Contacts of the strand formed by residues 146 - 154 (chain E) in PDB entry 1LNU
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 146 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E ILE* 5.7 0.2 - - + -
13E VAL* 4.0 28.3 - - + -
22E GLN* 5.8 0.7 - - - -
112E ASN 2.8 14.0 + - - -
113E ILE* 2.6 49.9 + - + +
114E PHE* 4.1 7.9 - + - -
116E PRO* 3.9 31.2 - - + -
138E PHE* 4.0 32.5 - - + -
139E PHE 3.0 23.8 - - - +
140E VAL* 4.1 11.2 - - + -
141E ASN* 2.8 9.4 - - - +
144E TYR 3.7 11.9 - - - -
145E SER* 1.3 79.6 - - - +
147E HIS* 1.3 53.5 + - - +
34F VAL* 4.8 2.5 - - + -
36F GLN* 3.3 31.2 - - + -
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Residues in contact with HIS 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E GLY* 5.3 3.5 + - - -
109E PHE* 3.6 24.3 - + + -
110E VAL 2.8 18.6 - - - +
111E ASP* 3.2 24.4 + - + +
113E ILE* 3.8 2.9 - - - -
138E PHE* 4.7 0.7 - - - -
139E PHE* 2.7 65.3 + + + +
140E VAL 3.9 8.3 - - - -
141E ASN* 2.7 29.9 + - - -
146E PHE* 1.3 72.3 - - - +
148E LYS* 1.3 58.5 + - - +
149E LEU* 4.0 5.1 - - + +
176F ARG* 5.9 4.0 - - - -
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Residues in contact with LYS 148 (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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108E CYS 3.9 0.4 - - - +
110E VAL* 2.9 32.6 + - - +
113E ILE* 3.4 14.0 - - + +
118E ILE* 4.3 6.1 - - + -
120E ILE* 3.0 26.9 - - + -
135E GLU* 2.8 32.8 + - - +
136E THR* 2.2 38.9 + - - +
137E SER* 4.2 6.7 - - - +
138E PHE* 4.1 34.4 - - + +
147E HIS* 1.3 74.7 - - - +
149E LEU* 1.3 89.0 + - - +
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Residues in contact with LEU 149 (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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93E PHE* 5.2 1.8 - - + -
107E ILE* 4.1 11.9 - - + -
108E CYS 3.7 2.0 - - - +
109E PHE* 3.2 46.7 - - + +
120E ILE* 5.2 0.2 - - - -
135E GLU* 3.3 6.9 - - - +
136E THR* 2.8 52.2 + - + +
139E PHE* 3.9 19.1 - - + -
147E HIS* 4.0 13.5 - - + +
148E LYS* 1.3 91.6 - - - +
150E SER* 1.3 60.0 + - - +
151E TYR* 3.7 17.5 - - + +
176F ARG 5.9 1.1 - - - +
177F ASN 4.6 2.5 - - - +
178F GLY* 4.6 9.9 - - - -
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Residues in contact with SER 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E LEU 3.8 0.3 - - - +
107E ILE* 3.5 4.0 - - - +
108E CYS* 3.0 35.0 + - - -
120E ILE* 4.0 29.6 + - - +
122E TRP* 3.3 21.3 + - - -
133E VAL* 4.3 5.2 - - - +
134E TYR 3.2 11.0 + - - -
135E GLU* 4.3 11.1 + - - +
149E LEU* 1.3 76.0 - - - +
151E TYR* 1.3 70.3 + - - +
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Residues in contact with TYR 151 (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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45E MET* 4.7 1.1 - - + +
95E LYS* 6.5 0.9 - - + -
105E THR* 3.7 16.6 - - + -
106E LEU 3.5 3.4 - - - -
107E ILE* 3.7 28.5 - - + -
122E TRP* 3.5 6.4 + - - -
132E GLY 3.7 1.0 - - - +
133E VAL* 3.2 6.8 - - - +
134E TYR* 2.5 71.1 + + + +
136E THR* 3.3 30.5 - - + +
149E LEU* 3.7 12.9 - - + +
150E SER* 1.3 76.7 + - - +
152E LEU* 1.3 59.9 + - - +
153E THR* 4.1 0.9 - - - +
177F ASN 2.6 29.6 + - - -
178F GLY* 3.2 20.8 - - - -
179F ASP* 4.3 15.3 - - + -
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Residues in contact with LEU 152 (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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105E THR* 3.2 5.7 - - - -
106E LEU* 2.8 48.1 + - + +
122E TRP* 3.3 54.3 - - + +
124E ARG* 4.5 8.1 - - - +
129E VAL* 5.0 8.7 - - + -
131E ASP 5.1 2.7 - - - +
132E GLY 4.0 2.0 - - - +
133E VAL* 4.5 6.7 - - + +
151E TYR* 1.3 71.0 - - - +
153E THR* 1.3 82.1 + - - +
154E PHE* 3.4 14.9 + - + -
162E TYR* 4.1 25.6 - - + -
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Residues in contact with THR 153 (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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103E PRO* 6.1 4.0 - - + -
104E ASN 3.9 7.0 - - - +
105E THR* 4.4 12.9 + - - +
124E ARG* 4.7 3.1 + - - -
131E ASP 4.8 1.9 - - - +
132E GLY* 2.9 35.2 + - - +
151E TYR* 4.1 0.9 - - - +
152E LEU* 1.3 77.7 - - - +
154E PHE* 1.3 61.6 + - - +
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Residues in contact with PHE 154 (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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94E PRO* 5.3 2.0 - - + -
98E VAL* 5.5 2.2 - - + -
103E PRO* 3.8 5.0 - - - +
104E ASN* 2.7 89.8 + - + +
105E THR 3.6 3.4 - - - -
106E LEU* 3.6 18.2 - - + -
124E ARG* 4.2 7.6 - - - +
152E LEU* 3.6 23.6 - - + -
153E THR* 1.3 77.2 - - - +
155E ILE* 1.3 72.1 + - - +
156E PRO* 3.7 22.2 - - + -
162E TYR* 3.2 35.9 - + + +
179E TRP* 3.8 29.8 - + - -
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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
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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