Contacts of the strand formed by residues 106 - 115 (chain F) in PDB entry 1E50
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 VAL 106 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8F GLN* 3.6 18.4 - - + +
11F LYS* 3.9 21.5 - - + -
12F PHE* 3.9 18.4 - - + +
18F PHE* 3.4 27.8 - - + -
102F ILE* 3.5 4.2 - - - +
103F LEU 2.9 25.2 + - - +
104F ASN 3.5 5.2 - - - +
105F GLY* 1.3 82.6 - - - +
107F CYS* 1.3 66.1 + - - +
108F VAL* 3.2 24.8 + - + +
127F PHE* 4.1 7.9 - - + -
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Residues in contact with CYS 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F VAL* 4.1 0.9 - - - -
8F GLN* 2.6 27.9 + - - +
101F MET 3.7 6.5 - - - +
102F ILE* 3.9 18.8 - - - +
106F VAL* 1.3 69.1 - - - +
108F VAL* 1.3 54.9 + - - +
127F PHE* 3.4 12.0 - - - -
128F ASP* 2.7 34.1 + - + +
131F ARG* 3.4 30.3 - - + -
132F ALA* 3.4 16.6 - - + +
135F GLU* 3.8 16.2 - - - -
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Residues in contact with VAL 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F PHE* 3.8 20.6 - - + -
18F PHE* 4.3 9.0 - - + -
100F PRO* 3.6 3.5 - - - +
101F MET* 3.0 55.1 + - + +
103F LEU* 3.9 12.8 - - + -
106F VAL* 3.3 32.1 - - + +
107F CYS* 1.3 73.7 - - - +
109F ILE* 1.3 65.0 + - - +
125F LEU* 4.0 24.0 - - + -
126F GLU 3.0 9.0 - - - +
128F ASP* 3.9 3.4 - - - +
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Residues in contact with ILE 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98F LYS* 3.9 37.5 - - + +
99F ALA 3.6 9.2 - - - +
100F PRO* 4.5 6.5 - - + -
108F VAL* 1.3 75.1 - - - +
110F TRP* 1.3 64.0 + - - +
111F LYS* 3.7 29.6 + - + +
125F LEU* 3.5 4.7 - - - -
126F GLU* 2.6 45.0 + - + +
127F PHE 5.7 0.7 - - - +
128F ASP* 3.0 40.8 - - + +
129F GLU* 5.9 0.4 - - - +
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Residues in contact with TRP 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F ILE* 3.6 28.7 - - + +
55F ILE* 3.5 45.7 + - + +
56F ALA 6.2 0.2 - - - -
57F PHE* 3.3 36.0 - + - -
64F LEU* 3.7 22.2 - - + +
66F LEU* 3.4 27.8 - - + +
68F PHE* 4.8 0.2 - + - -
97F LEU* 4.0 22.2 - - + -
98F LYS* 3.3 2.4 - - - -
99F ALA* 2.7 52.7 + - + +
101F MET* 4.8 3.8 - - - -
108F VAL 4.2 0.4 - - - -
109F ILE* 1.3 71.3 - - - +
111F LYS* 1.3 64.4 + - - +
112F GLY* 3.5 19.1 - - - -
124F CYS 3.6 3.4 - - - -
125F LEU* 3.9 9.6 - - + -
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Residues in contact with LYS 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F LEU 3.4 6.3 - - - +
98F LYS* 3.2 41.1 - - + +
109F ILE* 3.7 18.9 + - + +
110F TRP* 1.3 80.8 - - - +
112F GLY* 1.3 56.1 + - - +
123F GLY* 3.1 1.2 - - - -
124F CYS* 2.7 45.3 + - - +
126F GLU* 2.7 44.3 + - - +
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Residues in contact with GLY 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F ILE* 4.1 2.2 - - - -
96F TYR* 3.6 6.0 - - - -
97F LEU* 2.7 38.1 + - - +
110F TRP* 3.5 13.3 - - - -
111F LYS* 1.3 76.8 - - - +
113F TRP* 1.3 58.9 + - - -
122F MET 3.0 14.6 - - - -
123F GLY* 3.5 3.6 - - - -
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Residues in contact with TRP 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F GLU* 4.5 7.7 + - - -
27F ILE* 3.3 1.4 - - - +
94F LYS* 3.4 37.9 - - + -
95F VAL 3.0 14.4 - - - +
96F TYR* 3.6 44.7 + + + -
97F LEU* 5.6 0.7 - - - -
112F GLY* 1.3 75.6 - - - +
114F ILE* 1.3 73.9 + - - +
115F ASP* 3.9 10.1 - - + -
120F ASP 3.9 6.3 - - - -
121F GLY* 3.3 21.5 - - - -
122F MET* 2.9 59.8 + - + +
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Residues in contact with ILE 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F ILE* 3.7 13.5 - - + -
28F LYS 4.4 1.3 - - - -
29F TYR 3.8 22.9 - - - +
44F PHE* 3.7 33.2 - - + -
55F ILE* 3.6 36.3 - - + -
94F LYS* 3.0 19.0 - - - +
95F VAL* 3.0 20.4 + - + +
97F LEU* 5.1 2.7 - - + +
113F TRP* 1.3 83.2 - - - +
115F ASP* 1.3 76.9 + - - +
116F LEU* 3.3 1.2 + - - +
119F LEU* 3.6 7.9 - - - +
120F ASP* 3.4 15.5 - - - +
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Residues in contact with ASP 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F GLY 3.9 9.2 - - - +
94F LYS* 3.9 8.5 - - - +
113F TRP* 3.9 10.2 - - + -
114F ILE* 1.3 69.6 - - - +
116F LEU* 1.3 58.0 + - - +
117F GLN* 2.7 43.1 + - - +
118F ARG* 3.0 26.6 + - + +
119F LEU* 2.6 34.7 + - - -
120F ASP* 2.6 21.0 + - - +
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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