Contacts of the strand formed by residues 67 - 71 (chain D) in PDB entry 5LEZ
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 67 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48D LEU* 3.5 42.0 - - + +
49D ALA 4.2 0.2 - - - +
50D VAL* 3.5 20.0 - - + -
65D GLU* 4.4 5.9 - - - +
66D LYS* 1.3 79.6 + - - +
68D VAL* 1.3 67.2 + - - +
76D CYS 3.3 9.4 - - - +
77D ALA* 4.3 8.5 - - + -
216D GLU* 3.1 37.9 + - + +
217D LEU 4.1 0.4 - - - -
218D ALA* 3.7 26.2 - - + +
226D PHE* 4.0 14.1 - - + -
228D MET* 3.4 20.3 - - + +
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Residues in contact with VAL 68 (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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65D GLU* 3.9 31.9 - - + +
67D ILE* 1.3 78.5 - - - +
69D GLU* 1.3 60.0 + - - +
70D ILE* 3.7 3.5 + - + -
75D GLY* 3.5 2.9 - - - -
76D CYS* 2.9 42.1 + - + +
78D MET* 3.9 14.4 - - + -
89D ILE* 3.6 41.7 - - + -
93D ARG* 3.8 14.6 - - - +
226D PHE* 3.9 6.4 - - - -
228D MET* 5.1 0.9 - - - -
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Residues in contact with GLU 69 (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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68D VAL* 1.3 72.2 - - - +
70D ILE* 1.3 59.9 + - - +
71D ASP* 3.2 35.3 - - - +
72D ALA* 3.4 11.7 + - - +
74D ILE 4.0 2.9 - - - -
93D ARG* 2.8 36.0 + - - +
226D PHE* 3.6 38.3 - - + +
228D MET* 5.5 0.2 - - - +
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Residues in contact with ILE 70 (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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68D VAL* 4.3 1.1 - - + -
69D GLU* 1.3 77.0 - - - +
71D ASP* 1.3 60.7 + - - +
74D ILE* 2.9 34.0 + - + +
76D CYS* 3.8 30.5 - - + -
89D ILE* 3.9 30.3 - - + +
92D ALA* 3.8 42.6 - - + +
93D ARG* 3.4 18.3 - - + +
96D THR* 3.9 18.4 + - + -
97D GLN* 5.1 1.7 - - - +
112D VAL* 4.3 2.9 - - + -
143D PHE* 4.2 6.5 - - + -
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Residues in contact with ASP 71 (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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69D GLU* 3.2 18.1 - - - +
70D ILE* 1.3 77.8 - - + +
72D ALA* 1.3 77.9 + - - +
73D HIS* 3.1 32.3 + - + +
74D ILE* 3.0 18.8 + - + +
96D THR* 3.9 20.1 + - + +
97D GLN* 3.6 22.6 - - - +
100D TRP* 5.7 3.1 - - - +
106D THR* 5.3 4.3 - - - +
107D MET 5.7 0.2 + - - -
226D PHE* 4.1 1.2 - - - +
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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