Contacts of the helix formed by residues 185 - 200 (chain A) in PDB entry 2MYS
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 LYS 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A ILE* 3.6 19.7 - - + +
178A THR* 4.3 3.1 - - - -
179A GLY* 2.9 46.7 - - - +
180A GLU 3.9 4.0 - - - +
181A SER* 4.9 1.8 - - - +
184A GLY* 1.3 73.9 - - - +
186A THR* 1.3 53.9 + - - +
187A VAL 3.0 2.5 - - - -
188A ASN* 2.6 29.4 + - - +
189A THR* 2.5 23.5 + - - +
244A SER* 4.6 12.9 + - - -
463A ASP* 4.4 16.7 + - - +
464A ILE 3.8 17.6 + - - +
465A ALA* 4.6 8.3 - - - +
674A CYS* 4.2 6.5 - - + -
5000A SO4 2.5 33.2 + - - +
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Residues in contact with THR 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LYS* 1.3 74.3 - - - +
187A VAL* 1.3 55.8 - - - +
189A THR* 3.1 7.2 + - - -
190A MLY 2.6 47.1 + - + +
230A GLU* 3.6 23.1 - - + +
234A ASN* 4.6 5.1 + - - +
242A ASN* 4.5 7.4 + - - -
244A SER* 3.7 22.2 + - - +
248A MLY 3.3 31.9 - - - -
463A ASP* 3.8 5.2 + - - -
5000A SO4 2.9 17.7 + - - -
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Residues in contact with VAL 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A TYR* 5.5 6.3 - - + +
184A GLY* 3.3 33.0 - - - +
186A THR* 1.3 78.2 - - - +
188A ASN* 1.3 63.8 + - - +
190A MLY 3.7 16.4 - - - +
191A ARG* 3.0 48.1 + - - +
240A ASN* 5.5 4.5 - - - +
5000A SO4 5.0 0.7 - - - +
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Residues in contact with ASN 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A TYR* 4.4 1.0 + - - -
125A THR* 4.1 14.7 - - - +
135A TYR* 3.9 17.2 + - - -
155A ILE* 3.3 31.0 - - + +
177A ILE* 4.8 7.9 - - + -
183A ALA 5.1 0.2 + - - -
184A GLY 3.1 15.2 + - - -
185A LYS* 2.6 11.6 + - - +
187A VAL* 1.3 75.5 - - - +
189A THR* 1.3 55.3 + - - +
191A ARG* 2.8 7.2 + - - +
192A VAL* 2.6 40.8 + - + +
674A CYS* 2.9 35.5 - - - +
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Residues in contact with THR 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ILE* 4.4 9.9 - - + +
185A LYS* 2.5 27.0 + - - +
186A THR* 3.3 5.4 - - - -
188A ASN* 1.3 72.3 - - - +
190A MLY 1.3 65.1 + - - +
192A VAL* 3.0 10.3 + - - +
193A ILE* 2.9 31.0 + - + +
248A MLY 4.8 15.5 - - - -
250A ILE* 5.0 2.5 - - + -
461A VAL* 3.7 26.5 - - + +
463A ASP* 3.1 35.7 + - + +
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Residues in contact with MLY 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A THR* 2.6 39.4 + - + +
187A VAL* 3.7 15.3 - - - +
189A THR* 1.3 71.4 + - - +
191A ARG* 1.3 100.3 + - - +
193A ILE* 2.8 26.2 + - - +
194A GLN* 2.9 20.8 + - - +
226A ASN* 4.1 30.3 - - + +
227A PRO* 6.1 1.8 - - - -
230A GLU* 2.8 44.0 - - - +
242A ASN* 4.0 8.3 - - - -
248A MLY 4.8 6.0 - - - -
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Residues in contact with ARG 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A TYR* 3.1 48.9 - - + -
155A ILE* 5.8 4.3 - - + -
156A PHE* 4.4 15.3 - - + -
187A VAL* 3.0 36.8 + - - +
188A ASN* 2.8 6.5 + - - +
190A MLY 1.3 114.5 + - - +
192A VAL* 1.3 61.6 + - - +
194A GLN* 3.6 29.5 + - + +
195A TYR* 3.3 18.2 + - - +
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Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ILE* 4.4 27.1 - - + +
156A PHE* 5.9 0.4 - - - -
158A ILE* 6.5 0.7 - - + -
159A SER* 4.0 14.1 - - - -
175A ILE* 4.7 11.4 - - + -
177A ILE* 4.4 14.1 - - + -
188A ASN 2.6 24.6 + - - +
189A THR* 3.0 9.6 + - - +
191A ARG* 1.3 74.2 - - - +
193A ILE* 1.3 62.1 + - + +
195A TYR* 2.8 27.1 - - - +
196A PHE* 3.1 31.5 + - + -
461A VAL* 4.8 9.4 - - + -
672A VAL* 6.4 1.1 - - + -
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Residues in contact with ILE 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A THR* 3.0 19.7 - - + +
190A MLY 2.8 14.0 + - - +
192A VAL* 1.3 78.6 - - + +
194A GLN* 1.3 64.8 + - - +
196A PHE* 3.0 18.1 + - - +
197A ALA* 3.0 11.3 + - - +
222A ILE* 4.0 28.9 - - + +
223A ILE* 5.3 6.7 - - + -
226A ASN* 5.6 8.3 - - - +
248A MLY 5.6 2.2 - - - -
250A ILE* 3.1 38.1 - - + -
252A ILE* 3.9 23.8 - - + -
461A VAL* 4.7 8.3 - - + -
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Residues in contact with GLN 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A MLY 2.9 19.0 + - - +
191A ARG* 3.8 38.1 + - + +
192A VAL 3.3 0.2 - - - -
193A ILE* 1.3 73.5 - - - +
195A TYR* 1.3 53.7 + - - +
197A ALA* 2.9 5.6 + - - +
198A THR* 2.5 42.9 + - + +
223A ILE* 3.2 40.2 - - - +
226A ASN* 6.0 0.3 + - - -
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Residues in contact with TYR 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A VAL* 3.4 37.3 + - + -
143A TYR* 3.9 5.7 + - - +
144A ARG* 4.0 0.9 + - - -
156A PHE* 2.9 41.3 - + + -
159A SER* 2.8 34.3 - - - +
160A ASP* 2.4 33.0 + - + +
191A ARG 3.3 10.0 + - - +
192A VAL* 2.8 17.0 + - - +
194A GLN* 1.3 79.5 - - - +
196A PHE* 1.3 63.3 + + - -
198A THR* 3.0 14.1 + - - -
199A ILE* 3.0 54.0 + - + +
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Residues in contact with PHE 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A SER* 3.1 33.2 - - - -
162A ALA* 4.3 5.4 - - + -
163A TYR* 4.0 15.0 - + + -
175A ILE* 4.2 5.6 - - + -
192A VAL* 3.1 38.1 + - + -
193A ILE* 3.0 8.0 + - - +
195A TYR* 1.3 81.0 - + - +
197A ALA* 1.3 66.4 + - - +
199A ILE* 3.9 11.9 - - + +
200A ALA* 3.2 23.6 + - - +
252A ILE* 4.6 17.7 - - + -
254A PHE* 3.6 29.7 - + + -
260A LEU* 4.7 2.8 - - + +
459A ILE* 3.7 43.3 - - + -
461A VAL* 4.9 2.0 - - + -
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Residues in contact with ALA 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A ILE 3.0 9.8 + - - +
194A GLN* 2.9 12.4 + - - +
196A PHE* 1.3 79.6 - - - +
198A THR* 1.3 65.0 + - + +
201A ALA* 3.2 25.6 + - - +
219A GLU* 4.5 23.8 - - + +
222A ILE* 5.2 6.5 - - + -
223A ILE* 4.9 8.1 - - + -
260A LEU* 3.9 20.2 - - + +
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Residues in contact with THR 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A VAL* 5.1 11.3 - - + +
194A GLN* 2.5 33.1 + - + +
195A TYR* 3.0 12.0 + - - -
197A ALA* 1.3 76.5 - - + +
199A ILE* 1.3 60.9 + - - +
200A ALA 2.8 7.3 + - - -
201A ALA* 3.7 9.7 + - - +
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Residues in contact with ILE 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A VAL* 4.7 9.6 - - + +
144A ARG* 4.5 17.3 + - + +
160A ASP* 4.1 7.4 - - - +
163A TYR* 4.4 22.5 + - + -
195A TYR* 3.0 68.0 + - + +
196A PHE* 4.0 19.1 - - + +
198A THR* 1.3 75.3 - - - +
200A ALA* 1.3 64.6 + - + +
259A LYS* 4.5 5.4 + - - -
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Residues in contact with ALA 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A TYR* 3.1 34.8 - - + +
196A PHE 3.2 11.7 + - - +
197A ALA 3.8 3.6 - - - -
198A THR 2.8 8.1 + - - -
199A ILE* 1.3 81.1 - - + +
201A ALA* 1.3 56.2 + - - +
254A PHE* 4.4 5.6 - - + -
258A GLY 3.6 7.4 - - - +
259A LYS* 3.7 14.6 - - - +
260A LEU* 3.1 28.9 + - - +
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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