Contacts of the helix formed by residues 175 - 193 (chain D) in PDB entry 5CYP
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 THR 175 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173D THR 5.4 1.1 - - - +
174D LEU* 1.3 77.2 - - - +
176D LEU* 1.3 59.9 + - - +
177D GLU* 3.5 8.1 + - - +
178D GLU* 3.1 39.1 + - - +
179D ARG* 2.9 30.7 + - - +
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Residues in contact with LEU 176 (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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175D THR* 1.3 74.6 - - - +
177D GLU* 1.3 62.5 + - - +
179D ARG* 3.4 18.4 + - - +
180D VAL* 3.2 29.8 + - + +
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Residues in contact with GLU 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D THR* 3.3 7.5 + - - +
176D LEU* 1.3 81.3 - - - +
178D GLU* 1.3 62.3 + - + +
180D VAL* 3.4 7.7 + - - +
181D HIS* 3.3 21.1 + - - +
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Residues in contact with GLU 178 (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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301C GSP 2.3 42.4 + - - +
144D GLY* 5.9 1.5 - - - -
173D THR 4.3 2.3 - - - +
174D LEU* 3.4 25.9 - - + +
175D THR* 3.1 41.6 + - - +
177D GLU* 1.3 77.4 - - + +
179D ARG* 1.3 57.8 + - - +
181D HIS* 3.5 7.4 + - - +
182D PHE* 2.9 30.2 + - - +
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Residues in contact with ARG 179 (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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168D ILE* 4.7 4.7 - - + +
171D ALA* 2.6 36.5 + - - +
172D ASP* 4.5 2.6 - - - +
174D LEU* 3.6 17.3 + - + +
175D THR 2.9 18.3 + - - +
176D LEU* 3.7 25.9 - - - +
177D GLU 3.2 0.2 - - - -
178D GLU* 1.3 75.5 - - - +
180D VAL* 1.3 62.9 + - + +
182D PHE* 3.3 6.7 + - - +
183D LYS* 2.9 46.8 + - + +
223D ALA* 3.8 25.9 - - + +
256D CYS* 4.4 18.8 - - - -
257D GLU* 5.1 4.3 - - - -
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Residues in contact with VAL 180 (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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176D LEU* 3.2 16.9 + - + +
177D GLU* 3.8 8.3 - - - +
178D GLU 3.4 0.4 - - - -
179D ARG* 1.3 79.7 - - + +
181D HIS* 1.3 58.2 + - - +
183D LYS* 3.4 8.2 + - - +
184D GLN* 3.0 28.9 + - + +
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Residues in contact with HIS 181 (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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60C ARG* 3.3 47.1 + - + -
144D GLY 4.3 12.3 + - - -
177D GLU 3.3 11.2 + - - +
178D GLU* 3.9 9.4 - - - +
180D VAL* 1.3 76.9 - - - +
182D PHE* 1.3 63.8 + - - +
184D GLN* 3.4 8.3 + - + +
185D ARG* 3.0 45.5 + - + +
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Residues in contact with PHE 182 (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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140D ILE* 3.9 8.3 - - + -
141D PRO 3.4 21.3 - - - -
142D ALA* 3.8 11.0 - - - -
143D THR* 4.3 2.0 - - - -
144D GLY* 3.7 24.9 - - - -
145D HIS 3.4 24.7 - - - -
168D ILE* 3.5 43.1 - - + -
174D LEU* 3.7 18.4 - - + -
178D GLU 2.9 18.8 + - - +
179D ARG 3.6 4.5 - - - +
180D VAL 3.2 0.2 - - - -
181D HIS* 1.3 77.9 - + + +
183D LYS* 1.3 60.0 + - - +
185D ARG* 3.3 4.2 + - + -
186D ILE* 2.9 55.3 + - + +
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Residues in contact with LYS 183 (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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168D ILE* 3.8 7.6 - - + +
179D ARG* 2.9 30.3 + - + +
180D VAL* 3.7 6.7 - - - +
182D PHE* 1.3 77.4 - - - +
184D GLN* 1.3 53.6 + - - +
187D THR* 2.5 39.6 + - - +
218D GLU 4.8 8.1 - - - +
219D MET* 3.3 19.3 - - - +
220D ILE 4.8 1.6 - - - +
221D PRO* 3.1 42.8 + - + +
223D ALA* 3.4 18.2 - - - +
257D GLU* 3.3 27.1 + - - -
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Residues in contact with GLN 184 (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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180D VAL* 3.0 19.0 + - + +
181D HIS* 3.6 10.5 - - - +
182D PHE 3.3 0.2 - - - -
183D LYS* 1.3 76.8 - - - +
185D ARG* 1.3 60.7 + - - +
187D THR* 3.7 5.6 + - - -
188D ALA* 3.3 21.7 + - - +
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Residues in contact with ARG 185 (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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60C ARG* 5.6 4.8 - - - +
63C LYS* 6.1 0.2 - - - +
145D HIS* 4.4 6.5 - - - +
146D SER* 3.2 44.4 - - - +
181D HIS* 3.0 35.5 + - + +
182D PHE* 3.8 5.4 - - + +
184D GLN* 1.3 75.1 - - - +
186D ILE* 1.3 66.6 + - + +
188D ALA* 3.3 10.8 + - - +
189D ASP* 2.2 63.7 + - - +
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Residues in contact with ILE 186 (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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140D ILE* 3.7 20.2 - - + -
145D HIS 4.4 7.2 - - - +
147D LEU* 3.6 33.4 - - + +
182D PHE* 2.9 53.6 + - + +
183D LYS 4.0 0.2 - - - +
185D ARG* 1.3 76.5 - - - +
187D THR* 1.3 62.4 + - - +
189D ASP* 3.1 5.5 + - - +
190D LEU* 2.9 37.2 + - + +
221D PRO* 3.7 31.9 - - + -
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Residues in contact with THR 187 (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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183D LYS* 2.5 23.5 + - - +
184D GLN* 3.7 8.0 - - - -
186D ILE* 1.3 78.6 - - - +
188D ALA* 1.3 61.5 + - - +
190D LEU* 3.4 11.3 + - - +
191D LEU* 3.2 43.1 + - + +
217D ARG 5.8 2.9 - - - +
220D ILE* 3.5 19.6 + - - +
221D PRO* 5.3 0.2 - - - -
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Residues in contact with ALA 188 (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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184D GLN 3.3 11.6 + - - +
185D ARG* 3.6 19.3 - - - +
186D ILE 3.3 0.6 - - - -
187D THR* 1.3 78.8 - - - +
189D ASP* 1.3 58.7 + - - +
191D LEU* 3.4 10.3 + - - +
192D SER* 2.9 31.7 + - - -
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Residues in contact with ASP 189 (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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146D SER* 3.4 6.4 - - - -
147D LEU* 2.9 48.2 + - + +
152D ILE* 5.7 2.0 - - - -
185D ARG* 2.2 51.6 + - - +
186D ILE* 3.1 7.9 + - - +
188D ALA* 1.3 73.6 - - - +
190D LEU* 1.3 65.9 + - - +
192D SER* 3.0 20.5 + - - -
193D ASN* 3.0 26.9 + - - +
195D ILE* 5.4 0.4 - - - -
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Residues in contact with LEU 190 (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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147D LEU* 4.0 14.6 - - + -
155D MET* 3.6 27.1 - - + -
166D PRO* 3.8 23.8 - - + -
186D ILE* 2.9 30.9 + - + +
187D THR* 3.7 7.9 - - - +
188D ALA 3.4 0.2 - - - -
189D ASP* 1.3 77.6 - - - +
191D LEU* 1.3 62.5 - - + +
193D ASN 3.6 0.2 + - - -
194D GLY* 3.1 2.8 + - - -
195D ILE* 2.9 59.1 + - + +
197D VAL* 4.1 10.3 - - + -
220D ILE* 4.1 15.9 - - + -
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Residues in contact with LEU 191 (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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187D THR* 3.2 29.7 + - + +
188D ALA* 3.6 9.9 - - - +
190D LEU* 1.3 79.6 - - + +
192D SER* 1.3 61.2 + - - +
194D GLY* 3.2 13.5 + - - -
195D ILE 6.1 0.4 - - - +
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Residues in contact with SER 192 (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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188D ALA 2.9 13.7 + - - -
189D ASP* 3.0 23.6 + - - -
191D LEU* 1.3 78.0 - - - +
193D ASN* 1.3 64.8 + - - +
194D GLY 3.3 0.6 + - - -
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Residues in contact with ASN 193 (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 ILE* 3.3 44.5 - - + +
156D LYS* 5.5 4.0 - - + +
189D ASP* 3.0 31.7 + - - +
192D SER* 1.3 83.3 + - - +
194D GLY* 1.3 63.9 + - - +
195D ILE* 3.2 21.3 + - + +
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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