Contacts of the strand formed by residues 179 - 191 (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 LEU 179 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E PRO* 6.2 0.7 - - + -
132E ARG* 4.5 0.2 - - - +
133E SER* 2.7 36.1 + - - +
137E ARG* 3.2 52.1 - - + +
138E ASN 4.5 5.2 - - - +
139E ILE* 5.2 2.9 - - + -
172E ASN* 3.5 33.0 - - + +
173E PHE 3.4 11.9 - - - +
174E ALA* 4.4 3.1 - - + +
178E ARG* 1.3 74.3 - - - +
180E GLU* 1.3 88.9 + - - +
181E SER* 4.4 0.4 - - - +
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Residues in contact with GLU 180 (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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41B PHE* 4.0 6.9 - - - -
76E ARG* 2.8 30.4 + - - -
130E ILE* 3.2 24.6 - - + +
131E VAL 3.2 6.3 - - - +
132E ARG* 3.2 46.5 + - + +
171E ALA 3.9 0.2 - - - +
172E ASN* 3.4 4.3 - - - -
173E PHE* 2.9 44.1 + - + +
175E LEU* 4.1 18.6 - - + +
178E ARG 4.0 0.8 + - - +
179E LEU* 1.3 84.2 - - - +
181E SER* 1.3 62.0 + - - +
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Residues in contact with SER 181 (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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130E ILE* 3.0 23.9 - - - -
131E VAL* 3.0 15.0 + - - -
138E ASN 3.0 18.3 + - - -
139E ILE* 3.1 21.9 - - - +
140E VAL* 3.3 31.0 - - - +
170E PRO* 4.6 1.1 - - - -
172E ASN* 3.2 19.0 + - - -
179E LEU* 4.4 0.2 - - - +
180E GLU* 1.3 72.6 - - - +
182E LYS* 1.3 60.0 + - - +
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Residues in contact with LYS 182 (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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151B ASN* 5.3 4.8 + - - +
153B ASP* 4.2 16.8 + - - -
78E VAL* 4.5 19.5 - - - +
128E TYR* 4.0 33.8 - - + -
129E LEU 3.3 3.1 - - - -
130E ILE* 3.4 16.8 - - + -
140E VAL* 4.1 0.2 - - - -
169E LYS 4.5 0.7 - - - +
170E PRO* 3.2 6.6 - - - +
171E ALA* 2.9 52.6 + - + +
173E PHE* 3.7 35.4 - - + -
181E SER* 1.3 72.3 - - - +
183E LEU* 1.3 72.6 + - - +
184E ASP* 5.6 1.3 - - + -
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Residues in contact with LEU 183 (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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19E THR* 3.1 28.5 - - + +
127E ILE 3.6 1.0 - - - +
128E TYR* 3.1 10.4 - - - -
129E LEU* 2.8 36.2 + - + +
140E VAL* 3.5 22.0 - - + +
141E LEU* 3.4 27.4 - - - +
142E ALA* 3.8 3.8 - - + +
166E ALA* 6.3 0.2 - - + -
167E VAL 3.3 23.8 - - - +
168E VAL 4.0 7.0 - - - +
169E LYS 5.7 0.2 - - - -
170E PRO* 3.8 17.0 - - + -
182E LYS* 1.3 82.4 - - - +
184E ASP* 1.3 59.0 + - - +
185E TYR* 4.0 15.2 - - + +
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Residues in contact with ASP 184 (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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126E HIS* 3.3 16.9 + - - +
128E TYR* 3.2 32.7 + - + -
166E ALA 3.5 0.2 - - - -
167E VAL* 2.6 56.3 + - + +
169E LYS 5.9 0.2 + - - -
182E LYS* 4.4 1.5 + - + -
183E LEU* 1.3 73.9 - - - +
185E TYR* 1.3 71.3 + - - +
186E GLN* 3.3 21.0 + - - -
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Residues in contact with TYR 185 (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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19E THR* 2.3 35.4 + - - -
20E GLY* 3.0 16.3 + - - -
21E ILE* 3.7 38.4 - - + -
126E HIS* 3.6 2.1 - - - -
127E ILE* 2.9 50.0 + - + +
129E LEU* 4.0 17.9 - - + -
142E ALA* 4.3 4.7 - - + +
147E LYS* 4.5 7.4 - - + -
164E PHE* 4.0 23.6 - + + -
165E THR 3.3 7.9 - - - +
166E ALA* 3.5 28.5 - - + +
183E LEU* 4.1 15.7 - - + -
184E ASP* 1.3 81.5 - - - +
186E GLN* 1.3 59.8 + - - +
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Residues in contact with GLN 186 (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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124E THR* 4.4 9.6 + - - +
125E LEU 3.4 5.6 - - - +
126E HIS* 3.5 26.1 - - - +
163E SER 3.3 5.7 - - - +
164E PHE* 3.4 5.5 - - - -
165E THR* 2.7 52.6 + - + +
166E ALA 6.0 0.2 - - - -
167E VAL* 3.8 15.3 - - + +
184E ASP* 3.3 24.9 + - - +
185E TYR* 1.3 76.3 - - - +
187E LEU* 1.3 59.3 + - - +
188E ARG* 4.1 9.3 + - + +
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Residues in contact with LEU 187 (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* 4.1 20.0 - - + -
26E CYS* 4.3 9.4 - - - -
36E PHE* 5.0 6.1 - - + -
124E THR* 3.6 1.4 - - - -
125E LEU* 2.9 52.0 + - + +
156E LEU* 4.3 24.0 - - + -
161E ILE* 3.6 29.6 - - + -
163E SER 3.5 17.9 - - - +
164E PHE* 4.0 21.5 - - + -
185E TYR 4.4 0.2 - - - -
186E GLN* 1.3 71.8 - - - +
188E ARG* 1.3 62.1 + - - +
189E ILE* 3.7 9.4 + - + +
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Residues in contact with ARG 188 (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* 4.7 15.8 + - - -
123E GLN 3.5 10.1 + - - -
124E THR* 3.5 37.8 - - - +
161E ILE* 4.0 1.2 - - - +
162E GLU* 2.9 38.1 + - + +
163E SER* 3.0 29.7 + - - +
165E THR* 6.4 0.9 - - + -
186E GLN* 4.1 10.2 + - + +
187E LEU* 1.3 71.5 - - - +
189E ILE* 1.3 62.2 + - - +
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Residues in contact with ILE 189 (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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29E LEU* 3.4 33.2 - - + -
122E SER* 3.5 3.8 - - - -
123E GLN* 2.8 45.1 + - + +
125E LEU* 3.7 14.6 - - + -
156E LEU* 4.2 9.4 - - + -
159E TRP* 3.5 25.6 - - + -
160E ASP 3.3 11.9 - - - +
161E ILE* 4.1 16.2 - - + -
162E GLU* 3.8 3.8 - - - +
187E LEU* 4.0 23.3 - - + +
188E ARG* 1.3 79.9 - - - +
190E SER* 1.3 60.4 + - - +
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Residues in contact with SER 190 (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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120E PHE 5.4 1.6 - - - -
121E ASP 3.9 5.4 - - - -
122E SER* 3.5 20.0 - - - -
159E TRP* 3.3 4.7 - - - -
160E ASP* 2.9 46.4 + - - +
162E GLU* 3.5 15.7 + - - -
189E ILE* 1.3 75.1 - - - +
191E ARG* 1.3 66.8 + - - +
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Residues in contact with ARG 191 (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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31E ASP* 2.4 41.2 + - - -
113E LEU* 6.1 0.2 - - - +
115E PHE* 3.9 9.9 - - - -
118E TYR* 3.2 29.8 - - - -
119E PRO 3.1 24.0 + - - +
120E PHE 4.9 3.5 - - - +
121E ASP* 3.1 43.0 + - - +
123E GLN* 5.5 0.2 - - - +
158E GLY 3.8 6.1 - - - +
159E TRP* 3.2 34.2 - - + +
160E ASP* 5.3 0.5 - - - +
190E SER* 1.3 78.0 + - - +
192E GLN* 1.3 73.8 + - - +
193E TYR* 3.5 15.8 + - - +
196E TYR* 3.9 23.7 + - + -
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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