Contacts of the helix formed by residues 187 - 204 (chain A) in PDB entry 4K8T
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 ASP 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ALA 4.4 2.4 - - - +
32A ALA* 3.5 10.2 - - - +
33A MSE 3.0 34.4 + - - +
123A ARG* 5.5 2.1 + - - +
156A TYR* 3.6 20.7 + - + +
185A LEU 2.8 8.3 + - - +
186A SER* 1.3 77.7 - - - +
188A SER* 1.3 60.2 + - - +
189A PHE* 2.9 35.3 + - - +
190A CYS* 3.1 13.3 + - + +
191A VAL* 2.9 26.3 + - - +
193A ARG* 5.1 0.5 + - - -
216A GLU* 3.2 10.5 + - - -
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Residues in contact with SER 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ASP* 1.3 75.3 + - - +
189A PHE* 1.3 79.7 + - - +
191A VAL* 3.4 2.2 + - - +
192A ASP* 3.0 24.8 + - - -
215A GLN* 4.0 32.8 - - - +
216A GLU* 3.8 10.2 - - - +
219A SER* 3.1 21.4 + - - -
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Residues in contact with PHE 189 (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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29A THR* 4.0 21.3 - - + -
30A LYS 5.7 0.4 - - - -
32A ALA* 3.9 26.9 - - + -
33A MSE 5.4 3.4 - - - +
187A ASP* 2.9 13.6 + - - +
188A SER* 1.3 87.0 - - - +
190A CYS* 1.3 69.0 + - - +
191A VAL 3.1 1.1 - - - -
192A ASP* 3.2 24.3 + - + +
193A ARG* 2.9 40.1 + - - +
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Residues in contact with CYS 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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155A GLY* 3.4 35.2 - - - -
156A TYR* 3.8 13.5 - - + -
159A ASP* 4.5 0.7 - - - -
185A LEU 4.2 4.7 - - - +
187A ASP* 3.1 28.3 + - + +
189A PHE* 1.3 76.7 - - - +
191A VAL* 1.3 61.1 + - - +
193A ARG* 3.0 34.0 + - - +
194A TYR* 3.1 29.9 + - - +
198A PHE* 3.9 9.9 - - - -
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Residues in contact with VAL 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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185A LEU* 3.6 33.4 - - + +
187A ASP 2.9 19.3 + - - +
188A SER 3.5 8.1 - - - +
190A CYS* 1.3 73.2 - - - +
192A ASP* 1.3 59.1 + - - +
195A ARG* 2.8 36.3 + - + +
198A PHE* 4.0 14.4 - - + -
216A GLU* 4.3 10.5 - - + +
219A SER* 3.5 9.2 - - - +
220A LEU* 3.4 46.2 - - + +
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Residues in contact with ASP 192 (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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188A SER* 3.0 15.9 + - - +
189A PHE* 3.2 34.8 - - + +
191A VAL* 1.3 74.8 - - - +
193A ARG* 1.3 62.7 + - + +
194A TYR 3.5 0.2 + - - -
195A ARG* 2.9 45.0 + - - +
219A SER* 3.2 7.6 + - - -
222A GLN* 5.5 0.2 + - - -
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Residues in contact with ARG 193 (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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33A MSE 3.7 23.8 + - - +
35A LEU* 4.1 8.7 - - - +
159A ASP* 2.8 41.5 + - - -
187A ASP* 5.1 0.6 + - - -
189A PHE* 2.9 33.3 + - - +
190A CYS* 3.0 27.9 + - - +
192A ASP* 1.3 79.5 - - + +
194A TYR* 1.3 81.9 + - + +
195A ARG 3.7 0.4 - - - -
197A GLU* 4.3 2.8 - - - +
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Residues in contact with TYR 194 (chain A).
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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158A TRP* 3.2 55.0 + + + -
159A ASP* 2.7 34.6 + - - -
164A LYS* 5.5 2.9 - - - -
190A CYS* 3.1 30.9 + - - -
191A VAL 3.5 2.0 - - - -
193A ARG* 1.3 104.4 + - + +
195A ARG* 1.3 64.8 + - - +
197A GLU* 3.0 24.7 + - - +
198A PHE* 2.9 43.3 + - + -
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Residues in contact with ARG 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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191A VAL* 2.8 22.9 + - + +
192A ASP* 2.9 48.7 + - - +
193A ARG 3.7 1.6 - - - -
194A TYR* 1.3 71.2 - - - +
196A GLY* 1.3 62.7 + - - +
198A PHE* 3.4 4.5 + - - +
199A LEU* 3.0 40.4 + - + +
219A SER* 2.9 35.1 + - - +
220A LEU* 3.4 22.1 - - + +
222A GLN* 3.4 43.3 - - - +
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Residues in contact with GLY 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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194A TYR 3.4 0.6 - - - -
195A ARG* 1.3 79.6 - - - +
197A GLU* 1.3 65.5 + - - +
199A LEU* 3.6 7.2 + - - +
200A ASP* 3.1 24.0 + - - +
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Residues in contact with GLU 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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158A TRP* 3.5 29.2 - - + +
164A LYS* 4.6 9.9 + - - +
193A ARG 4.3 2.6 - - - +
194A TYR* 3.0 37.5 + - - +
196A GLY* 1.3 74.7 + - - +
198A PHE* 1.3 66.7 + - - +
200A ASP* 3.4 8.3 + - - +
201A LEU* 3.0 28.3 + - - +
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Residues in contact with PHE 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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155A GLY* 3.4 34.8 - - - -
158A TRP* 3.9 18.8 - + - -
183A MSE 4.0 15.3 - - + +
185A LEU* 3.9 41.3 - - + -
190A CYS* 3.9 7.2 - - - -
191A VAL* 4.0 29.8 - - + -
194A TYR* 2.9 36.6 + - + +
195A ARG 3.8 3.6 - - - +
197A GLU* 1.3 79.3 - - + +
199A LEU* 1.3 62.4 + - - +
201A LEU* 3.2 16.0 + - + +
202A MSE 3.1 26.9 + - - +
220A LEU* 4.6 6.1 - - + -
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Residues in contact with LEU 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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195A ARG* 3.0 42.1 + - + +
196A GLY* 4.0 6.3 - - - +
198A PHE* 1.3 76.6 - - - +
200A ASP* 1.3 57.0 + - - +
202A MSE 3.2 9.8 + - - +
203A ARG* 2.8 58.7 + - - +
220A LEU* 3.7 24.0 - - + +
221A TYR* 3.6 32.1 - - + +
232A ARG* 5.9 1.3 - - - +
236A ASP* 3.8 13.2 - - - +
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Residues in contact with ASP 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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196A GLY 3.1 19.3 + - - +
197A GLU* 3.6 8.2 - - - +
198A PHE 3.2 0.2 - - - -
199A LEU* 1.3 72.5 - - - +
201A LEU* 1.3 69.2 + - - +
203A ARG* 4.8 4.6 - - - +
204A SER* 2.9 39.6 + - - -
206A LYS* 5.3 5.7 + - - +
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Residues in contact with LEU 201 (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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153A PHE* 4.1 7.9 - - + -
158A TRP* 3.7 35.4 - - + -
167A ILE* 5.2 2.2 - - + -
168A LEU* 4.3 14.6 - - + -
183A MSE 4.0 22.0 - - - -
197A GLU 3.0 19.6 + - - +
198A PHE* 3.3 16.6 - - + +
200A ASP* 1.3 79.9 - - - +
202A MSE 1.3 59.1 + - - +
204A SER* 3.4 5.5 + - - -
206A LYS* 3.2 36.5 + - + -
207A VAL* 3.1 36.9 + - + -
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Residues in contact with MSE 202 (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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183A MSE 5.2 2.9 - - - +
185A LEU* 5.0 6.1 - - - -
198A PHE 3.1 21.0 + - - +
199A LEU* 3.5 11.7 - - - +
200A ASP 3.2 0.2 - - - -
201A LEU* 1.3 78.5 - - + +
203A ARG* 1.3 63.1 + - - +
205A GLY* 3.4 10.4 + - - -
207A VAL* 3.9 20.1 - - + +
210A VAL* 3.6 41.3 - - + -
220A LEU* 4.2 16.8 - - + -
221A TYR* 4.2 2.9 - - - +
233A ILE* 3.6 30.5 - - + -
236A ASP* 3.2 37.1 - - + +
237A CYS* 3.9 12.0 - - + -
238A LYS* 5.6 0.7 + - - -
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Residues in contact with ARG 203 (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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199A LEU* 2.8 46.8 + - - +
200A ASP* 4.4 4.5 - - - +
202A MSE 1.3 78.1 - - - +
204A SER* 1.3 59.0 + - - +
205A GLY* 3.5 0.5 + - - -
232A ARG* 4.2 19.0 - - - +
236A ASP* 2.9 48.3 + - + +
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Residues in contact with SER 204 (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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200A ASP* 2.9 32.5 + - - -
201A LEU 3.4 2.4 + - - -
203A ARG* 1.3 75.4 - - - +
205A GLY* 1.3 58.2 + - - +
206A LYS* 3.4 41.6 + - - +
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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