Contacts of the helix formed by residues 161 - 173 (chain D) in PDB entry 5CTR
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 161 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159D ALA 4.5 5.8 - - - +
160D ASP* 1.3 80.7 - - - +
162D ILE* 1.3 63.9 + - - +
163D ALA* 2.9 10.9 + - - +
164D THR* 2.6 47.0 + - - +
165D ILE* 3.4 18.2 + - - +
198D LEU 3.8 2.9 - - - -
199D ASP* 3.7 22.0 - - - +
200D ASN 3.7 5.8 - - - -
201D THR* 4.2 3.4 - - + +
202D VAL* 4.7 3.4 - - - -
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Residues in contact with ILE 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D THR* 1.3 74.1 - - - +
163D ALA* 1.3 62.9 + - - +
165D ILE* 3.4 10.9 + - + +
166D GLU* 3.2 20.0 + - + +
183D LEU* 4.2 23.2 - - + +
195D LEU* 4.5 23.3 - - + -
196D SER 5.3 1.1 - - - +
197D LYS* 2.8 34.8 - - + +
198D LEU* 4.2 1.8 - - - +
200D ASN* 2.9 34.0 + - - +
201D THR 4.0 8.7 - - - +
202D VAL* 5.6 2.0 - - + -
205D ALA* 4.8 11.2 - - + -
207D LEU* 6.1 3.4 - - + -
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Residues in contact with ALA 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D THR* 2.9 5.3 + - - +
162D ILE* 1.3 80.1 - - - +
164D THR* 1.3 63.4 + - - +
166D GLU* 3.4 10.5 + - - +
167D LYS* 3.1 49.8 + - - +
198D LEU* 3.3 39.0 + - + +
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Residues in contact with THR 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D PHE* 5.6 4.5 - - + -
160D ASP* 4.2 23.4 + - + +
161D THR* 2.6 41.0 + - - +
163D ALA* 1.3 71.0 - - - +
165D ILE* 1.3 67.0 + - + +
167D LYS* 3.2 12.3 + - - +
168D GLU* 3.2 18.5 + - + +
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Residues in contact with ILE 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D LEU* 5.7 0.2 - - + -
140D LEU* 3.9 26.0 - - + -
142D LEU* 5.1 0.9 - - + -
156D PHE* 4.0 40.2 - - + -
160D ASP* 5.5 0.9 - - + -
161D THR 3.4 14.7 + - - +
162D ILE* 3.8 9.4 - - - +
163D ALA 3.4 0.2 - - - -
164D THR* 1.3 73.9 - - + +
166D GLU* 1.3 55.4 + - - +
168D GLU* 2.8 9.5 + - + +
169D MET* 2.6 56.8 + - + +
183D LEU* 5.6 2.9 - - + -
202D VAL* 4.4 18.6 - - + -
207D LEU* 5.2 5.8 - - + -
213D LEU* 5.0 14.6 - - + -
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Residues in contact with GLU 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D ILE 3.2 11.9 + - - +
163D ALA* 3.4 10.7 - - - +
165D ILE* 1.3 79.1 - - - +
167D LYS* 1.3 72.6 + - - +
169D MET* 3.4 9.7 - - - +
170D ARG* 2.6 62.7 + - + +
181D THR* 2.8 31.3 + - + +
183D LEU* 4.5 19.6 - - + +
198D LEU* 5.9 1.2 - - - +
215D ILE* 4.5 4.3 - - + -
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Residues in contact with LYS 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D ALA* 3.1 47.4 + - - +
164D THR* 3.4 12.6 - - - +
165D ILE 3.2 0.2 - - - -
166D GLU* 1.3 90.1 + - - +
168D GLU* 1.3 57.9 + - - +
170D ARG* 4.0 19.2 - - - +
171D LYS* 3.0 28.9 + - - +
198D LEU* 5.7 2.6 - - - +
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Residues in contact with GLU 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D LEU* 5.5 5.4 - - + -
154D CYS* 4.1 20.4 - - + +
156D PHE* 4.4 20.9 - - + -
164D THR* 3.2 10.7 + - + +
165D ILE* 2.8 13.1 + - + +
167D LYS* 1.3 76.3 - - - +
169D MET* 1.3 65.3 + - + +
171D LYS* 4.4 16.8 + - - +
172D LEU* 3.0 44.4 + - + +
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Residues in contact with MET 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D LEU* 3.5 38.8 - - + -
143D CYS 3.7 20.9 - - - +
165D ILE* 2.6 42.0 + - + +
166D GLU* 3.4 4.9 - - - +
168D GLU* 1.3 73.8 - - - +
170D ARG* 1.3 60.6 + - - +
172D LEU* 4.4 1.4 - - - +
173D PHE* 3.1 45.3 + - + +
183D LEU* 5.5 0.7 - - + -
213D LEU* 4.6 7.9 - - + +
215D ILE* 2.3 64.6 - - + +
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Residues in contact with ARG 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D GLU* 2.6 50.9 + - + +
167D LYS* 4.0 18.7 - - - +
169D MET* 1.3 73.7 - - - +
171D LYS* 1.3 64.1 + - - +
173D PHE* 4.1 1.9 - - - -
174D ASN 3.4 3.1 + - - -
175D ILE* 3.3 49.9 + - + +
176D PRO 4.8 1.2 + - - -
177D ALA* 3.3 47.7 + - - +
179D ARG* 3.8 2.8 + - - +
181D THR* 3.4 25.6 + - + +
215D ILE* 6.1 0.4 - - - +
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Residues in contact with LYS 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D LYS 3.0 21.0 + - - +
168D GLU* 4.0 17.1 + - - +
169D MET 3.4 0.2 - - - -
170D ARG* 1.3 80.5 - - + +
172D LEU* 1.3 65.1 + - + +
174D ASN* 3.4 18.0 + - - +
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Residues in contact with LEU 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D LEU* 4.5 16.4 - - + -
152D LEU* 3.8 37.2 - - + -
154D CYS* 6.3 1.3 - - + -
168D GLU* 3.0 33.2 + - + +
169D MET* 4.4 1.8 - - - +
171D LYS* 1.3 77.5 - - + +
173D PHE* 1.3 65.9 + - + +
174D ASN* 3.0 23.1 + - - +
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Residues in contact with PHE 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D LEU* 4.9 3.4 - - + -
143D CYS* 3.3 31.0 - - - -
144D GLU* 3.2 43.3 - - + -
147D ASP* 6.4 0.2 - - + -
150D ASN* 4.8 7.9 - - + -
152D LEU* 4.4 20.4 - - + -
169D MET* 3.1 35.4 + - + +
170D ARG* 4.4 1.8 - - - +
172D LEU* 1.3 82.9 - - + +
174D ASN* 1.3 71.4 + - - +
175D ILE* 3.9 20.2 - - + +
215D ILE* 5.2 7.9 - - + -
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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