Contacts of the strand formed by residues 159 - 174 (chain E) in PDB entry 4LML
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 159 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29E LEU* 3.6 41.4 + - + +
31E ASP* 4.4 2.3 + - - -
113E LEU* 5.6 1.8 - - + -
121E ASP* 4.1 2.7 - - - -
123E GLN* 3.7 28.0 - - + -
155E PHE 3.8 8.7 - - - +
156E LEU* 3.0 29.9 + - + +
157E THR 3.4 16.8 + - - -
158E GLY* 1.3 82.6 + - - +
160E ASP* 1.3 62.5 + - - +
161E ILE* 4.1 1.1 + - - -
189E ILE* 3.5 35.4 - - + -
190E SER* 3.3 13.2 - - - -
191E ARG* 3.2 74.3 - - + +
192E GLN* 3.4 13.5 + - - -
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Residues in contact with ASP 160 (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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159E TRP* 1.3 71.4 - - - +
161E ILE* 1.3 62.6 + - - +
162E GLU* 3.7 10.7 + - - +
189E ILE* 3.3 6.2 - - - -
190E SER* 2.9 47.9 + - - +
191E ARG 5.3 0.7 - - - +
192E GLN* 2.4 38.8 + - - +
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Residues in contact with ILE 161 (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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23E LEU* 6.2 1.3 - - + -
26E CYS* 5.2 3.6 - - + -
150E LYS* 5.1 15.9 - - + -
154E VAL* 3.9 31.4 - - + +
155E PHE 4.2 13.0 - - - +
156E LEU* 4.1 26.2 - - + -
159E TRP 4.1 1.3 + - - +
160E ASP* 1.3 71.3 - - - +
162E GLU* 1.3 72.4 + - - +
163E SER 4.5 0.2 - - - +
187E LEU* 3.6 32.1 - - + -
188E ARG 4.0 2.2 - - - +
189E ILE* 4.1 11.0 - - + -
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Residues in contact with GLU 162 (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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122E SER* 5.1 1.0 + - - -
150E LYS* 5.3 6.4 + - - -
160E ASP* 3.7 14.3 - - - +
161E ILE* 1.3 82.1 - - - +
163E SER* 1.3 63.6 + - - +
188E ARG* 2.9 26.0 + - + +
189E ILE 3.8 3.3 + - - -
190E SER* 3.5 34.9 + - - -
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Residues in contact with SER 163 (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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150E LYS* 5.8 1.8 - - - +
161E ILE* 4.0 1.1 - - - +
162E GLU* 1.3 82.4 - - - +
164E PHE* 1.3 62.1 + - - +
165E THR* 4.6 10.7 - - - +
186E GLN 3.3 4.9 - - - +
187E LEU* 3.5 5.2 - - - -
188E ARG* 3.0 41.0 + - - +
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Residues in contact with PHE 164 (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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21E ILE* 3.4 39.7 - - + -
23E LEU* 3.9 44.9 - - + -
127E ILE* 5.3 8.5 - - + -
147E LYS* 3.8 32.0 - - + +
150E LYS* 4.6 26.8 - - + +
163E SER* 1.3 71.9 - - - +
165E THR* 1.3 62.6 + - - +
185E TYR* 4.0 31.0 - + + -
186E GLN 3.4 18.6 - - - -
187E LEU* 4.0 16.2 - - + -
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Residues in contact with THR 165 (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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144E ASP* 5.3 0.2 + - - -
147E LYS* 3.5 26.2 + - - +
163E SER* 4.6 13.7 - - - +
164E PHE* 1.3 78.1 - - - +
166E ALA* 1.3 84.3 + - - +
185E TYR* 3.3 7.6 - - - +
186E GLN* 2.7 49.8 + - + +
188E ARG* 6.4 0.7 - - + -
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Residues in contact with ALA 166 (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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142E ALA* 3.8 20.9 - - + -
144E ASP* 5.3 2.9 - - - +
147E LYS* 4.0 12.7 - - + +
165E THR* 1.3 92.9 + - - +
167E VAL* 1.3 64.4 + - - +
168E VAL* 3.1 13.0 + - + +
183E LEU* 6.3 0.2 - - + -
184E ASP 3.5 4.7 - - - +
185E TYR* 3.5 33.9 - - + -
186E GLN* 5.8 0.4 - - - -
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Residues in contact with VAL 167 (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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142E ALA* 4.7 0.9 - - - +
166E ALA* 1.3 70.3 - - - +
168E VAL* 1.3 65.8 + - + +
169E LYS* 3.3 21.8 + - + +
183E LEU* 3.3 21.0 - - - +
184E ASP* 2.6 50.1 + - + +
186E GLN* 3.8 17.5 - - - +
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Residues in contact with VAL 168 (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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141E LEU* 3.3 23.3 - - + +
142E ALA* 4.0 21.5 - - + +
144E ASP* 3.8 25.1 - - - +
166E ALA 3.1 10.9 + - - +
167E VAL* 1.3 74.8 - - + +
169E LYS* 1.3 88.3 + - + +
170E PRO* 3.1 14.2 - - - +
183E LEU* 4.0 3.1 - - - +
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Residues in contact with LYS 169 (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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141E LEU* 6.1 4.1 - - + +
167E VAL* 3.3 21.4 - - + +
168E VAL* 1.3 101.1 - - + +
170E PRO* 1.3 72.3 - - + +
171E ALA* 3.6 1.7 + - - +
182E LYS 4.5 0.7 - - - +
183E LEU* 4.5 0.7 - - - +
184E ASP 5.9 0.2 + - - -
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Residues in contact with PRO 170 (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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139E ILE* 3.6 20.6 - - + -
140E VAL 3.2 28.0 - - - +
141E LEU* 3.9 12.1 - - + -
168E VAL 3.1 11.4 - - - +
169E LYS* 1.3 90.3 - - + +
171E ALA* 1.3 59.8 + - - +
172E ASN* 3.6 16.4 + - - +
181E SER* 4.6 0.9 - - - -
182E LYS 3.2 17.9 - - - +
183E LEU* 3.8 4.0 - - + -
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Residues in contact with ALA 171 (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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169E LYS 3.6 2.7 + - - +
170E PRO* 1.3 70.9 - - - +
172E ASN* 1.3 63.4 + - - +
173E PHE* 3.6 18.5 + - + -
180E GLU 3.9 0.2 - - - +
182E LYS* 2.9 42.9 + - + +
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Residues in contact with ASN 172 (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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139E ILE* 3.3 25.2 - - - +
170E PRO* 3.6 20.9 + - - +
171E ALA* 1.3 74.9 - - - +
173E PHE* 1.3 64.1 + - - +
174E ALA 4.1 0.2 + - - -
179E LEU* 3.5 21.8 - - + +
180E GLU 3.4 2.5 - - - -
181E SER* 3.2 26.4 + - - -
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Residues in contact with PHE 173 (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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22B TYR* 5.8 4.9 - - - -
151B ASN* 5.3 8.5 - - - -
152B ASP* 6.1 1.3 - - - -
153B ASP* 6.0 0.4 - - - -
130E ILE* 5.6 3.4 - - + -
171E ALA* 3.9 20.2 - - + -
172E ASN* 1.3 74.6 - - - +
174E ALA* 1.3 66.9 + - - +
175E LEU* 4.8 11.2 - - + +
179E LEU* 3.4 10.3 - - - +
180E GLU* 2.9 38.8 + - + +
182E LYS* 3.7 43.1 - - + -
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Residues in contact with ALA 174 (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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172E ASN 4.1 0.4 + - - -
173E PHE* 1.3 75.9 - - - +
175E LEU* 1.3 62.9 + - - +
176E GLU 4.2 1.4 + - - -
177E ASP* 5.4 1.3 - - - +
178E ARG 3.3 12.6 - - - +
179E LEU* 4.4 2.2 - - + +
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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