Contacts of the strand formed by residues 68 - 73 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E ALA* 5.9 5.9 - - + +
53E PHE 3.8 8.1 - - - +
67E SER* 1.3 76.4 + - - +
69E MET* 1.3 59.6 + - - +
98E PRO* 3.3 6.8 - - + +
345F ARG* 2.9 54.9 + - + +
347F ARG* 3.2 6.7 + - - +
352F ARG* 2.9 42.9 + - - -
354F PRO* 3.5 2.4 - - - +
355F ILE* 3.1 35.6 + - + +
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Residues in contact with MET 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E ALA* 3.3 8.3 - - - +
53E PHE* 3.1 55.3 + - + -
55E GLY* 3.9 7.6 - - - -
61E PHE* 5.2 2.0 - - + -
62E GLN* 3.6 22.0 - - + -
67E SER 3.6 9.2 - - - +
68E ASP* 1.3 74.3 - - - +
70E LEU* 1.3 63.3 + - - +
95E VAL* 3.8 5.8 - - + -
96E HIS 3.6 21.8 - - - +
97E ASP* 4.2 4.5 - - - +
98E PRO* 4.0 7.9 - - - -
104E TYR* 3.4 40.8 - - + -
345F ARG* 3.3 26.9 - - - -
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Residues in contact with LEU 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E ASP 3.4 26.5 - - - +
50E GLY 4.1 1.1 - - - +
51E LEU 3.5 19.7 - - - +
52E ALA* 4.6 3.8 - - + +
69E MET* 1.3 76.7 - - - +
71E LEU* 1.3 66.5 + - - +
72E LEU* 4.6 11.4 - - + -
95E VAL* 3.4 7.4 - - - +
96E HIS* 2.7 56.0 + - + +
97E ASP 4.4 1.6 - - - +
98E PRO* 4.2 14.1 - - + +
101E LEU* 3.6 31.2 - - + -
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Residues in contact with LEU 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E VAL* 4.0 8.7 - - + -
25E PHE* 3.6 35.0 - - + -
35E PHE* 3.7 24.9 - - + -
50E GLY* 3.1 8.7 - - - -
51E LEU* 2.7 38.5 + - + +
53E PHE* 3.5 39.3 - - + -
70E LEU* 1.3 72.9 - - - +
72E LEU* 1.3 62.5 + - - +
93E PHE* 3.6 20.3 - - + -
94E PHE 3.2 7.0 - - - +
95E VAL* 3.7 20.2 - - + -
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Residues in contact with LEU 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E VAL 4.5 0.4 - - - +
47E PHE 3.9 17.5 - - - +
48E ASP 4.5 4.3 - - - +
49E ASP 4.1 5.6 - - - +
50E GLY* 3.7 29.2 - - - +
70E LEU* 4.6 9.6 - - + -
71E LEU* 1.3 72.3 - - - +
73E PRO* 1.4 71.2 - - + +
93E PHE* 3.4 3.6 - - - -
94E PHE* 2.8 38.3 + - + +
96E HIS* 3.6 44.0 - - + +
101E LEU* 5.1 6.5 - - + +
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Residues in contact with PRO 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E PHE* 5.7 0.4 - - + -
46E VAL* 3.5 23.3 - - + +
47E PHE* 3.4 51.3 - - + +
72E LEU* 1.4 92.3 - - + +
74E ASP* 1.3 59.3 + - - +
75E PRO* 3.4 8.4 - - - +
91E ILE* 4.3 8.3 - - + -
92E ASN 3.9 0.4 - - - +
93E PHE* 3.3 33.4 - - + -
94E PHE* 4.7 4.0 - - - -
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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