Contacts of the helix formed by residues 180 - 191 (chain L) in PDB entry 5GJQ
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 LYS 180 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172L LEU* 3.0 35.9 - - + +
174L GLY 3.1 32.7 + - - +
175L PRO 3.9 2.8 + - - -
178L THR* 3.2 21.3 - - - +
179L GLY* 1.3 74.8 - - - +
181L THR* 1.3 70.0 + - - +
182L LEU 3.1 0.7 - - - -
183L LEU* 3.0 19.1 + - - +
184L ALA* 3.4 6.1 + - - +
231L PHE* 4.7 2.4 - - - -
278L ALA* 6.0 4.3 - - + -
279L THR 3.2 23.2 + - - +
280L ASN* 2.3 35.0 + - - +
301L ILE* 3.4 9.4 - - + -
401L ADP 2.6 27.1 + - - +
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Residues in contact with THR 181 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180L LYS* 1.3 80.0 - - - +
182L LEU* 1.3 59.1 + - - +
183L LEU 3.4 0.7 + - - -
184L ALA* 3.6 3.6 + - - +
185L ARG* 3.3 26.3 + - - +
231L PHE* 4.7 11.4 - - + -
233L ASP* 3.9 19.8 + - - +
401L ADP 2.4 47.8 + - - +
319M GLY* 3.7 30.7 - - - -
320M PHE* 4.0 8.7 - - + +
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Residues in contact with LEU 182 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135L ILE* 3.1 35.1 - - + +
179L GLY* 4.4 9.2 - - - -
180L LYS 3.1 0.2 - - - -
181L THR* 1.3 76.9 - - - +
183L LEU* 1.3 61.0 + - - +
185L ARG* 2.9 38.9 + - + +
186L ALA* 3.3 20.4 + - - +
316L HIS* 5.6 0.7 - - + -
401L ADP 3.3 69.9 + - + +
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Residues in contact with LEU 183 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132L TYR* 6.5 0.4 - - + -
135L ILE* 4.1 16.8 - - + -
138L LEU* 6.4 1.6 - - + -
141L GLN* 4.8 13.5 - - + -
142L ILE* 5.4 14.1 - - + +
145L LEU* 4.0 16.2 - - + -
172L LEU* 3.7 32.3 - - + -
179L GLY 3.7 8.4 + - - +
180L LYS 3.0 12.0 + - - +
182L LEU* 1.3 76.5 - - - +
184L ALA* 1.3 60.0 + - - +
185L ARG 3.1 1.6 - - - -
186L ALA* 2.9 4.6 + - + +
187L VAL* 2.8 52.4 + - + +
276L ILE* 6.3 0.2 - - + -
301L ILE* 4.1 9.0 - - + -
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Residues in contact with ALA 184 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172L LEU* 5.4 0.4 - - - +
180L LYS 3.4 2.8 + - - -
181L THR 3.9 4.9 - - - +
183L LEU* 1.3 77.4 - - - +
185L ARG* 1.3 56.9 + - - +
187L VAL* 3.8 7.6 - - - +
188L ALA* 3.1 30.5 + - - +
195L PHE* 5.7 0.2 - - - -
197L LYS* 3.9 3.4 + - - -
231L PHE* 2.6 62.7 - - + -
276L ILE* 4.7 4.9 - - + +
320M PHE* 4.3 5.6 - - + -
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Residues in contact with ARG 185 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128L GLY* 6.0 0.7 - - - -
129L ASN* 3.6 38.1 + - + +
181L THR* 3.3 24.8 + - - +
182L LEU* 2.9 36.2 - - - +
183L LEU 3.1 0.8 - - - -
184L ALA* 1.3 74.6 - - - +
186L ALA* 1.3 61.3 + - - +
188L ALA* 4.0 1.0 - - - +
189L SER* 3.0 32.2 + - - -
401L ADP 4.7 7.2 + - - -
319M GLY 4.6 10.6 + - - -
320M PHE* 3.1 36.8 - - + -
321M GLN 4.8 4.8 - - - +
322M PRO* 4.9 20.8 - - - +
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Residues in contact with ALA 186 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130L VAL 3.9 1.0 - - - +
131L SER 3.7 19.1 - - - +
132L TYR* 3.9 18.4 + - + +
135L ILE* 4.1 14.4 - - + -
182L LEU 3.3 12.8 + - - +
183L LEU* 2.9 11.7 + - + +
185L ARG* 1.3 78.3 - - - +
187L VAL* 1.3 60.2 + - + +
189L SER* 2.7 19.6 + - - -
190L GLN* 3.1 18.5 + - - +
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Residues in contact with VAL 187 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145L LEU* 3.9 17.7 - - + -
149L ILE* 5.2 4.5 - - + -
183L LEU* 2.8 41.8 + - + +
184L ALA* 3.8 8.3 - - - +
186L ALA* 1.3 75.4 - - - +
188L ALA* 1.3 61.6 + - - +
190L GLN* 5.0 1.6 - - - -
191L LEU* 2.8 51.5 + - + +
195L PHE* 3.7 22.2 - - + -
276L ILE* 4.5 12.3 - - + -
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Residues in contact with ALA 188 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184L ALA 3.1 8.2 + - - +
185L ARG 4.4 1.6 - - - +
187L VAL* 1.3 80.5 - - - +
189L SER* 1.3 50.3 - - - +
192L ASP* 2.2 36.6 + - - +
195L PHE* 3.5 32.8 - - + -
197L LYS* 3.5 29.4 - - - +
320M PHE* 5.3 0.4 - - + -
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Residues in contact with SER 189 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128L GLY* 5.9 1.6 - - - -
129L ASN 2.9 31.1 - - - +
130L VAL 1.7 34.7 + - - -
185L ARG 3.0 17.2 + - - -
186L ALA* 2.7 21.1 + - - -
188L ALA* 1.3 78.7 - - - +
190L GLN* 1.3 57.5 + - - +
192L ASP* 3.0 22.7 - - - +
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Residues in contact with GLN 190 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131L SER* 4.1 24.2 - - - +
132L TYR* 4.5 10.3 + - + +
146L ARG* 2.3 44.1 + - - +
150L GLU* 4.0 10.0 + - - +
186L ALA 3.1 14.0 + - - +
187L VAL* 4.2 2.1 - - - +
189L SER* 1.3 83.6 + - - +
191L LEU* 1.3 79.5 + - - +
192L ASP* 4.0 3.8 - - - +
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Residues in contact with LEU 191 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146L ARG* 5.8 0.2 - - - +
149L ILE* 4.1 20.4 - - + -
150L GLU* 3.6 45.1 - - + +
153L LEU* 5.1 7.9 - - + -
187L VAL* 2.8 33.3 + - + +
190L GLN* 1.3 82.6 + - - +
192L ASP* 1.3 73.7 + - - +
193L CYS* 5.3 0.7 - - + -
195L PHE* 3.2 27.4 - - + -
229L ILE* 4.6 3.1 - - + -
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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