Contacts of the helix formed by residues 175 - 193 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A THR 5.5 1.3 - - - +
174A LEU* 1.3 78.4 - - - +
176A LEU* 1.3 63.8 + - - +
177A GLU* 3.5 7.6 + - - +
178A GLU* 3.2 38.2 + - - +
179A ARG* 3.0 22.3 + - - +
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Residues in contact with LEU 176 (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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175A THR* 1.3 74.5 - - - +
177A GLU* 1.3 63.0 + - - +
179A ARG* 3.5 5.5 + - - +
180A VAL* 3.3 27.2 + - - +
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Residues in contact with GLU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A THR* 3.3 7.0 + - - +
176A LEU* 1.3 79.9 - - - +
178A GLU* 1.3 62.8 + - + +
180A VAL* 3.3 9.4 + - - +
181A HIS* 3.2 20.7 + - - +
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Residues in contact with GLU 178 (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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144A GLY* 6.0 1.0 - - - -
173A THR 4.7 1.6 - - - +
174A LEU* 3.6 24.1 - - + +
175A THR* 3.2 40.3 + - - +
177A GLU* 1.3 75.1 - - + +
179A ARG* 1.3 61.0 + - - +
181A HIS* 3.3 7.5 + - - +
182A PHE* 2.8 32.3 + - - +
301B GSP 2.4 41.0 + - - +
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Residues in contact with ARG 179 (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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168A ILE* 4.8 5.1 - - + +
171A ALA* 5.7 4.5 - - + +
174A LEU* 4.3 17.4 - - + +
175A THR 3.0 18.7 + - - +
176A LEU* 3.8 7.6 - - - +
177A GLU 3.3 0.2 - - - -
178A GLU* 1.3 75.8 - - - +
180A VAL* 1.3 57.5 + - + +
182A PHE* 3.8 1.4 - - - +
183A LYS* 3.0 41.2 + - + +
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Residues in contact with VAL 180 (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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176A LEU 3.3 16.2 - - - +
177A GLU* 3.3 9.6 + - - +
178A GLU 3.2 0.4 - - - -
179A ARG* 1.3 79.7 - - + +
181A HIS* 1.3 60.4 + - - +
183A LYS* 3.8 7.0 - - + +
184A GLN* 3.1 44.3 + - + +
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Residues in contact with HIS 181 (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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144A GLY 4.2 13.9 + - - -
145A HIS* 6.0 0.2 - - - -
177A GLU 3.2 11.0 + - - +
178A GLU* 3.7 10.1 - - - +
180A VAL* 1.3 79.1 - - - +
182A PHE* 1.3 63.7 + - - +
184A GLN* 3.5 15.2 + - - +
185A ARG* 3.2 28.5 + - + +
60B ARG* 3.1 49.8 + - + -
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Residues in contact with PHE 182 (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 ILE* 3.8 11.2 - - + -
141A PRO 3.6 24.7 - - - -
142A ALA* 4.1 4.5 - - - -
143A THR* 4.3 2.2 - - - -
144A GLY* 3.7 26.5 - - - -
145A HIS 3.1 27.8 - - - -
168A ILE* 3.6 40.8 - - + -
174A LEU* 3.9 18.8 - - + -
178A GLU 2.8 17.5 + - - +
179A ARG 3.8 3.8 - - - +
181A HIS* 1.3 77.6 - - + +
183A LYS* 1.3 59.8 + - - +
185A ARG* 3.1 5.1 + - + +
186A ILE* 2.9 54.1 + - + +
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Residues in contact with LYS 183 (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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168A ILE* 3.8 13.2 - - + -
179A ARG* 3.0 25.3 + - + +
180A VAL* 3.8 7.6 - - - +
181A HIS 3.4 0.2 - - - -
182A PHE* 1.3 77.5 - - - +
184A GLN* 1.3 56.9 + - + +
186A ILE 3.5 0.2 + - - -
187A THR* 2.7 34.9 + - - -
218A GLU 4.7 7.9 + - - +
219A MET* 3.5 15.9 + - - +
220A ILE 4.9 2.0 - - - +
221A PRO* 3.2 37.7 - - + +
223A ALA* 4.4 10.3 - - - +
257A GLU* 2.4 42.0 + - - -
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Residues in contact with GLN 184 (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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180A VAL* 3.1 35.2 + - + +
181A HIS* 3.7 16.1 + - - +
182A PHE 3.3 0.2 - - - -
183A LYS* 1.3 78.7 - - + +
185A ARG* 1.3 60.7 + - - +
187A THR* 3.7 7.5 - - - -
188A ALA* 3.4 19.8 + - - +
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Residues in contact with ARG 185 (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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145A HIS* 4.2 6.5 - - - +
146A SER* 3.3 43.9 - - - +
147A LEU 5.1 0.2 - - - +
181A HIS* 3.2 20.5 + - + +
182A PHE* 3.1 11.5 + - + +
184A GLN* 1.3 77.8 - - - +
186A ILE* 1.3 65.4 + - - +
188A ALA* 3.2 21.8 + - - +
189A ASP* 2.8 38.3 + - - +
192A SER* 5.1 0.8 + - - -
60B ARG* 5.9 4.3 - - - +
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Residues in contact with ILE 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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140A ILE* 3.7 20.0 - - + -
145A HIS 4.6 4.0 - - - +
147A LEU* 3.7 31.2 - - + +
182A PHE* 2.9 55.6 + - + +
185A ARG* 1.3 76.7 - - - +
187A THR* 1.3 62.7 + - - +
189A ASP* 3.1 7.0 + - - +
190A LEU* 3.1 36.9 + - + +
221A PRO* 3.6 35.2 - - + -
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Residues in contact with THR 187 (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 LYS 2.7 22.8 + - - -
184A GLN* 3.7 8.8 - - - -
186A ILE* 1.3 78.8 - - - +
188A ALA* 1.3 60.5 + - - +
190A LEU* 3.4 9.6 + - - +
191A LEU* 3.1 45.3 + - + +
217A ARG 5.5 2.6 + - - +
220A ILE* 3.6 18.2 + - - +
221A PRO* 4.8 0.4 - - - +
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Residues in contact with ALA 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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184A GLN 3.4 10.5 + - - +
185A ARG* 3.2 24.7 + - - +
187A THR* 1.3 80.1 - - - +
189A ASP* 1.3 52.1 + - - +
191A LEU* 3.5 8.6 + - - +
192A SER* 2.8 39.4 + - - -
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Residues in contact with ASP 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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146A SER* 3.9 0.6 - - - -
147A LEU* 2.7 60.5 + - + +
152A ILE* 4.9 3.9 - - - +
185A ARG* 2.8 43.3 + - - +
186A ILE* 3.1 6.3 + - - +
188A ALA* 1.3 74.5 - - - +
190A LEU* 1.3 57.8 + - - +
192A SER* 3.3 5.9 + - - -
193A ASN* 2.8 52.2 + - - +
195A ILE* 5.1 0.7 - - - -
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Residues in contact with LEU 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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147A LEU* 4.4 5.6 - - + -
155A MET* 4.1 21.1 - - + -
166A PRO* 3.8 24.0 - - + -
186A ILE* 3.1 24.1 + - + +
187A THR* 3.4 8.9 + - - +
189A ASP* 1.3 73.9 - - - +
191A LEU* 1.3 64.3 - - + +
194A GLY 3.1 1.7 + - - -
195A ILE* 2.7 74.9 + - + +
197A VAL* 4.1 12.1 - - + -
220A ILE* 4.0 15.3 - - + -
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Residues in contact with LEU 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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187A THR* 3.1 33.9 + - + +
188A ALA* 3.7 7.2 - - - +
190A LEU* 1.3 79.0 - - + +
192A SER* 1.3 63.7 + - - +
194A GLY* 3.3 12.3 + - - -
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Residues in contact with SER 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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185A ARG* 5.1 1.0 + - - -
188A ALA* 2.8 28.1 + - - -
189A ASP* 3.2 14.4 + - - -
191A LEU* 1.3 72.9 - - - +
193A ASN* 1.3 67.9 + - - +
194A GLY 3.2 0.6 + - - -
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Residues in contact with ASN 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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152A ILE* 3.3 42.8 - - + +
156A LYS* 3.7 26.1 + - + +
189A ASP* 2.8 39.1 + - - +
192A SER* 1.3 82.0 + - - +
194A GLY* 1.3 63.1 + - - +
195A ILE* 3.2 16.2 + - + -
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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