Contacts of the helix formed by residues 185 - 201 (chain n) in PDB entry 5GJQ
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 THR 185 (chain n).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41n CYS* 4.1 0.2 - - - -
42n LYS* 4.0 18.8 - - - +
43n ASP* 3.5 16.4 - - - +
183n GLU 5.2 0.4 - - - +
184n MET* 1.3 77.3 - - - +
186n CYS* 1.3 59.8 + - - +
187n ARG* 3.5 13.7 + - - +
188n ASP* 3.0 32.0 + - - +
189n ILE* 2.9 30.4 + - - +
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Residues in contact with CYS 186 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41n CYS* 3.6 15.7 - - - -
43n ASP* 2.8 42.2 + - - +
44n GLY* 3.6 19.3 - - - -
45n VAL 3.8 4.5 - - - -
46n VAL* 3.9 10.5 - - - +
185n THR* 1.3 70.0 - - - +
187n ARG* 1.3 66.8 + - + +
189n ILE* 3.3 7.9 + - - +
190n VAL* 3.1 23.7 + - - +
215n TRP* 3.3 21.3 - - + -
216n VAL 4.9 1.8 - - - -
217n GLY* 5.1 3.1 - - - -
219n LEU* 5.4 7.0 - - + -
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Residues in contact with ARG 187 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185n THR* 3.1 12.2 + - - +
186n CYS* 1.3 81.3 - - + +
188n ASP* 1.3 68.3 + - - +
190n VAL* 3.9 12.6 + - - +
191n LYS* 4.0 20.3 + - - +
215n TRP* 3.5 20.7 - - - -
219n LEU* 3.8 22.0 - - + +
231n ILE* 3.9 32.7 - - - +
234n GLU* 3.9 24.7 + - - -
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Residues in contact with ASP 188 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184n MET* 4.0 21.7 - - + +
185n THR* 3.0 35.8 + - - +
187n ARG* 1.3 82.9 - - - +
189n ILE* 1.3 65.1 + - - +
190n VAL 3.3 0.7 + - - -
191n LYS* 3.4 27.6 + - - +
192n GLU* 3.7 7.6 + - - +
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Residues in contact with ILE 189 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39n ILE* 3.7 41.7 - - + +
41n CYS* 3.6 21.3 - - + -
46n VAL* 4.1 12.8 - - + -
179n LEU* 4.9 4.7 - - + -
181n MET* 4.2 5.2 - - + -
184n MET* 3.7 37.0 - - + -
185n THR 2.9 19.5 + - - +
186n CYS* 3.3 8.7 + - - +
188n ASP* 1.3 74.9 - - - +
190n VAL* 1.3 67.8 + - - +
192n GLU* 2.9 14.7 + - + +
193n VAL* 2.9 24.5 + - + +
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Residues in contact with VAL 190 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46n VAL* 4.1 20.6 - - + -
186n CYS 3.1 17.7 - - - +
187n ARG 4.0 7.0 - - - +
188n ASP 3.3 0.4 - - - -
189n ILE* 1.3 76.7 - - - +
191n LYS* 1.3 63.8 + - + +
193n VAL* 3.2 3.7 + - - +
194n ALA* 2.9 22.5 + - - +
213n LEU* 4.0 24.4 - - + +
215n TRP* 3.5 30.3 - - + -
227n VAL* 4.7 6.7 - - + -
231n ILE* 4.3 14.6 - - + +
235n ALA* 3.9 16.6 - - + -
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Residues in contact with LYS 191 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187n ARG* 4.0 23.6 + - - +
188n ASP* 3.4 14.8 + - - +
189n ILE 3.2 0.4 - - - -
190n VAL* 1.3 77.7 - - + +
192n GLU* 1.3 60.9 + - - +
194n ALA* 3.4 2.4 + - - +
195n LYS* 2.8 29.3 + - - +
231n ILE* 5.6 2.8 - - + +
234n GLU* 3.0 38.4 + - - -
235n ALA* 3.8 21.3 - - + -
238n TYR* 3.8 43.3 - - + -
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Residues in contact with GLU 192 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179n LEU* 3.6 44.8 - - + +
184n MET* 4.1 14.9 - - + +
188n ASP 4.0 10.9 - - - +
189n ILE* 2.9 9.9 + - + +
191n LYS* 1.3 77.5 - - - +
193n VAL* 1.3 61.7 + - - +
195n LYS* 3.3 27.5 + - - +
196n ILE* 2.9 38.9 + - - +
238n TYR* 3.0 25.5 + - - -
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Residues in contact with VAL 193 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37n ILE* 3.8 19.0 - - + +
39n ILE* 3.3 33.4 - - + -
46n VAL* 4.0 14.1 - - + +
47n PHE 4.5 0.9 - - - -
48n GLY* 3.8 31.4 - - - +
189n ILE* 2.9 23.4 + - + +
190n VAL* 3.4 7.2 - - - +
192n GLU* 1.3 76.0 - - - +
194n ALA* 1.3 65.2 + - - +
196n ILE* 3.2 5.0 + - - +
197n ILE* 2.9 28.2 + - + +
213n LEU* 3.9 11.7 - - + -
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Residues in contact with ALA 194 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190n VAL 2.9 12.9 + - - +
191n LYS 3.6 7.4 - - - +
193n VAL* 1.3 76.7 - - - +
195n LYS* 1.3 57.1 + - - +
197n ILE* 3.3 4.0 + - - +
198n TYR* 2.9 35.2 + - - -
211n LEU* 3.7 28.7 - - + -
213n LEU* 5.2 1.3 - - + -
235n ALA* 3.7 30.7 - - + +
236n GLU* 4.4 0.4 - - - +
239n ALA* 3.9 4.7 - - + -
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Residues in contact with LYS 195 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175n GLU* 5.5 1.5 + - - -
191n LYS 2.8 18.2 + - - +
192n GLU* 3.3 28.0 + - - +
194n ALA* 1.3 74.0 - - - +
196n ILE* 1.3 68.1 + - + +
198n TYR* 3.0 4.3 + - - +
199n ILE* 2.9 45.7 + - + +
238n TYR* 3.9 21.7 + - + -
239n ALA* 3.8 10.9 - - - +
242n SER* 4.1 28.5 - - - -
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Residues in contact with ILE 196 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37n ILE* 3.9 19.7 - - + -
39n ILE* 6.1 2.0 - - + -
172n ALA* 4.1 20.9 - - + +
175n GLU* 3.8 31.0 - - + +
176n ILE* 3.4 36.1 - - + -
179n LEU* 4.1 14.8 - - + -
192n GLU* 2.9 26.8 + - - +
193n VAL* 3.7 4.5 - - - +
195n LYS* 1.3 74.9 - - + +
197n ILE* 1.3 57.8 + - - +
199n ILE* 3.5 9.4 - - + +
200n VAL* 2.9 29.2 + - + +
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Residues in contact with ILE 197 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35n THR 4.6 4.7 - - - +
37n ILE* 3.9 33.9 - - + -
48n GLY 4.7 5.8 - - - -
50n GLU* 4.1 29.4 - - + +
193n VAL* 2.9 22.7 + - + +
194n ALA 3.4 8.3 - - - +
196n ILE* 1.3 76.5 - - - +
198n TYR* 1.3 58.8 + - + +
200n VAL* 3.3 10.0 + - + +
201n HIS* 2.9 28.6 + - - +
209n PHE* 3.8 26.5 - - + -
211n LEU* 3.9 26.0 - - + -
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Residues in contact with TYR 198 (chain n).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194n ALA 2.9 27.2 + - - +
195n LYS 3.0 3.8 + - - +
197n ILE* 1.3 75.2 - - + +
199n ILE* 1.3 67.2 + - - +
201n HIS* 3.8 15.0 + + + +
209n PHE* 3.7 37.2 + + - -
211n LEU* 4.5 11.4 - - + +
236n GLU* 3.9 26.4 + - + -
239n ALA* 3.5 27.4 - - + +
240n LYS* 3.6 37.4 + - + -
243n LEU* 4.1 37.0 - - + +
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Residues in contact with ILE 199 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175n GLU* 3.2 47.1 - - + +
195n LYS* 2.9 40.8 + - + +
196n ILE* 3.5 10.8 - - + +
198n TYR* 1.3 80.5 - - + +
200n VAL* 1.3 66.5 + - + +
201n HIS 3.2 7.4 + - - +
242n SER 6.1 1.8 - - - +
243n LEU* 4.4 15.4 - - + +
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Residues in contact with VAL 200 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35n THR* 4.1 20.2 - - + +
37n ILE* 6.0 0.2 - - + -
50n GLU* 4.6 4.7 - - - +
168n ALA* 3.5 33.4 - - + +
171n ALA* 3.7 10.1 - - + -
172n ALA* 3.5 38.6 - - + +
175n GLU* 5.3 1.1 - - + -
196n ILE* 2.9 14.1 + - + +
197n ILE* 4.0 11.9 - - + +
199n ILE* 1.3 81.5 - - + +
201n HIS* 1.3 68.0 + - - +
202n ASP* 3.5 5.4 + - - +
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Residues in contact with HIS 201 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50n GLU* 2.4 37.0 + - - +
52n LEU* 4.1 3.4 - - + -
197n ILE 2.9 17.9 + - - +
198n TYR* 3.9 12.2 - + - +
199n ILE 3.2 9.6 - - - +
200n VAL* 1.3 80.0 - - - +
202n ASP* 1.3 66.0 + - - +
203n GLU* 3.8 16.6 + - + +
206n ASP* 3.7 22.8 + - + -
207n LYS 3.2 26.0 + - - -
209n PHE* 3.3 41.3 - + + -
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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