Contacts of the strand formed by residues 192 - 199 (chain E) in PDB entry 4CQM
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 ILE 192 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E ALA* 4.2 5.2 - - - +
142E LEU* 3.7 37.2 - - + -
143E VAL* 4.0 22.9 - - + +
147E CYS 4.4 3.4 - - - -
149E GLY 3.5 11.0 - - - +
151E ILE* 3.9 33.4 - - + -
184E ALA 4.6 0.9 - - - +
187E LEU* 3.0 44.6 + - + +
188E GLY* 3.9 6.6 + - - -
190E HIS* 3.6 15.0 - - + +
191E GLY* 1.3 79.2 - - - +
193E ARG* 1.3 64.9 + - - +
194E CYS* 4.1 2.0 + - - -
249E THR* 4.5 2.4 + - - -
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Residues in contact with ARG 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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149E GLY 3.0 13.4 + - - +
150E SER* 3.6 17.2 + - - -
151E ILE 2.6 34.2 + - - -
191E GLY 5.1 3.6 - - - +
192E ILE* 1.3 75.9 - - - +
194E CYS* 1.3 60.3 + - - +
195E ASN* 4.0 7.1 - - - +
240E LEU* 2.9 22.8 + - - +
241E ALA 3.8 3.0 + - - -
242E SER 2.9 25.9 + - - -
243E GLU* 4.1 14.3 + - - +
245E SER* 3.1 23.5 + - - -
246E GLY* 3.4 28.8 - - - +
248E ILE 3.4 26.0 + - - +
249E THR* 3.6 10.1 - - - +
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Residues in contact with CYS 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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151E ILE* 3.2 34.8 - - + +
180E THR* 3.6 26.9 - - + +
183E ALA* 4.0 6.5 - - + -
184E ALA* 3.6 16.1 - - + +
187E LEU* 3.9 17.9 - - - -
192E ILE* 4.2 4.0 - - - -
193E ARG* 1.3 82.0 - - - +
195E ASN* 1.3 57.3 + - - +
249E THR* 3.0 7.7 + - - -
250E GLY* 2.5 36.9 + - - -
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Residues in contact with ASN 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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150E SER* 5.1 1.8 + - - -
151E ILE 3.0 8.0 + - - +
152E ILE* 3.6 4.2 - - + +
153E ASN 3.0 24.8 + - - +
180E THR* 3.4 11.8 - - - +
193E ARG* 4.0 12.7 - - - +
194E CYS* 1.3 80.9 + - - +
196E SER* 1.3 59.5 + - - +
240E LEU* 3.9 29.1 - - + +
248E ILE* 3.0 30.4 + - - +
249E THR* 3.2 9.9 - - - +
251E THR* 2.9 39.6 + - - +
253E VAL* 5.6 0.2 - - + -
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Residues in contact with SER 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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153E ASN 3.2 7.2 + - - -
155E SER* 4.5 7.6 - - - -
176E VAL* 4.6 1.6 - - - +
177E ILE* 3.9 13.5 + - - +
180E THR* 3.1 29.8 + - - +
195E ASN* 1.3 72.8 - - - +
197E VAL* 1.3 57.8 + - - +
198E LEU* 3.9 17.0 - - - -
251E THR 2.8 10.4 + - - +
252E SER* 3.3 12.0 - - - -
253E VAL* 2.7 35.7 + - - +
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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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152E ILE* 3.9 9.0 - - + -
153E ASN 2.9 7.3 + - - -
154E ILE* 3.6 23.7 - - + -
155E SER* 2.7 31.0 + - - -
196E SER* 1.3 75.9 - - - +
198E LEU* 1.3 62.7 + - - +
199E PRO* 3.2 10.2 - - + +
233E VAL* 4.0 21.1 - - + -
236E VAL* 4.1 13.5 - - + -
237E VAL* 4.4 4.0 - - + -
240E LEU* 3.8 24.5 - - + -
253E VAL 3.4 3.8 - - - +
255E VAL* 3.9 24.9 - - + -
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Residues in contact with LEU 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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155E SER* 3.9 12.1 - - - -
156E SER 3.3 28.5 - - - +
157E ILE* 4.0 4.9 - - - +
160E LYS* 4.4 17.5 - - + -
177E ILE* 4.0 17.9 - - + -
196E SER* 3.9 11.7 - - - +
197E VAL* 1.3 80.3 - - - +
199E PRO* 1.3 65.6 - - - +
252E SER* 3.7 28.3 - - - +
253E VAL 2.6 14.7 + - - +
254E GLU* 3.4 23.7 - - + +
255E VAL 3.1 18.8 + - - -
256E THR* 3.3 9.7 - - - +
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Residues in contact with PRO 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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23E ILE* 4.5 6.1 - - + -
154E ILE* 3.9 19.3 - - + -
155E SER 3.4 15.7 - - - +
156E SER* 3.7 5.5 + - - -
157E ILE* 3.1 21.3 + - - +
197E VAL* 3.2 22.2 - - + +
198E LEU* 1.3 84.2 - - - +
200E GLY* 1.3 65.0 + - - +
202E ILE* 3.9 24.7 - - + -
233E VAL* 4.2 12.8 - - + -
255E VAL* 3.3 10.8 - - + +
256E THR* 4.1 0.7 - - - -
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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