Contacts of the strand formed by residues 700 - 707 (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 GLY 700 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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696B SER* 4.2 0.3 - - - -
697B GLY* 2.8 35.6 + - - +
699B PHE* 1.3 80.4 - - - +
701B THR* 1.3 65.4 + - - -
702B VAL* 5.4 1.8 - - - +
721B LYS* 4.9 8.1 - - - +
722B GLU 3.1 13.9 - - - -
723B LEU* 4.2 4.5 - - - -
724B ARG* 4.3 7.4 - - - +
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Residues in contact with THR 701 (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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693B VAL* 3.5 21.1 - - + -
695B GLY 3.2 13.0 - - - +
696B SER* 2.8 20.4 + - - +
700B GLY* 1.3 76.7 - - - -
702B VAL* 1.3 66.7 + - - +
703B TYR* 3.6 31.1 - - + +
720B ILE 3.7 0.9 - - - +
721B LYS* 3.3 3.4 - - - +
722B GLU* 2.8 35.8 + - - -
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Residues in contact with VAL 702 (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 3.7 68.0 - - + +
693B VAL* 3.5 4.7 - - - +
694B LEU* 2.6 42.7 + - + -
695B GLY* 2.8 25.1 + - - +
696B SER* 5.9 0.4 - - - -
700B GLY 5.4 1.8 - - - +
701B THR* 1.3 76.7 - - - +
703B TYR* 1.3 64.2 + - - +
719B ALA* 5.1 0.4 - - + -
720B ILE 3.4 8.3 - - - +
721B LYS* 3.8 14.8 - - + -
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Residues in contact with TYR 703 (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* 3.3 47.7 - - + -
692B LYS 3.1 24.7 - - - +
693B VAL* 3.2 25.5 - - + +
694B LEU* 3.7 8.0 - - - +
701B THR* 3.6 34.9 - - + +
702B VAL* 1.3 74.3 - - - +
704B LYS* 1.3 68.4 + - - +
719B ALA* 3.5 5.0 - - - -
720B ILE* 2.8 45.9 + - + +
722B GLU* 3.9 22.3 + - + -
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Residues in contact with LYS 704 (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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691B ILE* 2.8 40.9 + - + -
692B LYS* 2.9 29.1 + - + +
694B LEU* 3.5 27.9 - - + +
703B TYR* 1.3 76.4 - - - +
705B GLY* 1.3 65.6 + - - +
706B LEU* 5.8 4.3 - - + -
717B PRO* 5.3 2.9 - - + -
718B VAL 3.7 4.7 - - - -
768B LEU* 3.7 28.0 - - + +
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Residues in contact with GLY 705 (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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689B LYS 3.1 8.7 - - - -
691B ILE* 4.3 0.9 - - - -
704B LYS* 1.3 78.4 - - - +
706B LEU* 1.3 66.5 + - - +
717B PRO* 3.4 6.1 - - - +
718B VAL* 2.8 32.3 + - - +
720B ILE* 3.1 25.6 - - - +
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Residues in contact with LEU 706 (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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688B PHE* 3.2 5.9 - - - +
689B LYS* 3.0 32.0 + - + +
691B ILE* 3.4 32.8 - - + -
704B LYS* 5.8 4.7 - - + -
705B GLY* 1.3 81.5 - - - +
707B TRP* 1.3 60.6 + - - +
708B ILE* 4.0 4.2 + - + +
715B LYS* 4.2 50.3 - - + +
716B ILE 3.2 6.7 - - - +
717B PRO* 4.3 14.8 - - + -
718B VAL* 4.3 3.8 - - - -
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Residues in contact with TRP 707 (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* 4.4 33.6 - - - +
683B LEU* 3.9 24.8 - - + +
687B GLU* 3.3 25.1 + - - +
688B PHE* 4.4 3.8 - - + -
706B LEU* 1.3 73.4 - - - +
708B ILE* 1.3 69.9 + - - +
709B PRO* 3.3 40.9 - - + +
715B LYS* 3.5 1.7 - - - -
716B ILE* 2.6 68.0 + - + +
718B VAL* 3.9 16.6 - - + -
765B ILE* 6.3 0.2 - - + -
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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