Contacts of the strand formed by residues 700 - 707 (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 GLY 700 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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696D SER* 3.6 0.2 - - - -
697D GLY* 2.8 34.4 + - - +
699D PHE* 1.3 80.0 - - - +
701D THR* 1.3 62.6 + - - -
702D VAL* 5.3 2.1 - - - +
721D LYS* 5.0 7.0 - - - +
722D GLU 3.2 13.7 - - - -
723D LEU* 4.2 4.9 - - - +
724D ARG* 4.3 6.7 - - - -
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Residues in contact with THR 701 (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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693D VAL* 3.5 21.1 - - + -
695D GLY 3.2 13.5 - - - +
696D SER* 2.8 20.8 + - - +
700D GLY* 1.3 75.0 - - - -
702D VAL* 1.3 67.2 + - - +
703D TYR* 3.6 30.9 - - + +
720D ILE 3.7 0.5 - - - +
721D LYS* 3.3 3.3 - - - -
722D GLU* 2.8 36.4 + - - -
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Residues in contact with VAL 702 (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 3.6 69.5 - - + +
693D VAL* 3.5 4.0 - - - +
694D LEU* 2.6 41.9 + - + -
695D GLY* 2.8 25.8 + - - +
696D SER* 5.9 0.2 - - - -
697D GLY 6.2 0.4 - - - +
700D GLY 5.3 2.0 - - - +
701D THR* 1.3 76.0 - - - +
703D TYR* 1.3 64.5 + - - +
719D ALA* 5.2 0.7 - - + -
720D ILE 3.5 7.4 - - - +
721D LYS* 3.9 15.3 - - + -
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Residues in contact with TYR 703 (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* 3.3 46.1 - - + -
692D LYS 3.1 24.9 - - - +
693D VAL* 3.2 26.7 - - + +
694D LEU* 3.7 8.4 - - - +
701D THR* 3.6 34.3 + - + +
702D VAL* 1.3 76.3 - - - +
704D LYS* 1.3 68.3 + - - +
719D ALA* 3.5 5.4 - - - -
720D ILE* 2.8 45.6 + - + +
722D GLU* 3.9 22.2 + - + -
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Residues in contact with LYS 704 (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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691D ILE* 2.8 47.7 + - + -
692D LYS* 2.9 27.0 + - + +
694D LEU* 3.5 29.0 - - + +
703D TYR* 1.3 75.9 - - - +
705D GLY* 1.3 61.2 + - - +
706D LEU* 5.8 2.5 - - + -
717D PRO* 5.3 3.8 - - + -
718D VAL 3.7 4.9 - - - +
768D LEU* 4.1 27.1 - - + +
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Residues in contact with GLY 705 (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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689D LYS 3.2 7.0 - - - -
691D ILE* 4.3 1.1 - - - -
704D LYS* 1.3 81.5 - - - +
706D LEU* 1.3 71.0 + - - +
717D PRO* 3.3 2.4 - - - +
718D VAL* 2.8 31.6 + - - +
720D ILE* 3.0 26.5 - - - +
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Residues in contact with LEU 706 (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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688D PHE* 3.2 5.5 - - - +
689D LYS* 2.9 32.7 + - + +
691D ILE* 3.8 30.5 - - + -
704D LYS* 5.8 2.9 - - + -
705D GLY* 1.3 81.2 - - - +
707D TRP* 1.3 61.4 + - - +
708D ILE* 3.9 6.3 + - + +
715D LYS* 3.6 33.9 - - + -
716D ILE 3.6 3.6 - - - -
717D PRO* 3.7 26.0 - - + -
718D VAL* 4.0 2.6 - - - +
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Residues in contact with TRP 707 (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* 2.7 58.3 - - + -
683D LEU* 5.1 13.9 - - + -
687D GLU* 3.6 13.0 + - + +
688D PHE* 4.3 5.8 - - + +
706D LEU* 1.3 74.3 - - - +
708D ILE* 1.3 74.4 + - - +
709D PRO* 3.2 35.2 - - + +
710D GLU* 4.6 7.5 + - - -
715D LYS* 3.7 1.5 - - - -
716D ILE* 2.7 53.1 + - + +
718D VAL* 3.9 19.7 - - + +
765D ILE* 6.1 0.9 - - + -
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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