 96.8 - - - +
717D PRO* 1.3 81.4 - - + +
718D VAL* 3.3 9.5 - - + +
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Residues in contact with PRO 717 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704D LYS* 5.3 3.6 - - + -
705D GLY 3.3 11.4 - - - +
706D LEU* 3.7 9.1 - - + -
715D LYS* 3.6 10.1 - - + +
716D ILE* 1.3 98.8 - - + +
718D VAL* 1.3 66.0 + - - +
767D GLN* 5.6 0.7 - - - -
768D LEU* 3.8 28.6 + - + +
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Residues in contact with VAL 718 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681D ARG* 6.1 0.4 - - - +
688D PHE* 5.4 3.8 - - + -
704D LYS* 3.7 4.2 - - - -
705D GLY 2.8 37.6 + - - +
706D LEU 4.0 3.6 - - - +
707D TRP* 3.9 24.5 - - + +
716D ILE* 3.3 15.5 - - + +
717D PRO* 1.3 82.2 - - - +
719D ALA* 1.3 58.4 + - - +
720D ILE* 3.7 24.0 - - + -
765D ILE* 3.7 25.8 - - + -
766D THR 3.8 6.5 - - - +
767D GLN* 5.3 0.9 - - - +
768D LEU* 3.7 14.3 - - - +
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Residues in contact with ALA 719 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D ITI 3.0 51.8 - - + +
702D VAL* 5.2 1.3 - - + -
703D TYR 3.5 6.3 - - - +
718D VAL* 1.3 74.3 - - - +
720D ILE* 1.3 61.7 + - - +
721D LYS 4.3 0.2 - - - -
764D LEU 3.6 0.2 - - - +
765D ILE* 3.3 7.6 - - - +
766D THR* 2.9 39.8 + - - +
768D LEU* 3.8 6.9 - - + +
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Residues in contact with ILE 720 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D ITI 4.5 2.7 - - - -
688D PHE* 4.4 11.4 - - + -
689D LYS 4.2 7.4 - - - +
690D LYS* 4.3 17.7 - - + -
701D THR 3.7 0.9 - - - +
702D VAL* 3.5 2.8 - - - +
703D TYR* 2.8 43.7 + - + +
704D LYS 4.3 2.0 - - - -
705D GLY* 3.0 39.9 - - - +
706D LEU 4.5 0.2 - - - +
718D VAL* 3.7 10.3 - - + -
719D ALA* 1.3 76.3 - - - +
721D LYS* 1.3 64.4 + - - +
722D GLU 4.5 1.1 - - - +
763D GLN* 3.9 33.0 - - + +
764D LEU 3.2 2.2 - - - -
765D ILE* 3.2 30.3 - - + -
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Residues in contact with LYS 721 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D ITI 2.9 61.6 + - + -
699D PHE 6.1 0.2 - - - -
700D GLY* 5.0 5.2 - - - +
701D THR 3.3 13.0 - - - +
702D VAL* 3.9 9.0 - - + -
720D ILE* 1.3 73.5 - - - +
722D GLU* 1.3 62.6 + - - +
723D LEU* 3.7 23.9 + - + +
762D VAL 3.6 1.4 - - - +
763D GLN* 3.4 1.6 - - - -
764D LEU* 2.7 49.2 + - + +
818D ASN* 5.3 1.0 + - - -
830D THR* 4.4 1.6 + - - +
831D ASP* 2.7 41.7 + - - +
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Residues in contact with GLU 722 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690D LYS* 3.8 21.9 + - - -
700D GLY* 3.2 3.1 - - - -
701D THR* 2.8 37.5 + - - +
703D TYR* 3.9 31.4 + - + -
720D ILE* 4.0 1.8 + - + -
721D LYS* 1.3 71.2 - - - +
723D LEU* 1.3 63.9 + - - +
724D ARG* 5.8 0.2 - - - +
761D THR* 2.6 43.1 + - - +
762D VAL 3.6 2.2 - - - -
763D GLN* 3.5 15.4 + - + +
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Residues in contact with LEU 723 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699D PHE* 3.5 18.4 - - + +
721D LYS* 4.0 26.9 - - + +
722D GLU* 1.3 76.2 - - - +
724D ARG* 1.3 65.7 + - - +
725D GLU 3.3 3.6 + - - -
761D THR* 4.1 19.4 - - - +
762D VAL* 2.9 48.2 + - + +
764D LEU* 4.2 17.7 - - + -
831D ASP* 5.8 0.2 - - - +
834D LEU* 3.9 30.5 - - + -
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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