Contacts of the strand formed by residues 688 - 696 (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 PHE 688 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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683D LEU* 3.6 25.4 - - + -
684D LYS 3.4 20.2 - - - -
685D GLU* 2.9 27.4 - - + +
686D THR 4.5 0.5 - - - -
687D GLU* 1.3 78.1 - - - +
689D LYS* 1.3 76.9 + - - +
690D LYS* 4.9 4.3 - - + -
706D LEU 3.2 14.6 - - - +
707D TRP* 4.3 7.9 - - + -
708D ILE* 3.9 5.9 - - - +
718D VAL* 5.4 3.4 - - + -
720D ILE* 4.4 19.7 - - + -
757D CYS* 3.4 41.7 - - + -
763D GLN* 3.6 26.7 - - + -
765D ILE* 4.5 10.8 - - + -
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Residues in contact with LYS 689 (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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685D GLU 5.3 0.4 - - - +
688D PHE* 1.3 85.5 - - - +
690D LYS* 1.3 68.1 + - - +
691D ILE* 3.0 20.5 - - + +
705D GLY* 3.2 2.8 - - - -
706D LEU* 2.9 33.9 + - + +
708D ILE* 4.7 9.6 - - + -
720D ILE* 4.5 2.5 - - - -
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Residues in contact with LYS 690 (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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685D GLU* 5.4 3.6 + - - -
688D PHE* 4.9 5.0 - - + -
689D LYS* 1.3 79.6 - - - +
691D ILE* 1.3 66.6 + - - +
703D TYR* 3.3 55.4 - - + -
704D LYS 3.8 4.9 - - - -
705D GLY* 4.3 1.3 - - - -
720D ILE* 4.3 11.4 - - + -
722D GLU* 3.8 17.9 + - - +
763D GLN* 2.5 36.8 + - - +
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Residues in contact with ILE 691 (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* 3.0 42.4 - - + +
690D LYS* 1.3 78.9 - - - +
692D LYS* 1.3 102.6 + - + +
703D TYR* 5.5 0.4 - - - -
704D LYS* 2.8 27.0 + - + +
705D GLY* 4.8 0.2 - - - -
706D LEU* 3.8 33.7 - - + +
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Residues in contact with LYS 692 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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691D ILE* 1.3 109.0 + - + +
693D VAL* 1.3 67.6 + - - +
694D LEU* 4.9 4.3 - - + -
703D TYR* 3.1 13.4 - - - -
704D LYS* 2.9 48.5 + - + +
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Residues in contact with VAL 693 (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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692D LYS* 1.3 78.1 - - - +
694D LEU* 1.3 67.6 + - - +
695D GLY* 3.8 12.3 - - - +
696D SER* 4.5 3.1 - - - +
701D THR* 3.5 25.1 - - + -
702D VAL 3.6 3.1 - - - -
703D TYR* 3.2 26.9 - - + +
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Residues in contact with LEU 694 (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 66.3 + - + +
692D LYS* 4.9 4.9 - - + -
693D VAL* 1.3 79.9 - - - +
695D GLY* 1.3 55.7 + - - +
702D VAL* 2.6 19.0 + - + +
703D TYR 3.7 7.2 - - - +
704D LYS* 3.5 50.0 - - + +
768D LEU* 4.1 17.0 - - + -
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Residues in contact with GLY 695 (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 4.4 8.5 - - - -
693D VAL* 3.7 4.9 - - - +
694D LEU* 1.3 82.2 - - - +
696D SER* 1.3 59.5 + - - -
701D THR* 3.2 7.3 - - - +
702D VAL* 2.8 35.6 + - - +
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Residues in contact with SER 696 (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* 4.5 3.6 - - - +
695D GLY* 1.3 70.8 - - - -
697D GLY* 1.3 60.4 + - - +
700D GLY 3.6 4.5 - - - -
701D THR* 2.8 31.3 + - - +
702D VAL* 5.9 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