Contacts of the strand formed by residues 189 - 198 (chain E) in PDB entry 4NQD
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 TYR 189 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111E ARG* 4.9 6.1 + - - -
150E GLY 2.8 25.3 + - - -
151E PHE* 2.6 49.5 + + + +
152E TYR* 3.6 27.6 - + - -
154E ASP* 3.6 34.2 - - + +
177E PRO* 3.6 30.5 - - + -
178E LEU 3.3 14.8 - - - -
179E LYS* 4.0 29.9 + - + -
180E GLU* 3.9 4.0 - - - -
185E ASN 5.5 1.0 + - - -
187E SER 3.8 7.4 - - - -
188E ARG* 1.3 77.4 - - - +
190E ALA* 1.3 57.3 + - - +
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Residues in contact with ALA 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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152D TYR* 5.4 0.9 - - + -
154D THR* 6.0 0.2 - - - -
174D TRP* 3.5 33.4 - - + -
148E ALA 3.3 5.8 - - - -
149E THR* 4.0 3.8 - - + +
151E PHE* 4.0 1.3 - - - -
174E ASP* 5.4 0.3 - - - +
177E PRO* 3.4 6.2 - - - +
178E LEU* 2.8 44.9 + - + +
180E GLU* 3.9 16.8 - - + +
189E TYR* 1.3 74.1 - - - +
191E LEU* 1.3 59.1 + - - +
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Residues in contact with LEU 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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174D TRP* 5.3 1.1 - - - -
146E CYS 3.7 0.7 - - - +
147E LEU* 3.5 4.1 - - - +
148E ALA* 2.8 43.4 + - + +
149E THR* 5.7 0.2 - - - +
151E PHE* 3.9 15.0 - - + -
154E ASP* 6.0 0.4 - - - +
156E VAL* 4.1 23.6 - - + +
158E LEU* 4.2 23.4 - - + +
173E THR* 4.0 16.6 - - + -
174E ASP* 3.5 41.1 - - + +
176E GLN 4.2 9.9 - - - +
177E PRO* 4.2 9.9 - - + -
190E ALA* 1.3 74.4 - - - +
192E SER* 1.3 64.3 + - - +
213E VAL* 6.0 0.2 - - + -
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Residues in contact with SER 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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154D THR* 3.3 18.9 + - - +
172D VAL* 4.0 9.8 - - - +
174D TRP* 4.4 0.2 - - - -
145E VAL* 5.0 0.2 - - - -
146E CYS 3.3 4.5 - - - -
147E LEU* 3.6 22.7 - - - -
158E LEU* 5.0 0.2 - - - -
173E THR* 3.6 3.8 - - - +
174E ASP* 2.6 57.7 + - - -
191E LEU* 1.3 76.1 - - - +
193E SER* 1.3 63.3 + - - +
194E ARG* 3.2 8.5 + - - -
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Residues in contact with SER 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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145E VAL* 3.4 6.5 - - - +
146E CYS 2.9 31.8 + - - -
158E LEU* 3.5 24.2 - - - -
160E TRP* 2.9 25.8 + - - -
171E VAL* 4.0 0.3 - - - +
172E CYS 3.2 10.1 + - - -
173E THR* 2.7 27.7 + - - -
192E SER* 1.3 75.9 - - - +
194E ARG* 1.3 64.8 + - - +
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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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133D LEU* 4.4 1.8 - - + -
154D THR* 3.4 17.4 + - - -
155D ASP 3.5 13.3 + - - -
157D CYS* 3.4 12.2 - - - +
159D LEU* 3.9 11.0 - - + -
170D SER* 2.8 37.0 + - - +
171D ALA* 3.7 6.1 - - - +
172D VAL* 3.9 9.3 - - + +
143E THR* 3.8 22.7 - - + -
144E LEU 3.4 4.3 - - - -
145E VAL* 4.4 10.1 - - + -
160E TRP* 4.1 2.7 - - - -
170E GLY 3.8 0.2 - - - +
171E VAL* 3.2 5.7 - - - +
172E CYS* 2.7 59.0 + - - -
174E ASP* 2.8 29.6 + - - -
192E SER* 3.2 19.0 + - - -
193E SER* 1.3 79.1 + - - +
195E LEU* 1.3 59.3 + - - +
196E ARG 4.2 0.2 - - - -
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Residues in contact with LEU 195 (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 3.7 1.6 - - - +
143E THR* 3.4 2.0 - - - -
144E LEU* 2.9 37.2 + - + +
160E TRP* 3.7 44.1 - - + -
162E VAL* 3.7 27.8 - - + -
167E VAL* 4.4 7.2 - - + -
169E SER 4.1 10.3 - - - +
170E GLY 3.4 9.4 - - - +
171E VAL* 4.0 12.8 - - + -
194E ARG* 1.3 71.9 - - - +
196E ARG* 1.3 65.9 + - - +
197E VAL* 3.9 18.5 + - + -
209E PHE* 3.8 18.4 - - + -
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Residues in contact with ARG 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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135D THR* 4.1 7.5 + - - +
136D ASP* 2.7 43.7 + - - -
159D LEU* 3.7 28.4 - - + +
161D MET* 3.8 27.8 - - - +
166D PHE* 3.4 13.5 - - - -
168D SER* 3.1 15.3 + - - -
135E GLU* 2.9 28.9 + - - +
139E THR* 3.7 16.0 + - - +
141E LYS* 3.5 13.3 - - + +
142E ALA 3.3 7.6 - - - +
143E THR* 3.2 17.0 + - - +
169E SER 5.1 0.2 - - - +
170E GLY* 2.8 20.7 + - - +
195E LEU* 1.3 76.0 - - - +
197E VAL* 1.3 71.1 + - - +
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Residues in contact with VAL 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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161D MET* 3.8 8.5 - - - -
141E LYS* 3.4 5.7 - - - +
142E ALA* 2.8 41.8 + - + +
144E LEU* 4.8 4.5 - - + -
162E VAL* 5.7 1.1 - - + -
195E LEU* 3.9 24.2 - - + -
196E ARG* 1.3 79.6 - - - +
198E SER* 1.3 67.4 + - - +
201E PHE* 4.1 24.2 - - + -
202E TRP* 3.9 24.0 - - + +
209E PHE* 4.4 12.8 - - + -
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Residues in contact with SER 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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161D MET* 4.0 7.4 - - - +
164D MET* 4.7 16.4 - - - -
140E GLN 3.8 7.6 - - - -
141E LYS* 4.5 1.6 - - - +
197E VAL* 1.3 81.2 - - - +
199E ALA* 1.3 63.7 + - - +
200E THR* 3.2 12.4 + - - -
201E PHE* 3.1 22.7 + - - +
202E TRP* 3.2 15.8 + - - +
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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