Contacts of the helix formed by residues 202 - 218 (chain A) in PDB entry 5C6P
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 CYS 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A MET* 3.5 42.2 - - + -
48A ALA* 4.2 12.1 - - - -
56A VAL* 3.6 35.4 - - + -
145A LEU* 5.4 1.1 - - + -
185A TYR* 4.7 3.3 - - + -
199A GLY 5.2 0.2 - - - -
200A ALA* 2.4 36.6 + - - -
201A GLY 1.3 65.4 - - - -
203A GLY* 1.3 54.7 + - - +
205A ALA 2.3 8.5 + - - -
206A THR* 2.3 40.5 + - + -
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Residues in contact with GLY 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 3.1 14.9 - - - +
145A LEU* 2.9 49.1 + - - +
200A ALA 2.9 6.9 + - - -
202A CYS* 1.3 79.6 - - - +
204A VAL* 1.3 54.3 + - - -
206A THR* 3.3 3.2 + - - -
207A MET* 3.0 22.7 - - - +
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Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 3.3 16.8 - - + +
144A SER* 3.3 31.9 - - - +
188A VAL* 3.3 35.7 - - + +
198A GLY* 5.1 4.5 - - - +
201A GLY* 3.5 18.6 - - - -
203A GLY* 1.3 75.5 - - - +
205A ALA* 1.3 63.6 + - - +
207A MET* 3.5 7.6 - - - +
208A ALA* 3.5 17.7 + - - +
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Residues in contact with ALA 205 (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 ASN* 2.8 34.8 + - - +
185A TYR* 3.5 12.6 - - + -
188A VAL* 4.5 3.4 - - + -
201A GLY* 2.8 27.4 - - - +
202A CYS 2.3 18.6 + - - +
204A VAL* 1.3 74.1 - - + +
206A THR* 1.3 65.8 + - - +
208A ALA* 2.9 22.2 - - - +
209A VAL* 3.4 3.3 - - - +
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Residues in contact with THR 206 (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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40A VAL* 4.7 8.5 - - + -
41A ASP* 6.4 0.4 - - - -
44A MET* 3.3 42.8 - - + +
145A LEU* 4.3 9.4 + - + +
177A PHE* 5.4 1.6 - - - -
181A VAL* 4.2 6.3 - - - -
202A CYS* 2.3 32.6 + - + +
203A GLY* 3.3 13.0 + - - +
205A ALA* 1.3 66.9 - - - +
207A MET* 1.3 63.6 + - - +
209A VAL* 2.7 29.5 + - - +
210A PHE* 3.4 15.1 + - - +
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Residues in contact with MET 207 (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 SER* 3.1 16.8 - - - +
145A LEU* 4.5 1.3 - - - -
147A MET* 4.0 7.9 - - - -
148A PRO* 3.2 46.8 - - + +
203A GLY 3.0 17.5 + - - +
204A VAL* 3.5 10.5 - - - +
205A ALA 3.2 0.4 - - - -
206A THR* 1.3 82.0 + - - +
208A ALA* 1.3 87.7 + - + +
210A PHE* 3.2 10.2 + - - +
211A TRP* 3.1 39.0 - - + +
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Residues in contact with ALA 208 (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 ASN* 4.9 5.4 - - + +
188A VAL* 6.4 1.3 - - + -
204A VAL 3.5 8.2 + - - +
205A ALA* 2.9 19.9 + - - +
207A MET* 1.3 98.4 - - + +
209A VAL* 1.3 60.8 + - + +
211A TRP* 3.2 24.4 + - - +
212A PHE* 3.3 4.4 + - - +
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Residues in contact with VAL 209 (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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177A PHE* 2.9 48.3 - - + +
180A ASN* 4.3 8.5 - - + +
181A VAL* 3.9 8.5 - - + -
184A ASN* 3.2 28.3 - - + +
205A ALA 3.4 13.2 - - - +
206A THR 2.7 10.1 + - - +
208A ALA* 1.3 74.3 - - + +
210A PHE* 1.3 60.8 + - - +
212A PHE* 3.3 31.9 - - + -
213A SER 2.8 21.1 + - - -
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Residues in contact with PHE 210 (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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37A ILE* 4.8 18.8 - - + -
63A PHE* 4.8 18.6 - + - -
67A TYR* 5.1 17.5 - + - -
148A PRO* 3.8 15.0 - - + -
151A MET* 4.0 5.6 - - + -
152A VAL* 3.2 44.6 - - + -
155A ALA* 4.4 4.0 - - + +
174A PHE* 5.6 4.5 - + - -
177A PHE* 4.1 21.3 - + - -
206A THR* 3.4 8.9 + - - -
207A MET* 3.2 14.2 + - - +
208A ALA 3.2 0.8 - - - -
209A VAL* 1.3 74.6 - - - +
211A TRP* 1.3 54.2 + - + +
212A PHE 2.9 1.1 - - - -
213A SER* 2.6 12.6 + - - -
214A ALA* 2.5 34.3 + - - +
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Residues in contact with TRP 211 (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 MET 3.8 15.3 - - - -
148A PRO* 3.3 23.4 - - + +
150A ALA* 5.0 6.1 - - + -
151A MET* 3.2 53.0 - - + +
207A MET* 3.1 34.6 - - + -
208A ALA 3.2 9.6 - - - +
210A PHE* 1.3 73.3 - - - +
212A PHE* 1.3 56.8 + - - +
214A ALA* 3.7 0.9 - - - -
215A LEU* 3.2 38.1 + - + +
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Residues in contact with PHE 212 (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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173A SER* 4.3 7.4 - - - -
176A ALA* 3.0 37.5 - - + -
177A PHE* 3.5 16.8 - + - -
179A LEU* 5.6 1.6 - - + -
180A ASN* 4.1 14.4 - - - +
208A ALA 3.3 4.1 + - - +
209A VAL* 3.3 33.6 + - + +
210A PHE 2.9 1.4 - - - -
211A TRP* 1.3 78.5 - - - +
213A SER* 1.3 64.0 + - - +
215A LEU* 3.6 4.7 - - - +
216A ALA* 3.1 29.9 + - + +
219A ILE* 5.6 5.2 - - + -
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Residues in contact with SER 213 (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 ALA* 4.1 13.1 + - - -
173A SER* 4.3 3.8 + - - -
174A PHE* 3.6 23.8 - - - -
177A PHE* 3.2 28.5 - - - -
209A VAL 2.8 5.8 + - - -
210A PHE* 2.6 15.6 + - - -
212A PHE* 1.3 74.0 - - - +
214A ALA* 1.3 55.9 - - - -
216A ALA* 2.7 27.2 + - - +
217A LEU* 2.8 16.1 + - - +
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Residues in contact with ALA 214 (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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151A MET* 2.4 45.8 - - + -
154A ARG* 5.1 4.7 + - - +
155A ALA* 3.3 18.4 - - + +
210A PHE 2.5 16.9 + - - +
211A TRP 3.4 7.0 - - - +
213A SER* 1.3 73.8 - - - +
215A LEU* 1.3 62.7 + - + +
217A LEU* 3.0 22.7 - - - +
218A TRP* 3.4 3.6 + - - +
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Residues in contact with LEU 215 (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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151A MET* 4.0 7.2 - - + -
154A ARG* 3.5 17.3 - - - +
211A TRP* 3.2 24.4 + - + +
212A PHE* 3.6 6.5 - - - +
213A SER 3.2 0.2 - - - -
214A ALA* 1.3 89.9 - - + +
216A ALA* 1.3 59.1 + - - +
217A LEU 3.8 0.7 - - - +
218A TRP* 3.5 33.9 - - + +
219A ILE* 3.0 27.3 - - + +
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Residues in contact with ALA 216 (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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169A ILE* 4.2 6.1 - - - +
173A SER* 3.4 32.1 - - - +
212A PHE* 3.1 18.9 + - + +
213A SER* 2.7 14.5 + - - +
215A LEU* 1.3 78.8 - - - +
217A LEU* 1.3 65.0 + - - +
219A ILE* 3.0 16.4 - - + -
220A TYR* 3.2 23.0 - - - +
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Residues in contact with LEU 217 (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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101A ILE* 3.7 21.5 - - + -
154A ARG* 3.5 14.6 - - - +
155A ALA* 3.6 17.3 - - - +
157A HIS* 4.4 1.8 - - - +
158A ALA* 2.6 52.0 - - + +
161A SER* 6.0 3.1 - - - -
169A ILE* 6.0 0.7 - - - -
213A SER* 2.8 15.5 + - - +
214A ALA 3.0 10.8 - - - +
216A ALA* 1.3 75.7 - - - +
218A TRP* 1.3 59.0 + - + +
219A ILE 2.5 0.2 + - - -
220A TYR* 2.3 43.1 + - - +
221A ILE* 5.9 0.2 - - - -
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Residues in contact with TRP 218 (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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101A ILE* 4.7 17.9 - - + -
154A ARG* 3.1 38.4 - - - +
214A ALA 3.4 3.2 + - - -
215A LEU* 3.5 37.4 - - + +
217A LEU* 1.3 82.8 - - + +
219A ILE* 1.3 60.1 - - + +
220A TYR 2.9 6.8 + - - -
221A ILE* 3.2 55.8 + - + +
222A ALA 4.7 0.2 + - - -
227A PHE 5.6 2.9 - - - -
228A ARG* 4.7 10.3 - - + -
230A PHE* 4.0 30.5 - + + -
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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