Contacts of the helix formed by residues 152 - 170 (chain D) in PDB entry 3K75
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 ARG 152 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150D ILE 3.6 0.2 + - - -
151D PRO* 1.3 69.4 - - - +
153D GLU* 1.3 61.3 + - + +
155D MET* 3.3 9.3 - - - +
156D LEU* 2.8 45.8 + - + +
181D PHE* 3.0 55.4 + - + -
182D ARG 5.5 0.8 + - - -
184D GLY* 3.4 15.8 - - - -
185D ALA 3.1 24.5 + - - +
186D GLU* 2.8 38.7 + - - +
187D SER* 5.0 0.4 - - - +
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Residues in contact with GLU 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D PRO* 3.2 11.4 - - + +
152D ARG* 1.3 79.6 - - + +
154D GLU* 1.3 63.5 + - + +
156D LEU* 3.3 13.6 + - + +
157D GLN* 3.1 33.8 + - - +
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Residues in contact with GLU 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D ILE* 4.0 7.6 - - + -
151D PRO* 3.0 31.2 + - + +
153D GLU* 1.3 77.4 - - + +
155D MET* 1.3 66.3 + - - +
157D GLN* 3.1 7.1 + - - +
158D MET* 2.8 29.6 + - - +
241D LEU* 3.6 20.5 - - + +
250D TYR* 3.3 36.5 - - + +
251D PRO* 4.9 1.7 - - - +
253D ARG* 2.9 36.2 + - - -
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Residues in contact with MET 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D ILE* 3.3 26.5 - - + +
151D PRO 3.0 17.4 + - - +
152D ARG* 3.3 13.5 - - - +
154D GLU* 1.3 77.8 - - - +
156D LEU* 1.3 52.6 + - - +
158D MET* 2.9 15.6 + - - +
159D GLN* 2.7 35.6 + - - +
177D VAL* 4.3 4.3 - - + -
178D CYS 5.6 0.2 - - - +
181D PHE* 3.6 34.3 - - + -
188D SER* 3.4 35.0 - - - +
190D ASP 4.3 0.7 - - - +
191D MET* 3.7 37.2 - - + +
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Residues in contact with LEU 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ARG* 2.8 39.1 + - + +
153D GLU* 3.5 16.8 - - + +
155D MET* 1.3 73.1 - - - +
157D GLN* 1.3 62.8 + - + +
159D GLN* 3.0 23.0 + - - +
160D ASP* 2.9 34.3 + - - +
181D PHE* 4.2 15.3 - - + -
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Residues in contact with GLN 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D GLU* 3.1 26.8 + - - +
154D GLU* 3.1 9.1 + - - +
156D LEU* 1.3 75.7 - - + +
158D MET* 1.3 63.0 + - - +
160D ASP* 3.2 11.9 + - - +
161D ILE* 3.2 25.2 + - + +
241D LEU* 3.4 30.9 - - + +
242D PRO* 5.5 1.8 + - - +
250D TYR* 3.6 26.8 + - - -
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Residues in contact with MET 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D ILE* 4.3 18.2 - - + -
154D GLU* 2.8 22.1 + - - +
155D MET* 3.1 28.0 - - - +
157D GLN* 1.3 74.8 - - - +
159D GLN* 1.3 67.2 + - - +
160D ASP 3.1 0.9 + - - -
161D ILE* 3.1 12.6 + - - +
162D VAL* 3.1 16.2 + - - +
191D MET* 3.3 41.1 - - + -
223D PHE* 3.8 22.2 - - + -
239D CYS* 5.0 4.5 - - - -
241D LEU* 3.9 25.1 - - + +
253D ARG* 4.4 18.2 - - + -
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Residues in contact with GLN 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D MET 2.7 16.4 + - - +
156D LEU* 3.0 20.5 + - - +
158D MET* 1.3 72.3 - - - +
160D ASP* 1.3 67.8 + - - +
162D VAL* 3.4 2.9 + - - +
163D LEU* 2.8 54.5 + - + +
176D THR* 5.9 0.2 - - - -
177D VAL* 3.9 25.4 + - + +
181D PHE* 3.7 30.7 - - + -
191D MET* 3.6 8.0 - - + +
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Residues in contact with ASP 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D LEU* 2.9 23.4 + - - +
157D GLN* 3.5 10.0 - - - +
159D GLN* 1.3 86.2 + - - +
161D ILE* 1.3 67.9 + - + +
163D LEU* 3.8 3.8 - - - -
164D ASN* 2.8 38.6 + - - +
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Residues in contact with ILE 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D GLN* 3.3 9.6 - - + +
158D MET* 3.1 5.3 + - - +
160D ASP* 1.3 78.3 - - + +
162D VAL* 1.3 66.6 + - - +
164D ASN* 3.7 3.9 - - - +
165D GLU* 3.3 27.6 + - + +
218D LEU* 4.7 1.6 - - + -
221D VAL* 4.7 12.6 - - + +
223D PHE* 3.5 44.9 - - + -
241D LEU* 3.5 32.5 - - + -
242D PRO* 4.0 16.6 - - + -
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Residues in contact with VAL 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D MET 3.1 8.6 + - - +
159D GLN* 3.7 8.1 - - - +
161D ILE* 1.3 78.2 - - - +
163D LEU* 1.3 72.4 + - + +
164D ASN 3.1 1.4 + - - -
165D GLU* 3.4 1.6 + - - +
166D VAL* 2.9 38.0 + - + +
175D ALA* 4.9 0.4 - - + -
177D VAL* 5.8 1.6 - - + -
191D MET* 4.3 13.7 - - - -
193D VAL* 4.4 25.4 - - + -
214D VAL* 5.8 0.7 - - + -
218D LEU* 4.2 17.7 - - + +
223D PHE* 3.4 32.5 - - + -
255D ILE* 4.5 6.1 - - + -
257D ILE* 5.8 2.0 - - + -
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Residues in contact with LEU 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D GLN* 2.8 50.3 + - + +
160D ASP* 4.2 3.4 - - - +
162D VAL* 1.3 79.0 - - + +
164D ASN* 1.3 62.3 + - - +
166D VAL* 3.9 3.7 - - + +
167D LYS* 3.1 22.7 + - - +
175D ALA* 3.0 48.0 - - + +
176D THR* 5.2 0.2 - - - -
177D VAL* 5.5 4.7 - - + +
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Residues in contact with ASN 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D ASP* 2.8 35.1 + - - +
161D ILE* 3.7 4.5 - - - +
163D LEU* 1.3 74.3 - - - +
165D GLU* 1.3 73.7 + - - +
166D VAL 3.1 1.3 - - - -
167D LYS* 2.8 8.3 + - - +
168D LYS* 2.8 38.1 + - + +
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Residues in contact with GLU 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D ILE* 3.3 19.8 + - + +
162D VAL 3.9 2.2 - - - +
164D ASN* 1.3 83.2 - - - +
166D VAL* 1.3 58.8 + - + +
168D LYS* 3.5 31.8 + - - +
169D LEU* 2.9 35.3 + - - +
214D VAL* 6.0 0.4 - - + +
217D GLN* 3.4 25.1 + - + +
218D LEU* 4.1 22.2 - - + -
221D VAL* 3.4 37.0 - - + +
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Residues in contact with VAL 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D VAL* 2.9 31.6 + - + +
163D LEU* 3.9 7.2 - - + +
164D ASN 3.1 0.4 - - - -
165D GLU* 1.3 78.7 - - + +
167D LYS* 1.3 58.3 + - - +
169D LEU* 4.4 5.6 - - - -
170D ASP 2.9 24.3 + - - +
173D TYR* 3.3 40.7 - - + -
175D ALA* 4.5 10.1 - - + +
195D LEU* 3.9 16.8 - - + -
214D VAL* 3.8 25.6 - - + -
218D LEU* 5.6 0.7 - - + -
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Residues in contact with LYS 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D LEU 3.1 18.5 + - - +
164D ASN* 2.8 7.5 + - - +
166D VAL* 1.3 75.2 - - - +
168D LYS* 1.3 65.6 + - + +
169D LEU 3.4 0.2 + - - -
170D ASP 4.1 3.4 - - - -
171D PRO* 3.5 30.7 - - + +
173D TYR* 5.5 1.1 - - - -
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Residues in contact with LYS 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D ASN* 2.8 27.2 + - + +
165D GLU* 3.5 37.0 + - - +
167D LYS* 1.3 75.8 - - + +
169D LEU* 1.3 65.9 + - - +
170D ASP* 4.7 0.2 - - - -
221D VAL* 5.9 0.4 - - - +
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Residues in contact with LEU 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D GLU 2.9 17.6 + - - +
166D VAL* 3.8 5.6 - - - +
167D LYS 3.2 0.2 - - - -
168D LYS* 1.3 81.4 - - - +
170D ASP* 1.3 60.7 + - - +
173D TYR* 4.3 2.9 - - + -
213D ARG* 3.1 81.7 + - + +
214D VAL* 3.8 16.4 - - + -
217D GLN* 3.7 32.1 - - + +
220D LYS* 5.7 0.9 - - - +
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Residues in contact with ASP 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D VAL 2.9 15.3 + - - +
167D LYS* 3.5 2.9 - - - -
169D LEU* 1.3 82.2 - - - +
171D PRO* 1.3 97.1 - - - +
172D GLU* 3.0 15.1 + - - +
173D TYR* 3.2 20.6 - - + +
197D HIS* 2.7 30.6 + - - -
210D LEU* 5.8 0.3 - - - +
213D ARG* 3.7 16.7 + - - +
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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