Contacts of the helix formed by residues 177 - 188 (chain J) in PDB entry 5G04
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 177 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175J MET 4.0 0.4 + - - -
176J LEU* 1.3 75.9 - - - +
178J ALA* 1.3 77.2 + - - +
179J GLN* 3.3 8.5 + - + +
180J GLU* 3.0 36.4 + - + +
181J GLU* 3.0 21.5 + - - +
210J LYS* 4.3 0.2 - - - -
366J GLY* 3.2 27.4 + - - -
397J ILE* 3.4 25.5 - - + +
398J ALA 4.2 2.8 + - - -
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Residues in contact with ALA 178 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177J THR* 1.3 75.9 + - - +
179J GLN* 1.3 60.5 + - + +
181J GLU* 3.5 3.6 + - - +
182J LYS* 3.2 22.1 + - - +
210J LYS* 3.6 28.2 - - + +
213J ASN* 3.3 44.6 + - + +
398J ALA* 4.0 13.2 - - + -
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Residues in contact with GLN 179 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177J THR* 3.3 8.1 + - + +
178J ALA* 1.3 77.6 - - + +
180J GLU* 1.3 69.9 + - - +
182J LYS* 3.4 7.6 + - - +
183J GLU* 2.8 30.0 + - - +
396J SER 4.9 9.5 + - - -
397J ILE 4.9 1.2 + - - -
398J ALA* 5.1 3.1 - - - +
399J PRO* 4.2 29.5 - - + +
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Residues in contact with GLU 180 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154J LYS* 4.9 5.6 - - - +
176J LEU* 4.3 21.3 - - + -
177J THR* 3.0 35.5 + - + +
179J GLN* 1.3 85.8 - - - +
181J GLU* 1.3 53.0 + - - +
183J GLU* 2.9 29.2 + - - +
184J LEU* 2.4 40.1 + - - +
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Residues in contact with GLU 181 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167J PHE* 5.6 8.1 - - + -
170J LEU* 4.0 3.3 - - + +
171J THR* 3.4 35.6 + - - +
174J HIS* 5.4 0.7 - - - -
176J LEU* 3.5 44.0 - - + +
177J THR 3.0 10.4 + - - +
178J ALA* 3.8 5.2 - - - +
180J GLU* 1.3 73.8 - - - +
182J LYS* 1.3 57.0 + - - +
184J LEU* 3.3 8.1 + - + +
185J LEU* 3.0 30.3 + - - +
209J LEU* 3.9 18.6 - - + +
210J LYS* 3.0 38.2 + - - +
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Residues in contact with LYS 182 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178J ALA 3.2 12.4 + - - +
179J GLN* 3.6 10.5 - - - +
180J GLU 3.2 0.2 - - - -
181J GLU* 1.3 76.2 - - - +
183J GLU* 1.3 63.4 + - - +
185J LEU* 3.4 10.2 + - - +
186J GLU* 3.3 31.3 + - - +
209J LEU* 5.0 19.0 - - + +
214J LYS* 5.9 3.2 - - - +
217J GLU* 5.9 1.2 + - - -
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Residues in contact with GLU 183 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154J LYS* 4.4 13.9 + - - -
179J GLN 2.8 16.0 + - - +
180J GLU* 3.2 33.5 - - - +
182J LYS* 1.3 79.2 - - - +
184J LEU* 1.3 63.5 + - - +
186J GLU* 3.3 21.3 + - - +
187J SER* 3.2 21.5 + - - -
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Residues in contact with LEU 184 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154J LYS* 3.6 33.2 - - + +
157J LEU* 4.0 17.9 - - + -
158J LYS* 5.1 6.5 - - + -
167J PHE* 5.1 9.0 - - + -
170J LEU* 3.8 15.0 - - + -
176J LEU* 3.4 25.6 - - + -
180J GLU 2.4 30.3 + - - +
181J GLU* 3.6 6.7 - - + +
183J GLU* 1.3 69.2 - - - +
185J LEU* 1.3 65.7 + - - +
187J SER* 3.1 24.7 + - - +
188J LEU* 3.2 24.3 + - + +
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Residues in contact with LEU 185 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167J PHE* 4.8 8.1 - - + -
181J GLU 3.0 14.2 + - - +
182J LYS* 3.8 5.8 - - - +
183J GLU 3.4 0.2 - - - -
184J LEU* 1.3 76.4 - - - +
186J GLU* 1.3 62.5 + - + +
188J LEU* 3.5 37.6 + - + +
190J LEU* 3.7 21.6 - - + +
202J ARG* 4.8 8.1 - - + -
205J PHE* 3.5 32.8 - - + -
206J GLU* 2.8 31.6 - - - +
209J LEU* 3.4 25.8 - - + -
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Residues in contact with GLU 186 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182J LYS* 3.3 33.8 - - + +
183J GLU* 3.5 17.1 - - - +
184J LEU 3.2 0.4 - - - -
185J LEU* 1.3 77.4 - - + +
187J SER* 1.3 60.0 + - - +
188J LEU 3.2 9.9 - - - +
190J LEU* 5.7 0.2 - - - +
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Residues in contact with SER 187 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158J LYS* 3.8 26.8 + - - +
183J GLU* 3.2 14.1 + - - -
184J LEU* 3.1 19.9 + - - +
186J GLU* 1.3 74.2 - - - +
188J LEU* 1.3 65.4 + - - +
189J PRO* 3.5 4.3 - - - +
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Residues in contact with LEU 188 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157J LEU* 4.0 28.3 - - + +
158J LYS* 5.3 4.9 - - + +
161J VAL* 3.7 33.9 - - + -
167J PHE* 5.9 4.0 - - + -
184J LEU* 3.2 47.0 + - + +
185J LEU* 3.5 34.2 - - + +
186J GLU 3.2 11.7 - - - +
187J SER* 1.3 77.2 - - - +
189J PRO* 1.4 78.3 - - + +
190J LEU* 3.3 15.0 + - + +
205J PHE* 4.7 9.0 - - + -
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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