Contacts of the strand formed by residues 106 - 115 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5D VAL* 4.8 0.2 - - + -
8D GLN* 3.6 17.3 - - + -
11D LYS* 4.0 17.9 - - + -
12D PHE* 3.9 18.4 - - + +
18D PHE* 3.5 23.8 - - + -
102D ILE* 3.8 4.1 - - - +
103D LEU 3.0 23.0 + - - +
104D ASN 3.5 13.5 - - - +
105D GLY* 1.3 82.0 - - - +
107D CYS* 1.3 67.4 + - - +
108D VAL* 3.2 24.8 + - + +
127D PHE* 4.1 8.5 - - + -
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Residues in contact with CYS 107 (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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4D VAL* 4.1 1.6 - - - -
8D GLN* 2.6 24.6 + - - +
101D MET 3.7 7.0 - - - +
102D ILE* 4.0 17.9 - - - +
106D VAL* 1.3 69.4 - - - +
108D VAL* 1.3 63.9 + - - +
127D PHE* 3.3 10.9 - - - -
128D ASP* 3.0 26.2 + - + +
131D ARG* 3.5 17.3 - - + -
132D ALA* 3.4 27.8 - - + +
135D GLU* 3.8 16.6 - - - -
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Residues in contact with VAL 108 (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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12D PHE* 3.7 20.0 - - + -
18D PHE* 4.1 9.2 - - + -
100D PRO* 3.5 1.4 - - - +
101D MET* 3.0 59.6 + - + +
103D LEU* 3.8 13.7 - - + -
106D VAL* 3.2 24.2 - - + +
107D CYS* 1.3 81.9 - - - +
109D ILE* 1.3 70.9 + - - +
125D LEU* 4.2 17.0 - - + -
126D GLU 3.1 9.9 - - - +
128D ASP* 3.9 3.5 - - - +
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Residues in contact with ILE 109 (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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98D LYS* 3.9 45.1 - - + +
99D ALA 3.4 9.6 - - - +
100D PRO* 4.4 9.4 - - + -
108D VAL* 1.3 77.3 - - - +
110D TRP* 1.3 64.4 + - - +
111D LYS* 3.7 17.4 + - + +
124D CYS 3.7 0.3 - - - +
125D LEU* 3.5 4.7 - - - -
126D GLU* 2.6 46.0 + - + +
127D PHE 5.6 0.4 - - - +
128D ASP* 3.1 39.5 - - + +
131D ARG* 5.7 0.7 - - - +
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Residues in contact with TRP 110 (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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27D ILE* 3.6 28.6 - - + +
55D ILE* 3.5 47.9 + - + +
57D PHE* 3.3 38.4 - + - -
64D LEU* 3.9 13.6 - - + +
66D LEU* 3.5 32.8 - - + +
68D PHE* 4.8 2.5 - + - -
97D LEU* 3.8 25.6 - - + -
98D LYS* 3.3 1.7 - - - -
99D ALA* 2.7 45.0 + - + +
101D MET* 4.9 4.0 - - - -
108D VAL* 4.3 0.8 - - - +
109D ILE* 1.3 72.5 - - - +
111D LYS* 1.3 63.8 + - - +
112D GLY* 3.7 16.6 - - - -
124D CYS 3.5 4.3 - - - -
125D LEU* 3.6 15.5 - - + -
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Residues in contact with LYS 111 (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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97D LEU 3.3 9.4 - - - +
98D LYS* 3.1 44.2 - - + +
109D ILE* 3.7 16.0 + - + +
110D TRP* 1.3 81.6 - - - +
112D GLY* 1.3 57.2 + - - +
123D GLY* 3.1 0.9 - - - -
124D CYS* 2.7 44.5 + - - +
126D GLU* 2.7 43.9 + - - +
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Residues in contact with GLY 112 (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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27D ILE* 4.1 7.0 - - - -
96D TYR* 3.6 6.9 - - - -
97D LEU* 2.8 31.9 + - - +
110D TRP* 3.7 6.7 - - - -
111D LYS* 1.3 77.2 - - - +
113D TRP* 1.3 63.5 + - - -
122D MET 3.0 14.8 - - - -
123D GLY* 3.5 4.0 - - - -
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Residues in contact with TRP 113 (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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24D GLU* 4.5 6.7 + - - -
27D ILE* 3.3 1.6 - - - +
94D LYS* 3.4 37.6 - - + +
95D VAL 3.0 15.0 - - - +
96D TYR* 3.7 41.0 + + + -
97D LEU* 5.7 1.1 - - - -
112D GLY* 1.3 76.5 - - - +
114D ILE* 1.3 76.2 + - - +
115D ASP* 3.9 16.2 - - + -
120D ASP 4.0 1.1 - - - -
121D GLY* 3.5 19.7 - - - -
122D MET* 2.8 62.4 + - + +
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Residues in contact with ILE 114 (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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27D ILE* 3.8 15.0 - - + -
28D LYS* 4.4 1.3 - - - -
29D TYR* 3.9 18.8 - - + +
44D PHE* 3.6 33.4 - - + -
55D ILE* 3.6 40.6 - - + -
94D LYS* 3.1 17.7 - - - +
95D VAL* 3.1 19.9 + - + +
97D LEU* 5.1 2.7 - - + +
113D TRP* 1.3 82.3 - - - +
115D ASP* 1.3 76.3 + - - +
116D LEU* 3.2 2.8 + - - +
119D LEU* 3.6 17.5 - - - +
120D ASP 3.5 5.4 - - - -
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Residues in contact with ASP 115 (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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93D GLY 3.8 10.8 - - - +
94D LYS* 4.0 6.3 - - - +
113D TRP* 3.8 13.1 - - + -
114D ILE* 1.3 70.6 - - - +
116D LEU* 1.3 56.4 + - - +
117D GLN* 2.8 40.3 + - - +
118D ARG* 3.6 29.7 - - + +
119D LEU* 2.5 35.2 + - - -
120D ASP* 2.7 19.5 + - - +
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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
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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