Contacts of the helix formed by residues 185 - 202 (chain T) 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 SER 185 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42T CYS* 4.1 0.7 - - - -
43T ASN* 3.8 12.2 + - - +
184T LEU* 1.3 76.3 - - - +
186T ALA* 1.3 65.2 + - - +
187T ARG* 3.6 9.8 + - - +
188T GLU* 3.0 33.0 + - - +
189T ALA* 2.9 22.9 + - - +
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Residues in contact with ALA 186 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42T CYS* 3.6 22.4 - - - -
43T ASN* 4.1 3.6 - - - +
44T ASP* 4.6 2.7 - - - +
47T VAL* 4.0 2.6 - - + +
185T SER* 1.3 71.2 - - - +
187T ARG* 1.3 63.0 + - - +
189T ALA* 3.2 2.4 + - - +
190T VAL* 3.0 29.6 + - - +
214T TRP* 3.8 23.1 - - + -
216T SER* 3.8 26.0 - - - +
218T GLU* 4.0 7.2 - - - +
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Residues in contact with ARG 187 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185T SER* 3.2 8.8 + - - +
186T ALA* 1.3 80.2 - - - +
188T GLU* 1.3 62.2 + - + +
190T VAL* 3.3 19.8 - - - +
191T LYS* 3.5 19.8 + - - +
214T TRP* 4.1 5.1 - - + -
218T GLU* 2.8 44.9 - - - +
228T LEU* 3.9 35.6 - - + +
231T GLU* 4.9 5.9 + - - +
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Residues in contact with GLU 188 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180T HIS* 6.4 0.2 - - - -
184T LEU* 4.1 20.1 - - + +
185T SER* 3.0 25.1 + - - +
187T ARG* 1.3 74.0 - - + +
189T ALA* 1.3 55.2 + - - +
191T LYS* 3.1 35.3 + - - +
192T GLN* 2.8 53.0 + - - +
235T PHE* 5.0 7.4 - - - -
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Residues in contact with ALA 189 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40T ILE* 3.5 25.1 - - + +
42T CYS* 4.1 11.2 - - + -
47T VAL* 3.7 18.4 - - + -
184T LEU* 4.2 8.9 - - + +
185T SER 2.9 16.0 + - - +
186T ALA 3.2 4.7 + - - +
188T GLU* 1.3 76.8 - - - +
190T VAL* 1.3 53.0 + - - +
192T GLN* 4.1 7.4 - - - -
193T ALA* 2.7 35.9 + - - +
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Residues in contact with VAL 190 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47T VAL* 3.9 19.3 - - + -
186T ALA 3.0 16.9 + - - +
187T ARG* 3.3 9.4 - - - +
189T ALA* 1.3 74.1 - - - +
191T LYS* 1.3 65.2 + - + +
193T ALA* 3.5 3.6 - - - +
194T ALA* 3.1 19.6 + - - +
212T ILE* 3.8 12.8 - - + +
214T TRP* 3.4 31.9 - - + -
224T VAL* 4.2 25.4 - - + -
228T LEU* 4.6 12.8 - - + -
232T ALA* 4.3 13.2 - - + -
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Residues in contact with LYS 191 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187T ARG* 3.5 18.1 + - - +
188T GLU* 3.1 30.6 + - - +
190T VAL* 1.3 76.6 - - + +
192T GLN* 1.3 61.6 + - - +
194T ALA* 2.8 20.6 + - - +
195T LYS* 2.9 13.7 + - - +
228T LEU* 5.6 1.6 - - + -
231T GLU* 3.4 31.3 + - + +
232T ALA* 4.1 18.8 - - + -
235T PHE* 3.7 53.4 - - + -
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Residues in contact with GLN 192 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40T ILE* 4.2 4.9 - - + -
179T LEU* 3.5 46.0 - - + +
180T HIS* 5.5 2.3 - - - +
184T LEU* 4.9 9.2 - - + +
188T GLU* 2.8 39.7 + - - +
189T ALA* 3.7 9.0 - - - +
191T LYS* 1.3 72.5 - - - +
193T ALA* 1.3 57.4 + - - +
195T LYS* 2.8 36.4 + - - +
196T ILE* 2.9 34.0 + - - +
235T PHE* 3.9 16.5 - - - -
239T GLU* 5.6 1.0 + - - -
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Residues in contact with ALA 193 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38T ILE* 3.7 14.6 - - + +
40T ILE* 3.6 18.2 - - + +
47T VAL* 3.9 17.3 - - + -
49T ALA* 4.0 12.1 - - + +
189T ALA 2.7 21.9 + - - +
190T VAL 3.5 6.3 - - - +
192T GLN* 1.3 71.2 - - - +
194T ALA* 1.3 63.6 + - - +
196T ILE 3.3 0.7 + - - -
197T ILE* 3.0 29.9 + - - +
212T ILE* 4.8 1.6 - - + -
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Residues in contact with ALA 194 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190T VAL 3.1 9.6 + - - +
191T LYS 2.8 13.3 + - - +
193T ALA* 1.3 75.9 - - - +
195T LYS* 1.3 63.2 + - - +
197T ILE* 3.9 1.4 - - - +
198T TYR* 3.1 29.6 + - - -
210T LEU* 3.9 24.7 - - + -
212T ILE* 4.1 3.5 - - + +
232T ALA* 3.4 35.7 - - + +
236T ALA* 3.7 3.8 - - + -
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Residues in contact with LYS 195 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175T GLU* 3.1 27.9 + - - +
179T LEU* 5.2 6.6 - - - +
191T LYS 2.9 10.8 + - - +
192T GLN* 2.8 43.3 - - - +
194T ALA* 1.3 76.3 - - - +
196T ILE* 1.3 61.4 + - - +
198T TYR* 3.1 6.5 + - - +
199T LEU* 2.8 52.0 + - + +
235T PHE* 4.4 14.1 - - + -
236T ALA* 3.8 17.7 - - + +
239T GLU* 4.6 23.8 - - + +
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Residues in contact with ILE 196 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38T ILE* 4.1 16.6 - - + -
40T ILE* 4.4 4.9 - - + -
172T ALA* 3.8 34.7 - - + +
175T GLU* 3.7 22.2 - - + -
176T LEU* 3.6 28.5 - - + -
179T LEU* 3.7 20.2 - - + -
192T GLN 2.9 22.6 + - - +
193T ALA 3.9 3.4 - - - +
195T LYS* 1.3 84.3 - - - +
197T ILE* 1.3 57.4 + - - +
199T LEU* 3.9 6.5 - - - +
201T ALA* 2.9 28.1 + - - +
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Residues in contact with ILE 197 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36T THR* 4.1 30.3 - - + +
37T SER* 4.6 0.4 - - - -
38T ILE* 3.7 24.0 - - + -
49T ALA* 3.6 26.2 - - + +
50T VAL 3.9 9.0 - - - +
51T GLU* 4.3 11.6 - - + +
193T ALA 3.0 21.0 + - - +
194T ALA 3.9 1.1 - - - +
196T ILE* 1.3 75.8 - - - +
198T TYR* 1.3 59.8 + - + +
201T ALA* 3.3 4.2 + - + +
202T HIS* 3.0 27.2 + - - +
208T PHE* 3.8 18.8 - - + -
210T LEU* 3.7 24.2 - - + -
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Residues in contact with TYR 198 (chain T).
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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194T ALA 3.1 24.1 + - - +
195T LYS 3.1 8.4 + - - +
197T ILE* 1.3 76.3 - - + +
199T LEU* 1.3 63.2 + - + +
202T HIS* 3.2 16.1 + - - +
203T GLU* 3.9 5.7 + - - +
208T PHE* 3.5 38.4 - + - -
210T LEU* 4.2 21.6 - - + +
233T ILE* 3.4 33.1 - - + +
236T ALA* 3.4 24.0 - - + +
237T GLN* 3.5 29.2 - - - +
240T ILE* 4.2 25.1 - - + +
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Residues in contact with LEU 199 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171T SER* 4.7 8.7 - - - -
175T GLU* 3.5 43.1 - - + +
195T LYS* 2.8 42.7 + - + +
196T ILE* 3.9 5.6 - - - +
198T TYR* 1.3 73.4 - - + +
201T ALA* 1.3 61.8 + - - +
203T GLU* 3.3 28.8 + - - +
239T GLU 4.9 2.9 - - - +
240T ILE* 3.7 31.9 - - + -
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Residues in contact with ALA 201 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36T THR* 4.2 21.7 - - + +
51T GLU* 4.9 0.2 - - - +
168T GLY* 3.5 35.5 - - - +
171T SER* 4.3 10.7 - - - -
172T ALA* 4.3 10.1 - - + +
196T ILE 2.9 19.7 + - - +
197T ILE* 3.3 6.3 + - + +
199T LEU* 1.3 71.6 - - - +
202T HIS* 1.3 60.7 + - - +
203T GLU 3.0 6.5 + - - -
204T ASP* 3.4 12.2 + - - +
205T ASN* 4.6 0.7 + - - +
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Residues in contact with HIS 202 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51T GLU* 2.8 31.8 + - + +
53T LEU* 4.5 3.6 - - + -
197T ILE 3.0 12.5 + - - +
198T TYR 3.4 12.8 - - - +
199T LEU 3.2 1.0 - - - -
201T ALA* 1.3 74.6 - - - +
203T GLU* 1.3 61.9 + - - +
204T ASP 3.3 0.7 - - - -
205T ASN 3.1 18.7 + - - -
206T LYS* 2.9 64.0 + - + +
207T ASP* 4.5 2.8 + - - -
208T PHE* 3.3 46.5 + + + -
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Residues in contact with GLU 203 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198T TYR 4.3 5.5 - - - +
199T LEU* 3.3 21.4 + - - +
201T ALA 3.0 0.2 - - - -
202T HIS* 1.3 77.9 - - - +
204T ASP* 1.3 64.2 + - - +
205T ASN 3.0 9.5 + - - -
206T LYS* 3.1 59.6 + - - +
240T ILE* 4.0 23.3 - - - +
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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