Contacts of the helix formed by residues 187 - 202 (chain M) in PDB entry 5IYB
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 187 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181M CYS* 3.8 1.1 - - - -
185M ARG 4.2 0.6 + - - -
186M ILE* 1.3 78.6 - - - +
188M LYS* 1.3 65.1 + - - +
189M LYS* 3.9 14.8 + - - +
190M GLU* 3.2 29.8 + - - +
191M ILE* 3.2 14.7 + - - +
156T VAL 3.8 4.9 - - - -
157T ALA* 3.8 25.8 - - - +
161T TYR* 4.2 23.0 + - - -
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Residues in contact with LYS 188 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177M PHE* 4.5 19.4 - - + -
178M LYS* 4.4 22.3 - - + +
181M CYS* 3.4 11.1 - - - -
187M SER* 1.3 73.6 - - - +
189M LYS* 1.3 59.6 + - + +
191M ILE* 3.7 4.0 + - - +
192M GLY* 3.0 26.9 + - - -
286P GLU* 3.3 30.3 + - - -
287P LEU* 3.9 29.1 - - + +
156T VAL* 2.9 42.4 + - + +
10X T 6.3 3.6 - - - -
11X A 5.0 0.3 + - - -
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Residues in contact with LYS 189 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187M SER* 3.2 10.6 + - - +
188M LYS* 1.3 79.9 - - + +
190M GLU* 1.3 59.3 + - + +
193M ARG* 2.8 63.7 + - - +
287P LEU* 6.5 0.2 - - - -
165T TYR* 4.5 21.4 + - - -
10X T 3.1 58.4 + - - +
11X A 3.6 7.9 + - - +
76Y C 5.4 4.2 + - - -
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Residues in contact with GLU 190 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154M ARG* 5.8 4.9 - - - +
155M ALA* 5.0 9.2 - - - +
158M ALA* 4.7 7.1 - - + +
186M ILE* 3.7 27.9 - - + +
187M SER* 3.2 21.0 + - - +
189M LYS* 1.3 76.3 - - + +
191M ILE* 1.3 61.5 + - - +
193M ARG* 3.3 12.8 + - - +
194M CYS* 2.9 37.2 + - - +
161T TYR* 3.7 15.8 + - - -
75Y C 6.0 1.1 - - - +
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Residues in contact with ILE 191 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158M ALA 5.2 2.2 - - - +
161M SER* 4.5 8.5 - - - +
162M ALA* 4.3 23.1 - - + +
165M TYR* 5.0 3.1 - - + -
177M PHE* 4.1 23.8 - - + +
180M ILE* 3.7 31.0 - - + +
181M CYS* 4.1 15.0 - - - +
184M SER* 5.0 0.7 - - - -
186M ILE* 3.6 34.3 - - + +
187M SER 3.2 12.5 + - - +
188M LYS* 4.1 3.4 - - - +
190M GLU* 1.3 76.4 - - - +
192M GLY* 1.3 57.8 + - - +
194M CYS* 3.7 4.9 - - - +
195M PHE* 2.7 30.1 + - + +
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Residues in contact with GLY 192 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177M PHE* 4.6 11.1 - - - -
188M LYS 3.0 18.9 + - - -
189M LYS 3.8 1.3 - - - -
191M ILE* 1.3 77.3 - - - +
193M ARG* 1.3 60.5 + - - +
195M PHE* 3.5 8.1 + - - +
196M LYS* 3.2 33.7 + - - +
287P LEU* 4.4 18.1 - - - +
11X A 5.1 1.3 - - - -
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Residues in contact with ARG 193 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154M ARG* 4.5 18.6 - - - +
189M LYS* 2.8 51.0 + - - +
190M GLU* 3.7 11.2 - - - +
192M GLY* 1.3 73.6 - - - +
194M CYS* 1.3 60.8 - - - +
196M LYS* 3.3 11.9 + - - +
197M LEU* 2.9 31.2 + - - +
11X A 2.8 44.9 + - - +
12X T 5.5 7.4 - - - +
75Y C 4.4 17.5 + - - -
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Residues in contact with CYS 194 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151M LEU* 5.7 3.1 - - + -
154M ARG* 4.1 28.7 - - - -
158M ALA* 4.1 27.1 - - - +
159M ILE* 4.4 7.2 - - - -
162M ALA* 3.7 19.1 - - + -
190M GLU* 2.9 21.1 + - - +
191M ILE 3.8 1.1 - - - +
193M ARG* 1.3 72.6 - - - +
195M PHE* 1.3 61.1 + - - +
197M LEU* 4.3 7.0 - - - -
198M ILE* 2.8 43.0 + - + +
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Residues in contact with PHE 195 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162M ALA* 4.0 10.2 - - + +
165M TYR* 3.7 23.3 - + + -
166M ILE* 3.7 27.4 - - + -
169M ARG* 4.3 15.0 - - - -
177M PHE* 4.2 17.5 - + + -
191M ILE* 2.7 22.7 + - + +
192M GLY* 3.6 7.2 - - - +
194M CYS* 1.3 73.4 - - - +
196M LYS* 1.3 77.2 + - + +
198M ILE* 3.8 4.1 - - - +
199M LEU* 3.1 54.4 + - + +
206M VAL* 4.3 9.4 - - + -
284P GLU* 3.5 29.6 - - + -
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Residues in contact with LYS 196 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192M GLY 3.2 23.6 + - - +
193M ARG* 3.8 9.3 - - - +
195M PHE* 1.3 93.4 - - + +
197M LEU* 1.3 63.1 + - - +
199M LEU* 3.5 8.6 + - + +
200M LYS* 3.1 22.9 + - - +
282P SER* 5.6 14.8 - - - +
284P GLU* 5.7 8.7 - - + -
287P LEU* 4.3 10.5 - - + +
292P ILE* 6.3 1.8 - - + -
11X A 3.3 26.1 + - - -
12X T 2.6 40.1 + - - +
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Residues in contact with LEU 197 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150M SER 5.2 5.4 - - - +
151M LEU* 3.8 31.2 - - + -
154M ARG* 3.6 32.1 - - - +
193M ARG 2.9 17.5 + - - +
194M CYS* 3.8 5.6 - - - +
196M LYS* 1.3 77.1 - - - +
198M ILE* 1.3 58.2 + - - +
200M LYS* 3.3 34.7 + - - +
201M ALA* 2.9 32.9 + - + +
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Residues in contact with ILE 198 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141M LEU* 6.2 1.3 - - + -
145M VAL* 3.8 22.9 - - + -
151M LEU* 3.8 20.2 - - + -
159M ILE* 4.2 13.7 - - + +
162M ALA* 3.6 26.0 - - + -
163M CYS* 4.2 17.3 - - - +
166M ILE* 3.5 22.4 - - + -
194M CYS* 2.8 27.7 + - + +
195M PHE 3.8 2.9 - - - +
197M LEU* 1.3 69.6 - - - +
199M LEU* 1.3 57.9 + - + +
201M ALA* 3.8 4.2 - - - +
202M LEU* 2.6 45.4 + - + +
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Residues in contact with LEU 199 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166M ILE* 4.3 25.6 - - + -
195M PHE* 3.1 50.6 + - + +
196M LYS* 3.7 8.7 - - + +
197M LEU 3.4 0.2 - - - -
198M ILE* 1.3 77.5 - - + +
200M LYS* 1.3 61.0 + - - +
202M LEU* 4.6 3.4 - - + +
203M GLU* 3.3 14.4 + - - -
204M THR* 3.2 39.0 + - + +
205M SER* 4.3 8.3 - - - -
206M VAL* 4.5 13.9 - - + +
282P SER* 6.0 5.6 - - - +
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Residues in contact with LYS 200 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196M LYS 3.1 16.5 + - - +
197M LEU* 3.3 32.8 - - - +
199M LEU* 1.3 77.7 - - - +
201M ALA* 1.3 70.4 + - - +
203M GLU* 3.4 10.0 + - - +
294P ARG* 6.2 4.9 - - - -
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Residues in contact with ALA 201 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145M VAL* 6.3 1.8 - - + -
148M GLN* 3.0 34.4 + - - +
150M SER* 3.6 18.4 - - - +
151M LEU* 5.4 5.4 - - + -
197M LEU* 2.9 22.0 + - + +
198M ILE* 3.8 4.5 - - - +
200M LYS* 1.3 80.9 - - - +
202M LEU* 1.3 59.9 + - - +
203M GLU* 3.1 7.1 + - - +
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Residues in contact with LEU 202 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141M LEU* 3.6 29.8 - - + -
144M GLN* 3.6 38.4 - - + +
145M VAL* 4.7 11.9 - - + +
148M GLN* 4.3 12.6 - - - +
166M ILE* 5.8 3.4 - - + -
170M GLN* 5.6 0.9 - - - +
198M ILE* 2.6 37.4 + - + +
199M LEU* 4.7 2.9 - - + +
201M ALA* 1.3 71.8 - - - +
203M GLU* 1.3 70.5 + - - +
204M THR* 3.0 29.1 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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