Contacts of the strand formed by residues 67 - 72 (chain E) in PDB entry 4XXD
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 67 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E VAL* 3.4 27.1 - - + -
59E TYR* 3.4 22.5 - - + -
63E VAL* 3.0 36.9 + - + +
65E GLY 4.6 4.7 + - - -
66E ARG* 1.3 103.2 + - + +
68E THR* 1.4 65.8 + - - +
80E LEU* 4.2 9.0 - - + -
81E GLN 3.2 5.8 - - - +
82E MET* 3.7 64.4 - - + -
86E ASP* 3.5 24.9 - - - -
90E TYR* 4.0 7.4 - + - -
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Residues in contact with THR 68 (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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59E TYR* 3.3 10.3 - - - +
65E GLY 5.2 2.8 + - - -
66E ARG 5.1 1.9 + - - -
67E PHE* 1.4 76.6 + - - +
69E ILE* 1.3 70.7 + - - +
70E SER* 3.7 8.2 + - - -
79E TYR* 4.4 0.5 - - - +
80E LEU* 3.7 4.9 - - - +
81E GLN* 3.0 43.8 + - + +
82E ASN* 5.6 2.4 - - - -
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Residues in contact with ILE 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E MET 4.0 6.7 - - - +
35E SER* 4.2 2.0 - - - -
36E TRP* 3.5 22.9 - - + +
49E ALA* 3.4 38.1 - - + +
50E GLN 3.9 10.3 - - - +
51E ILE* 3.8 38.3 - - + +
57E THR* 3.1 29.0 + - - +
59E TYR* 2.8 23.4 + - + +
68E THR* 1.3 77.5 - - - +
70E SER* 1.3 63.1 + - - +
78E LEU* 4.2 6.1 - - + -
79E TYR 3.6 10.8 - - - +
80E LEU* 4.5 2.0 - - - +
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Residues in contact with SER 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E ARG* 5.0 4.5 + - - -
51E ILE* 4.2 6.5 - - - -
68E THR* 4.6 9.0 - - - -
69E ILE* 1.3 75.7 - - - +
71E ARG* 1.3 65.7 + - - +
78E LEU* 3.5 7.9 - - - +
79E TYR* 2.7 56.3 + - - +
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Residues in contact with ARG 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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29E PHE* 2.7 41.6 + - + -
32E TYR 2.8 19.2 + - - -
34E MET* 3.6 27.8 - - - +
51E ILE* 3.9 19.5 - - + +
52E ASN 2.7 50.0 + - - -
53E VAL 4.3 7.2 - - - +
54E GLY* 4.1 9.0 - - - +
70E SER* 1.3 82.1 + - - +
72E ASP* 1.3 59.7 + - - +
73E ASN* 2.8 21.3 + - - +
77E THR 3.4 10.1 - - - +
78E LEU* 3.9 11.0 - - + -
79E TYR* 4.8 2.9 - - - -
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Residues in contact with ASP 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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29E PHE* 4.2 0.2 - - - -
71E ARG* 1.3 72.3 - - - +
73E ASN* 1.3 57.1 + - - +
74E ALA* 3.2 22.0 + - - +
75E LYS* 3.1 28.2 + - + +
76E ASN 3.0 24.1 + - - -
77E THR* 2.9 31.1 + - + -
79E TYR* 4.4 9.5 + - + -
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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
------------------------------------------------------------
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