Contacts of the helix formed by residues 180 - 189 (chain A) in PDB entry 5FQU
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 HIS 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A SER 5.1 2.0 + - - -
151A ASN 5.2 1.1 - - - -
152A ARG* 3.6 37.9 + - - -
154A PHE* 4.0 2.4 - - - -
178A LYS 4.1 0.8 + - - -
179A GLY* 1.3 76.5 - - - -
181A LEU* 1.3 68.3 + - - +
182A PRO* 3.2 8.3 - - + -
183A GLN* 3.0 35.5 + - + +
184A ALA* 3.0 20.8 + - - +
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Residues in contact with LEU 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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67A GLY 4.1 17.3 - - - +
71A SER* 4.2 2.2 - - - -
145A LEU* 4.1 20.6 - - + -
148A THR* 4.3 13.4 + - - +
151A ASN* 5.5 2.4 + - - +
154A PHE* 3.6 31.6 - - + -
157A LEU* 3.7 31.2 - - + -
161A PHE* 3.6 34.5 - - + -
179A GLY 3.7 1.0 + - - -
180A HIS* 1.3 70.5 - - - +
182A PRO* 1.3 72.7 - - + +
184A ALA* 3.2 1.0 + - - +
185A ILE* 2.9 31.8 + - + +
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Residues in contact with PRO 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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138A ALA* 5.2 0.7 - - - +
141A LEU* 3.9 17.6 - - + +
142A GLU* 3.7 31.6 - - + +
145A LEU* 4.0 33.6 - - + +
148A THR* 4.8 6.1 - - - +
180A HIS* 3.3 10.1 - - + -
181A LEU* 1.3 95.3 - - + +
183A GLN* 1.3 57.0 + - - +
185A ILE* 3.4 3.1 + - + +
186A ARG* 2.9 31.0 + - - +
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Residues in contact with GLN 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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142A GLU* 5.7 2.7 + - - +
176A PHE* 5.9 0.3 - - - -
179A GLY* 5.6 0.3 - - - -
180A HIS* 3.0 38.5 + - + +
182A PRO* 1.3 77.5 - - - +
184A ALA* 1.3 64.1 + - - +
186A ARG* 3.2 11.9 + - + +
187A ALA* 3.0 21.0 + - - +
198A VAL* 5.8 1.6 - - + -
199A GLU 4.9 2.8 + - - -
200A ILE* 3.5 47.9 - - + +
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Residues in contact with ALA 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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154A PHE* 3.9 16.2 - - + -
163A ALA* 4.2 6.3 - - + +
176A PHE* 3.7 44.9 - - + -
178A LYS 5.5 0.7 - - - +
180A HIS 3.0 11.4 + - - +
181A LEU* 3.6 6.5 - - + +
183A GLN* 1.3 78.2 + - - +
185A ILE* 1.3 62.8 + - - +
187A ALA* 3.0 15.1 + - - +
188A SER* 3.1 13.0 + - - -
200A ILE* 4.9 0.4 - - - -
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Residues in contact with ILE 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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63A ALA* 3.5 21.6 - - - +
64A VAL* 3.7 32.8 - - + +
67A GLY* 3.7 21.5 - - - -
68A LEU* 4.5 2.0 - - + +
141A LEU* 3.8 18.4 - - + -
145A LEU* 4.3 11.0 - - + -
161A PHE* 4.0 14.6 - - + -
163A ALA* 4.6 2.0 - - + -
181A LEU* 2.9 37.8 + - + +
182A PRO* 3.7 4.3 - - + +
184A ALA* 1.3 72.0 - - - +
186A ARG* 1.3 62.7 + - - +
188A SER* 3.3 10.6 + - - -
189A MSE 3.1 20.6 + - - +
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Residues in contact with ARG 186 (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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134A GLY* 2.8 45.9 + - - -
137A LEU* 4.1 11.2 - - - +
138A ALA* 3.9 23.3 - - + +
141A LEU* 3.7 14.1 - - + +
182A PRO 2.9 14.8 + - - +
183A GLN* 3.4 13.2 - - + +
185A ILE* 1.3 76.1 - - - +
187A ALA* 1.3 56.1 + - - +
189A MSE 3.4 5.4 + - - +
190A SER* 2.5 65.3 + - - +
195A PHE* 3.6 11.7 - - - +
196A ALA* 2.8 25.5 + - - +
197A PRO 4.3 1.8 + - - -
198A VAL* 3.4 24.1 - - + +
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Residues in contact with ALA 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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165A SER* 3.2 20.7 + - - +
176A PHE* 3.7 22.4 - - + -
183A GLN 3.0 10.9 + - - +
184A ALA 3.0 8.7 + - - +
186A ARG* 1.3 76.5 - - - +
188A SER* 1.3 62.3 + - - +
190A SER* 3.0 18.6 + - - -
198A VAL* 3.6 27.6 - - + -
200A ILE* 4.1 2.0 - - + -
205A LEU* 4.3 2.7 - - + -
206A VAL* 3.4 5.5 - - - -
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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
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59A THR* 3.3 6.6 - - - -
60A SER* 3.0 37.9 + - - -
63A ALA* 3.6 14.9 - - - +
163A ALA* 4.1 7.6 - - - -
164A VAL 2.5 34.1 + - - -
165A SER* 3.6 4.8 + - - -
184A ALA 3.1 8.4 + - - -
185A ILE 3.6 8.3 - - - -
187A ALA* 1.3 77.6 - - - +
189A MSE 1.3 57.1 + - - +
207A ASP* 3.3 18.2 - - - +
208A GLY 3.7 1.2 + - - +
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Residues in contact with MSE 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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32A GLY 4.4 0.9 - - - +
33A ALA* 4.6 7.2 - - + -
60A SER* 3.6 30.5 - - - +
61A MSE 3.6 33.9 - - + -
64A VAL* 4.0 18.2 - - + -
87A TRP* 6.4 0.4 - - + -
137A LEU* 3.7 26.5 - - + -
141A LEU* 5.6 0.4 - - + -
185A ILE* 3.1 16.5 + - + +
186A ARG* 3.7 6.3 - - - +
187A ALA 3.1 0.4 - - - -
188A SER* 1.3 76.0 - - - +
190A SER* 1.3 58.8 + - - +
191A ILE* 2.8 30.0 + - + +
195A PHE* 3.3 32.8 - - + -
287A PHE* 5.8 1.3 - - + -
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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