Contacts of the helix formed by residues 177 - 187 (chain X) in PDB entry 3RCK
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 GLY 177 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61X ARG 3.4 17.7 - - - -
62X VAL* 4.0 1.9 - - - +
174X VAL* 4.2 2.5 - - - -
176X GLU* 1.3 80.8 - - - +
178X MET* 1.3 66.2 + - - +
179X ASP* 3.0 16.0 + - - -
180X VAL* 2.9 16.6 + - - +
181X VAL* 3.1 13.9 + - - +
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Residues in contact with MET 178 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137X PRO* 4.0 15.5 - - + -
138X GLY* 3.8 35.4 - - - +
157X CYS 3.8 6.7 - - - +
158X THR* 4.3 8.3 - - + -
174X VAL* 3.8 13.1 - - + +
176X GLU 3.6 1.8 - - - -
177X GLY* 1.3 77.5 - - - +
179X ASP* 1.3 57.3 + - - +
181X VAL* 3.2 34.1 + - + +
182X LYS* 2.8 47.8 + - + +
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Residues in contact with ASP 179 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59X LEU 5.0 0.2 - - - +
177X GLY* 3.4 17.0 + - - -
178X MET* 1.3 77.9 + - - +
180X VAL* 1.3 70.9 + - - +
182X LYS* 3.3 7.2 + - - +
183X LYS* 3.0 43.5 + - - +
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Residues in contact with VAL 180 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52X VAL* 4.5 4.5 - - + -
59X LEU* 3.4 38.1 - - + +
60X GLY* 3.8 10.3 - - - +
61X ARG 3.7 25.4 - - - +
62X VAL* 3.7 19.5 - - + -
177X GLY* 2.9 8.1 + - - +
179X ASP* 1.3 87.3 - - - +
181X VAL* 1.3 66.4 + - - +
183X LYS* 3.2 10.0 + - - +
184X ILE* 3.0 31.9 + - + +
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Residues in contact with VAL 181 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62X VAL* 4.0 25.8 - - + -
104X CYS* 3.8 9.4 - - + -
156X ILE* 3.9 28.7 - - + -
158X THR* 3.8 15.9 - - + -
174X VAL* 4.2 2.0 - - + -
177X GLY 3.1 12.6 + - - +
178X MET* 3.2 37.2 + - + +
180X VAL* 1.3 76.4 - - - +
182X LYS* 1.3 57.8 + - - +
184X ILE* 3.2 12.8 + - + +
185X GLU* 2.9 26.0 + - - +
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Residues in contact with LYS 182 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158X THR* 4.5 12.5 + - - -
178X MET* 2.8 38.4 + - + +
179X ASP* 3.9 6.5 - - - +
181X VAL* 1.3 73.9 - - + +
183X LYS* 1.3 64.5 + - - +
185X GLU* 2.7 37.1 + - - +
186X SER* 3.0 23.4 + - - -
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Residues in contact with LYS 183 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58X PRO 5.2 0.8 + - - -
59X LEU* 2.6 56.8 + - + +
179X ASP* 3.0 32.2 + - + +
180X VAL* 3.2 13.9 + - - +
182X LYS* 1.3 73.1 - - - +
184X ILE* 1.3 66.0 + - - +
186X SER* 2.6 26.6 + - - +
187X PHE* 3.2 18.8 - - + -
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Residues in contact with ILE 184 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52X VAL* 3.9 24.5 - - + -
59X LEU* 3.9 16.8 - - + -
62X VAL* 5.0 3.8 - - + -
95X PHE* 4.1 24.9 - - + -
98X VAL* 3.4 14.4 - - + +
104X CYS* 3.8 23.3 - - + -
156X ILE* 6.3 0.4 - - + -
180X VAL* 3.0 24.9 + - + +
181X VAL* 3.2 13.7 + - + +
183X LYS* 1.3 74.7 - - - +
185X GLU* 1.3 64.2 + - - +
187X PHE* 3.0 25.3 + - - +
198X ILE* 3.8 25.9 - - + +
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Residues in contact with GLU 185 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98X VAL* 3.6 10.8 - - - +
99X ILE 4.5 2.9 - - - +
100X PRO* 3.5 29.7 - - + +
101X SER* 2.8 20.8 + - - -
104X CYS* 3.8 7.4 - - - -
158X THR* 2.8 34.7 + - + +
181X VAL 2.9 16.3 + - - +
182X LYS* 2.7 41.8 + - - +
184X ILE* 1.3 75.3 - - - +
186X SER* 1.3 57.8 + - - +
188X GLY* 3.0 16.8 + - - -
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Residues in contact with SER 186 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100X PRO* 5.4 3.4 - - - +
182X LYS 3.0 12.7 + - - -
183X LYS* 2.6 23.5 + - - +
185X GLU* 1.3 75.6 - - - +
187X PHE* 1.3 74.5 + - - +
188X GLY 3.3 6.1 + - - +
195X SER* 4.8 1.2 + - - -
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Residues in contact with PHE 187 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54X ALA* 3.7 25.4 - - + -
59X LEU* 4.1 15.7 - - + -
98X VAL* 4.7 0.2 - - - -
183X LYS* 3.2 28.3 - - + -
184X ILE* 3.0 14.0 + - - +
186X SER* 1.3 88.9 - - - +
188X GLY* 1.3 61.2 + - - +
194X THR* 3.2 6.0 - - - -
195X SER* 2.8 42.4 + - - +
196X LYS* 3.3 44.0 - - + +
198X ILE* 4.1 13.7 - - + -
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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