Contacts of the strand formed by residues 188 - 201 (chain E) in PDB entry 4DEP
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 LYS 188 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183E TYR 3.8 0.2 - - - +
184E THR* 3.7 3.1 - - - -
185E TYR 3.0 28.4 + - - +
186E LEU* 2.8 11.3 + - + +
187E GLY* 1.3 80.6 - - - +
189E GLN* 1.3 62.7 + - - +
190E TYR* 3.6 32.2 - - + +
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Residues in contact with GLN 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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182E SER* 4.5 14.7 + - - +
183E TYR 3.4 4.6 - - - +
184E THR* 3.2 41.0 + - - +
187E GLY* 3.3 21.8 + - - +
188E LYS* 1.3 73.8 - - - +
190E TYR* 1.3 71.8 + - - +
191E PRO* 4.5 2.3 - - - +
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Residues in contact with TYR 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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22E ILE* 4.1 22.2 - - + +
67E VAL* 3.5 43.4 + - + +
68E PRO* 4.4 20.0 - - + -
182E SER* 3.4 8.0 - - - -
183E TYR* 2.8 40.1 + - + +
185E TYR* 3.6 29.0 + - + -
188E LYS* 3.6 36.3 - - + +
189E GLN* 1.3 78.8 - - - +
191E PRO* 1.3 72.2 - - + +
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Residues in contact with PRO 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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20E ASN 3.5 24.9 - - - +
21E GLU* 3.1 26.1 - - + +
22E ILE 3.3 16.8 + - - -
180E HIS* 4.0 15.5 - - + -
181E ALA 3.8 6.5 - - - +
182E SER* 5.0 1.1 - - - +
189E GLN 4.5 2.2 - - - +
190E TYR* 1.3 93.7 - - + +
192E ILE* 1.3 62.6 + - - +
193E THR* 5.4 0.2 - - + -
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Residues in contact with ILE 192 (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 GLU* 3.9 3.6 - - + +
22E ILE* 3.8 16.2 - - + +
128E MET* 3.9 12.1 - - + -
131E PHE* 3.4 43.5 - - + -
139E PRO* 5.6 0.2 - - + -
180E HIS* 3.1 8.5 + - - -
181E ALA* 3.0 50.0 + - + +
183E TYR* 3.6 23.8 - - + -
190E TYR 4.5 0.4 - - - +
191E PRO* 1.3 78.8 - - - +
193E THR* 1.3 66.2 + - - +
194E ARG* 3.5 30.7 - - - +
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Residues in contact with THR 193 (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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18E SER* 3.4 11.8 + - - -
21E GLU* 3.0 39.3 + - - +
104E CYS 5.0 9.4 + - - +
178E THR* 4.8 8.3 - - + -
179E CYS 3.4 12.3 - - - +
180E HIS* 3.9 16.6 - - + +
191E PRO* 5.4 0.7 - - + -
192E ILE* 1.3 81.1 - - - +
194E ARG* 1.3 87.5 + - - +
195E VAL* 5.2 4.3 - - - +
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Residues in contact with ARG 194 (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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17E SER* 5.3 3.8 + - - -
18E SER* 5.7 0.2 + - - -
21E GLU* 5.4 0.8 + - - -
22E ILE 5.4 1.6 + - - -
23E ASP* 3.8 20.0 + - - -
109E ALA 5.4 0.4 - - - -
111E PHE* 4.3 18.8 - - + -
125E CYS* 4.0 10.5 - - - -
126E PRO* 2.8 42.7 + - + +
127E TYR* 2.2 39.4 + - + +
128E MET* 3.6 8.3 - - - -
131E PHE* 3.7 13.5 - - - -
178E THR* 3.6 8.1 + - - +
179E CYS* 3.3 35.7 + - - +
192E ILE* 3.5 16.6 - - - +
193E THR* 1.3 95.9 + - - +
195E VAL* 1.3 67.3 + - - +
196E ILE* 4.2 1.0 + - + -
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Residues in contact with VAL 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E SER* 6.1 0.9 - - - +
105E TYR* 3.4 53.8 - - + -
106E ASN 4.6 0.7 - - - +
109E ALA* 3.7 31.2 + - + +
110E ILE* 3.6 13.2 - - + -
111E PHE* 2.8 28.6 + - - -
176E ASN* 4.4 8.7 - - + -
177E TYR 3.3 11.9 - - - +
178E THR* 4.2 3.4 - - - +
193E THR* 5.2 5.4 - - - +
194E ARG* 1.3 80.5 - - - +
196E ILE* 1.3 61.5 + - - +
197E GLU 4.1 0.2 - - - -
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Residues in contact with ILE 196 (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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110E ILE* 4.8 0.2 - - - -
111E PHE* 3.3 11.2 - - + +
113E GLN* 3.3 43.7 - - + +
123E LEU* 4.4 14.4 - - + -
124E VAL 3.2 26.0 - - - +
125E CYS* 4.3 1.1 - - - -
126E PRO* 4.1 13.5 - - + -
143E TRP* 3.9 29.2 - - + -
176E ASN* 4.3 2.0 - - - -
177E TYR* 2.4 48.6 + - + +
179E CYS* 4.7 4.7 - - - -
194E ARG 4.2 0.4 + - - +
195E VAL* 1.3 77.2 - - - +
197E GLU* 1.3 66.1 + - - +
198E PHE 3.5 1.0 + - - +
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Residues in contact with GLU 197 (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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110E ILE* 3.5 22.0 - - + +
111E PHE 2.8 9.4 + - - +
112E LYS* 3.5 30.2 - - + +
113E GLN 3.0 28.4 + - - +
175E GLY 3.6 1.1 - - - +
176E ASN* 3.2 15.2 + - - +
196E ILE* 1.3 72.5 - - - +
198E PHE* 1.3 60.0 + - - +
199E ILE* 4.2 25.9 - - + +
401E NAG 2.9 48.6 - - - +
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Residues in contact with PHE 198 (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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113E GLN 3.9 4.0 - - - -
115E LEU* 3.6 40.2 - - + -
123E LEU* 3.8 18.2 - - + -
166E VAL* 4.1 18.6 - - + -
169E VAL* 3.7 30.7 - - + -
173E HIS* 3.6 25.8 - - + +
174E ARG* 3.5 8.4 - - - +
175E GLY 2.7 32.3 + - - +
177E TYR* 3.5 33.7 - + + -
196E ILE* 3.5 2.6 + - - +
197E GLU* 1.3 70.9 - - - +
199E ILE* 1.3 78.3 + - - +
200E THR* 4.2 6.1 - - - -
401E NAG 5.2 0.7 + - - -
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Residues in contact with ILE 199 (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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112E LYS* 5.0 10.5 - - + +
113E GLN 3.2 12.5 + - - +
114E LYS* 3.3 65.1 - - + +
115E LEU 3.4 4.9 + - - -
174E ARG* 4.6 15.3 - - - +
197E GLU* 4.2 27.4 - - + +
198E PHE* 1.3 82.6 - - - +
200E THR* 1.3 62.7 + - - +
201E LEU* 6.1 0.4 - - + -
401E NAG 5.6 4.5 - - - -
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Residues in contact with THR 200 (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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115E LEU 3.4 4.8 + - - -
117E VAL* 3.7 18.8 - - + +
169E VAL* 3.6 26.9 - - - +
170E ALA 3.8 4.6 + - - -
171E GLU* 4.7 9.9 - - + -
174E ARG* 3.2 47.4 + - - +
198E PHE* 4.2 4.1 - - - -
199E ILE* 1.3 78.9 - - - +
201E LEU* 1.3 69.2 + - - +
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Residues in contact with LEU 201 (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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147D THR* 5.7 5.6 - - + -
149D GLN* 5.4 13.2 - - + +
114E LYS* 3.5 48.5 - - + +
115E LEU 2.8 11.9 + - - +
116E PRO* 3.6 15.9 - - + -
117E VAL* 2.8 32.5 + - - +
199E ILE* 6.1 0.2 - - + -
200E THR* 1.3 83.4 - - - +
202E GLU* 1.3 62.4 + - + +
203E GLU 3.4 0.9 + - - -
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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