Contacts of the helix formed by residues 192 - 204 (chain K) in PDB entry 3SDI
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 VAL 192 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159K ILE* 6.1 0.2 - - + -
160K LEU* 3.7 24.9 - - + -
163K ALA* 4.1 20.4 - - + -
164K HIS* 5.9 0.9 - - - +
170K GLY 4.7 0.7 - - - -
171K GLY 2.8 29.7 + - - +
172K SER* 4.3 6.3 - - - +
173K VAL* 4.4 10.8 - - + -
190K HIS 3.3 3.3 + - - +
191K ASP* 1.3 67.8 - - - +
193K GLY* 1.3 65.5 + - - +
195K LEU* 4.1 7.2 - - + -
196K PHE* 3.1 27.7 + - + +
192W ARG* 4.0 4.5 - - - +
193W GLN 5.0 4.4 + - - +
194W ASP* 3.9 27.8 - - + +
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Residues in contact with GLY 193 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191K ASP* 2.8 15.6 + - - -
192K VAL* 1.3 77.0 - - - +
194K GLU* 1.3 66.4 + - - +
197K TRP* 3.3 27.4 + - - -
144L TYR* 5.6 1.0 - - - +
190W LYS* 5.2 0.9 - - - -
192W ARG* 3.8 28.8 - - - +
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Residues in contact with GLU 194 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191K ASP* 3.0 26.5 + - + +
193K GLY* 1.3 81.0 - - - +
195K LEU* 1.3 67.7 + - - +
196K PHE 3.1 2.8 + - - -
197K TRP* 3.3 5.4 + - - +
198K LYS* 3.0 24.3 + - + +
144L LYS* 3.7 47.6 + - - +
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Residues in contact with LEU 195 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156K LYS* 3.5 45.1 - - + +
160K LEU* 3.9 31.4 - - + -
173K VAL* 4.2 20.4 - - + -
190K HIS* 4.5 13.5 - - + +
191K ASP 2.9 16.1 + - - +
192K VAL* 4.1 5.4 - - - -
194K GLU* 1.3 78.7 - - - +
196K PHE* 1.3 57.4 + - - +
198K LYS* 3.8 14.5 - - + +
199K VAL* 2.8 39.3 + - + +
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Residues in contact with PHE 196 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160K LEU* 4.2 19.4 - - + +
164K HIS* 3.6 18.6 - + + -
192K VAL* 3.1 22.5 + - + +
195K LEU* 1.3 74.2 - - - +
197K TRP* 1.3 89.5 + + + +
199K VAL* 3.3 2.1 + - - +
200K LYS* 2.9 32.9 + - + +
206K PHE* 3.4 50.0 - + + -
209K VAL* 3.5 28.9 - - + -
193W GLN* 3.4 35.7 - - + +
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Residues in contact with TRP 197 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193K GLY 3.3 23.7 + - - -
194K GLU* 3.3 5.2 + - - +
196K PHE* 1.3 95.9 - + + +
198K LYS* 1.3 61.3 + - - +
200K LYS* 3.7 15.7 - - + +
201K GLU* 3.1 24.8 + - - +
209K VAL* 3.9 25.1 - - + -
210K ILE 4.3 0.4 - - - -
211K GLY* 4.4 16.4 - - - -
214V LEU* 4.2 22.9 - - + -
190W LYS* 3.3 47.8 - - + +
191W MET 3.5 35.1 + - - -
192W ARG* 5.2 0.8 - - - +
193W GLN* 3.7 12.5 - - + +
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Residues in contact with LYS 198 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156K LYS* 5.7 5.2 - - - +
194K GLU* 3.0 17.9 + - + +
195K LEU* 3.8 18.8 - - + +
197K TRP* 1.3 78.5 - - - +
199K VAL* 1.3 66.4 + - + +
200K LYS 3.3 0.2 + - - -
201K GLU* 3.4 4.2 + - - +
202K GLU* 2.8 70.5 + - - +
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Residues in contact with VAL 199 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153K TYR* 3.5 27.8 - - + +
156K LYS* 5.8 0.7 - - + -
157K ARG* 3.7 15.3 - - - +
160K LEU* 3.8 20.0 - - + -
195K LEU* 2.8 39.1 + - + +
196K PHE 4.1 1.3 - - - +
198K LYS* 1.3 78.0 - - + +
200K LYS* 1.3 59.3 - - - +
202K GLU* 4.6 3.4 - - - +
203K GLU* 2.9 57.4 + - - +
205K SER* 4.1 3.5 + - - +
206K PHE* 4.4 3.1 - - + -
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Residues in contact with LYS 200 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196K PHE* 2.9 22.1 + - + +
197K TRP* 3.7 26.2 - - + +
199K VAL* 1.3 74.0 - - - +
201K GLU* 1.3 59.2 + - - +
204K GLY* 2.7 35.5 + - - -
205K SER 3.0 23.6 - - - +
206K PHE* 3.0 30.4 + - + +
207K ASN* 4.6 10.2 - - - +
209K VAL* 3.0 30.3 + - - +
211K GLY* 3.1 17.1 + - - +
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Residues in contact with GLU 201 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197K TRP 3.1 14.5 + - - +
198K LYS* 3.5 5.6 - - - +
200K LYS* 1.3 82.2 - - - +
202K GLU* 1.3 69.4 + - + +
203K GLU 3.2 0.5 + - - -
204K GLY* 3.8 4.5 + - - -
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Residues in contact with GLU 202 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198K LYS* 2.8 60.1 + - + +
199K VAL* 4.6 2.9 - - - +
201K GLU* 1.3 83.1 - - + +
203K GLU* 1.3 59.3 - - + +
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Residues in contact with GLU 203 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153K TYR* 3.0 32.3 + - - +
157K ARG* 3.0 18.7 + - - -
199K VAL* 2.9 19.8 + - + +
202K GLU* 1.3 79.2 - - + +
204K GLY* 1.3 60.7 + - - +
205K SER* 2.9 24.2 + - - +
140X HIS* 3.1 25.1 + - - -
143X ARG* 3.1 29.3 + - - +
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Residues in contact with GLY 204 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200K LYS* 2.7 17.2 + - - -
201K GLU 3.8 4.2 + - - -
203K GLU* 1.3 77.4 - - - +
205K SER* 1.3 58.1 + - - +
207K ASN* 3.2 19.7 + - - +
143X ARG* 3.1 22.3 + - - -
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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