Contacts of the strand formed by residues 106 - 111 (chain E) in PDB entry 4LOU
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 TRP 106 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B PRO* 4.7 8.9 - - + +
381B GLN 3.5 8.7 + - - -
382B TYR* 3.8 12.9 + - - +
383B HIS* 3.3 43.4 + + + -
33E TRP* 3.8 28.7 - + + -
99E LEU* 3.7 22.2 - - + -
100E TYR* 3.3 41.3 - + - -
101E TYR* 3.7 29.3 - + + +
104E GLY 2.8 28.1 + - - -
105E TYR* 1.3 72.3 - - - +
107E TYR* 1.3 59.4 + - - +
33F HIS* 3.4 2.9 + - - -
88F GLN* 3.1 20.8 + - - -
90F TRP* 3.3 34.6 + - + +
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Residues in contact with TYR 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A GLU* 3.8 11.6 + - - -
99E LEU* 3.4 11.6 - - - +
100E TYR* 2.7 52.4 + - + -
101E TYR* 3.5 32.2 + - - -
102E GLY 3.8 0.7 - - - -
105E TYR 4.4 2.0 - - - -
106E TRP* 1.3 71.9 - - - +
108E PHE* 1.3 63.8 + - - +
109E ASP* 3.4 21.5 + - + -
33F HIS* 3.2 27.1 - + + -
35F TYR* 3.5 7.6 - - - +
45F ARG* 3.5 42.9 + - - -
48F TYR* 3.7 38.8 - + + -
88F GLN* 4.0 2.0 - - - -
90F TRP* 5.1 0.2 - - - -
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Residues in contact with PHE 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E SER* 4.0 7.6 - - - -
37E VAL* 3.5 28.0 - - + -
47E TRP* 3.6 25.4 - + - -
97E ALA* 4.1 11.9 - - + -
98E ARG 4.1 2.9 - - - -
99E LEU* 3.9 15.9 - - + -
107E TYR* 1.3 73.1 - - - +
109E ASP* 1.3 65.9 + - - +
110E VAL 3.6 2.2 - - - -
111E TRP* 3.2 35.9 + + + +
35F TYR* 2.7 23.8 + - - +
45F ARG* 3.9 2.3 - - - +
88F GLN* 3.4 26.5 - - - -
90F TRP* 4.0 9.4 - + - -
95F GLN* 3.8 17.9 - - + -
97F PHE* 3.5 25.1 - + - -
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Residues in contact with ASP 109 (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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98E ARG* 2.3 56.9 + - - +
100E TYR* 4.0 12.3 - - + +
107E TYR* 3.4 27.3 + - + -
108E PHE* 1.3 74.9 - - - +
110E VAL* 1.3 68.0 + - - +
111E TRP* 4.8 1.0 - - - -
45F ARG* 3.1 37.1 + - - +
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Residues in contact with VAL 110 (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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2E VAL* 4.6 23.6 - - + +
4E LEU* 3.2 17.0 - - + +
97E ALA* 3.4 1.6 - - - -
98E ARG* 3.0 47.2 + - + +
109E ASP* 1.3 102.1 - - - +
111E TRP* 1.3 77.8 + - - +
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Residues in contact with TRP 111 (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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4E LEU* 4.1 6.2 + - - +
37E VAL* 3.8 31.6 - - + -
45E LEU* 4.0 17.9 - - + -
95E TYR* 3.5 40.4 - + + -
96E CYS 3.7 5.8 - - - +
97E ALA* 4.4 6.3 - - + -
108E PHE* 3.2 43.8 + + + +
109E ASP 4.7 1.1 - - - -
110E VAL* 1.3 92.9 - - - +
112E GLY* 1.3 66.9 + - - +
35F TYR* 3.7 18.1 - + - -
42F SER* 4.4 5.7 - - - -
43F PRO* 3.5 42.5 + - + +
45F ARG 5.1 2.5 - - - -
97F PHE* 4.1 10.8 - + - -
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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