Contacts of the strand formed by residues 192 - 199 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200C LEU* 5.5 0.8 - - - +
139D ALA* 4.1 7.2 - - - +
142D LEU* 3.7 35.4 - - + -
143D VAL* 4.0 22.2 - - + -
147D CYS 4.4 6.1 - - - +
149D GLY 3.3 13.0 - - - +
151D ILE* 3.8 33.9 - - + -
184D ALA 4.7 1.2 - - - +
187D LEU* 2.8 44.6 + - + +
188D GLY* 3.9 4.2 + - - -
190D HIS* 3.9 12.6 - - + +
191D GLY* 1.3 82.8 - - - +
193D ARG* 1.3 65.1 + - - +
194D CYS* 3.9 2.2 + - - -
249D THR* 4.4 2.4 + - - -
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Residues in contact with ARG 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C LEU* 4.5 10.8 - - + -
149D GLY 2.9 13.6 + - - +
150D SER* 3.4 16.0 + - - +
151D ILE* 2.5 35.5 + - - +
191D GLY 5.3 2.7 - - - +
192D ILE* 1.3 74.7 - - - +
194D CYS* 1.3 56.7 + - - +
195D ASN* 4.2 6.0 - - - +
240D LEU 3.1 16.5 + - - -
241D ALA 4.2 1.4 + - - -
242D SER 2.8 26.7 + - - -
243D GLU* 4.6 2.8 - - - +
245D SER* 2.7 35.5 + - - -
246D GLY* 3.3 30.6 + - - +
248D ILE 3.4 25.7 + - - +
249D THR* 3.5 12.3 - - - +
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Residues in contact with CYS 194 (chain D).
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* 5.2 0.2 - - - -
151D ILE* 3.3 21.3 - - + +
153D ASN* 5.6 0.4 - - - +
180D THR* 3.6 26.6 - - + +
183D ALA* 3.8 14.4 - - + -
184D ALA* 3.6 10.8 - - - +
187D LEU* 3.6 31.6 - - - -
192D ILE* 3.9 3.6 + - - -
193D ARG* 1.3 76.9 - - - +
195D ASN* 1.3 57.6 + - - +
249D THR* 3.0 7.7 + - - -
250D GLY* 2.6 35.0 + - - -
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Residues in contact with ASN 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D SER* 5.1 1.8 + - - -
151D ILE 2.9 10.8 + - - +
152D ILE* 3.5 3.0 - - - +
153D ASN 3.0 24.1 + - - -
180D THR* 3.5 10.1 - - - +
193D ARG* 4.2 9.7 + - - +
194D CYS* 1.3 78.9 - - - +
196D SER* 1.3 61.4 + - - +
197D VAL 4.3 0.2 + - - -
240D LEU* 3.9 30.3 - - + +
248D ILE* 2.8 30.0 + - - +
249D THR* 3.2 13.0 + - - +
251D THR* 2.8 40.8 + - - +
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Residues in contact with SER 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ASN* 3.2 6.3 + - - +
155D SER* 3.8 17.5 + - - -
177D ILE* 3.8 11.8 - - - +
180D THR* 3.1 31.1 + - - +
195D ASN* 1.3 74.8 - - - +
197D VAL* 1.3 62.5 + - - +
198D LEU* 4.0 4.0 - - - -
251D THR 3.1 6.8 + - - +
252D SER* 3.2 19.0 - - - -
253D VAL* 2.9 27.0 + - - +
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Residues in contact with VAL 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ILE* 3.8 17.0 - - + -
153D ASN 2.8 9.3 + - - -
154D ILE* 3.6 15.2 - - + -
155D SER* 2.6 31.9 + - - +
196D SER* 1.3 72.6 - - - +
198D LEU* 1.3 62.5 + - - +
199D PRO* 3.1 21.3 - - + +
233D VAL* 4.0 12.8 - - + -
236D VAL* 3.9 14.8 - - + -
237D VAL* 4.4 5.2 - - + -
240D LEU* 3.7 28.3 - - + -
253D VAL 3.7 9.2 - - - +
255D VAL* 4.0 13.2 - - + -
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Residues in contact with LEU 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D SER* 3.8 14.1 - - - +
156D OAS 3.5 26.0 - - - +
157D ILE* 4.3 4.7 - - - +
160D LYS* 4.3 18.8 - - + -
177D ILE* 4.0 16.8 - - + -
196D SER* 4.0 8.7 - - - +
197D VAL* 1.3 80.5 - - - +
199D PRO* 1.3 65.3 - - - +
252D SER* 3.6 31.2 - - - +
253D VAL 3.0 9.1 + - - -
254D GLU* 3.3 29.3 - - + +
255D VAL* 3.0 21.5 + - - -
256D THR* 3.4 6.1 - - - +
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Residues in contact with PRO 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ILE* 4.4 6.7 - - + -
154D ILE* 3.9 18.8 - - + -
155D SER 3.2 17.9 - - - -
156D OAS 3.5 7.0 - - - +
157D ILE 3.2 20.6 + - - -
197D VAL* 3.1 21.8 - - + +
198D LEU* 1.3 85.3 - - - +
200D GLY* 1.3 69.0 + - - +
202D ILE* 4.0 4.7 - - + -
233D VAL* 3.9 27.1 - - + -
255D VAL* 3.2 9.9 - - + +
256D THR* 3.9 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