Contacts of the strand formed by residues 68 - 73 (chain D) in PDB entry 3ZXR
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 ASP 68 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ALA* 5.7 7.0 - - + +
53D PHE 3.7 7.2 - - - -
67D SER* 1.3 76.7 + - - +
69D MET* 1.3 59.6 - - - +
98D PRO* 3.5 5.5 - - + +
345E ARG* 2.8 55.7 + - + +
347E ARG* 3.2 6.7 + - - +
352E ARG* 3.0 41.0 + - - -
354E PRO* 3.6 1.7 - - - +
355E ILE* 3.1 36.2 + - + +
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Residues in contact with MET 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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52D ALA* 3.3 8.5 - - - +
53D PHE* 3.1 55.2 + - + +
55D GLY* 4.0 7.4 - - - -
61D PHE* 5.2 2.0 - - + -
62D GLN* 3.6 22.4 - - + -
67D SER 3.6 8.5 - - - +
68D ASP* 1.3 74.5 - - - +
70D LEU* 1.3 61.1 + - - +
95D VAL* 3.7 6.7 - - + -
96D HIS 3.4 22.2 - - - +
97D ASP* 4.1 4.3 - - + +
98D PRO* 4.0 8.3 - - - -
104D TYR* 3.5 40.4 - - + -
345E ARG* 3.3 29.4 - - - -
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Residues in contact with LEU 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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49D ASP 3.4 26.5 - - - +
50D GLY 4.2 0.7 - - - +
51D LEU 3.4 18.8 - - - +
52D ALA* 4.6 4.3 - - + +
69D MET* 1.3 75.7 - - - +
71D LEU* 1.3 64.5 + - - +
72D LEU* 4.4 12.8 - - + -
95D VAL* 3.4 7.8 - - - +
96D HIS* 2.7 57.6 + - + +
97D ASP 4.5 1.1 - - - +
98D PRO* 4.2 15.7 - - + +
101D LEU* 3.6 31.4 - - + -
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Residues in contact with LEU 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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23D VAL* 3.9 8.3 - - + -
25D PHE* 3.5 40.4 - - + -
35D PHE* 3.7 31.0 - - + -
50D GLY* 3.1 9.0 - - - -
51D LEU* 2.7 37.6 + - + +
53D PHE* 3.5 35.2 - - + -
70D LEU* 1.3 72.1 - - - +
72D LEU* 1.3 63.4 + - - +
93D PHE* 3.6 22.3 - - + -
94D PHE 3.3 5.2 - - - +
95D VAL* 3.8 15.3 - - + -
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Residues in contact with LEU 72 (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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46D VAL 4.4 0.4 - - - +
47D PHE 4.0 17.0 - - - +
48D ASP 4.6 3.8 - - - +
49D ASP 4.1 5.8 - - - +
50D GLY* 3.7 28.7 - - - +
70D LEU* 4.4 10.5 - - + -
71D LEU* 1.3 73.0 - - - +
73D PRO* 1.3 71.8 - - + +
93D PHE* 3.3 4.2 - - - -
94D PHE* 2.8 38.2 + - + +
96D HIS* 3.5 44.2 - - + +
101D LEU* 5.0 6.1 - - + +
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Residues in contact with PRO 73 (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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42D PHE* 5.7 0.4 - - + -
46D VAL* 3.4 25.1 - - + +
47D PHE* 3.4 50.4 - - + +
72D LEU* 1.3 91.4 - - + +
74D ASP* 1.3 61.0 + - - +
75D PRO* 3.4 8.6 - - - +
91D ILE* 4.3 8.1 - - + -
92D ASN 3.9 0.2 - - - +
93D PHE* 3.3 32.9 - - + -
94D PHE* 4.7 4.4 - - - -
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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