Contacts of the helix formed by residues 176 - 188 (chain D) in PDB entry 4KEU
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 ASN 176 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172D ASN 4.1 1.8 + - - -
173D ALA 5.0 0.2 + - - -
174D HIS 3.8 1.2 - - - -
175D ASN* 1.3 80.5 + - - +
177D THR* 1.3 63.9 + - - +
178D GLY 3.3 2.7 - - - -
179D LEU* 3.3 32.2 + - - +
180D GLU* 3.2 33.9 + - - +
208D TYR* 3.4 24.8 + - + -
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Residues in contact with THR 177 (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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140D ALA* 4.0 17.6 + - + -
141D ASP 3.4 20.0 - - - +
144D GLY* 3.7 22.2 - - - -
145D ILE* 4.2 8.4 - - + +
171D SER* 3.5 1.4 - - - -
172D ASN 3.0 25.7 + - - -
175D ASN* 3.0 29.4 + - - +
176D ASN* 1.3 78.3 - - - +
178D GLY* 1.3 56.9 + - - +
180D GLU* 3.2 5.5 + - - +
181D GLN* 2.9 36.5 + - - +
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Residues in contact with GLY 178 (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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171D SER* 3.6 14.9 + - - -
172D ASN 4.7 0.6 + - - -
176D ASN 3.3 1.0 - - - -
177D THR* 1.3 81.7 + - - +
179D LEU* 1.3 61.3 + - - +
181D GLN* 3.3 4.1 + - - -
182D GLN* 3.1 19.2 + - - +
197D ILE* 3.5 36.8 - - - +
200D LEU* 5.2 0.2 - - - -
208D TYR* 3.4 7.5 + - - -
212D ILE* 4.3 2.0 - - - -
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Residues in contact with LEU 179 (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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176D ASN* 3.3 32.3 + - - +
178D GLY* 1.3 75.4 - - - +
180D GLU* 1.3 61.7 + - - +
182D GLN* 3.5 14.1 + - - +
183D ARG* 3.0 26.3 + - + +
208D TYR* 3.1 18.4 + - + +
211D LYS* 3.8 31.4 - - + +
212D ILE* 3.8 23.5 - - + +
215D LYS* 3.3 27.1 - - + +
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Residues in contact with GLU 180 (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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145D ILE* 3.9 25.4 - - + +
176D ASN* 3.2 28.8 + - - +
177D THR* 3.6 7.0 - - - +
178D GLY 3.2 0.4 - - - -
179D LEU* 1.3 79.9 - - - +
181D GLN* 1.3 65.3 + - - +
182D GLN 3.2 0.2 - - - -
183D ARG* 2.8 48.2 + - - +
184D ILE* 2.9 33.9 + - + +
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Residues in contact with GLN 181 (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 ILE* 3.3 26.8 - - + +
140D ALA* 3.3 20.6 - - - +
145D ILE* 4.5 3.6 - - + +
153D ILE* 4.0 20.4 - - + +
169D THR* 2.7 25.5 + - + -
170D HIS 2.8 24.8 + - - -
171D SER* 3.6 12.5 - - - -
177D THR 2.9 17.9 + - - +
178D GLY* 3.3 8.0 + - - +
180D GLU* 1.3 76.3 - - - +
182D GLN* 1.3 58.0 + - - +
184D ILE* 4.0 1.0 - - - +
185D LEU* 3.0 41.7 + - + +
197D ILE* 4.0 6.6 - - + +
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Residues in contact with GLN 182 (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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178D GLY 3.1 10.0 + - - +
179D LEU* 3.6 13.4 - - - +
181D GLN* 1.3 78.0 - - - +
183D ARG* 1.3 66.1 + - - +
185D LEU* 3.9 5.5 - - - +
186D THR* 3.0 40.4 + - + +
195D ILE* 4.8 2.5 - - + -
197D ILE* 3.9 13.2 - - + +
212D ILE* 2.8 38.2 + - + +
215D LYS* 3.3 41.3 + - + +
217D SER* 2.8 34.4 + - - +
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Residues in contact with ARG 183 (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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154D ARG* 5.6 2.6 - - - +
179D LEU* 3.0 15.3 + - + +
180D GLU* 2.8 44.9 + - - +
182D GLN* 1.3 76.7 - - - +
184D ILE* 1.3 87.5 + - - +
186D THR* 2.8 20.3 + - - +
187D GLU* 2.9 61.2 + - + +
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Residues in contact with ILE 184 (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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145D ILE* 4.3 17.7 - - + -
150D GLU* 4.2 23.8 - - + +
153D ILE* 3.6 28.7 - - + -
154D ARG* 4.0 36.3 - - + +
180D GLU* 2.9 21.7 + - + +
183D ARG* 1.3 105.5 - - - +
185D LEU* 1.3 63.3 + - - +
187D GLU* 3.4 6.3 + - - +
188D GLU* 3.0 25.2 + - + +
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Residues in contact with LEU 185 (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 ILE* 5.3 2.9 - - + -
153D ILE* 3.4 36.3 - - + +
156D ALA* 4.5 2.9 - - + -
157D ALA* 4.2 7.2 - - + +
167D ILE* 3.8 35.7 - - + -
169D THR* 4.5 7.6 - - + -
181D GLN* 3.0 31.5 + - + +
182D GLN 3.9 0.4 - - - +
184D ILE* 1.3 75.8 - - - +
186D THR* 1.3 59.0 + - - +
188D GLU* 3.3 9.6 + - - +
189D GLY 3.4 0.3 + - - -
190D VAL* 2.9 29.8 + - + +
195D ILE* 3.7 40.4 - - + -
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Residues in contact with THR 186 (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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182D GLN* 3.0 27.5 + - + +
183D ARG* 2.8 23.0 + - - -
185D LEU* 1.3 72.4 - - - +
187D GLU* 1.4 61.1 + - - +
189D GLY* 2.8 21.1 + - - -
190D VAL 3.5 20.3 + - - +
192D PRO* 4.0 21.5 - - + -
195D ILE* 4.1 11.7 - - + -
215D LYS* 5.4 1.3 - - + +
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Residues in contact with GLU 187 (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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154D ARG* 5.2 9.3 + - - +
183D ARG* 2.9 61.7 + - + +
184D ILE* 3.7 6.3 - - - +
186D THR* 1.4 78.4 + - - +
188D GLU* 1.3 60.1 + - + +
189D GLY* 3.2 4.3 + - - -
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Residues in contact with GLU 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D ARG* 2.4 53.0 + - + +
157D ALA* 3.4 28.3 - - + -
158D ILE* 5.6 3.1 - - - +
161D LYS* 2.4 47.2 + - - +
184D ILE* 3.0 24.2 + - + +
185D LEU 3.6 1.8 - - - +
186D THR 3.2 0.4 - - - -
187D GLU* 1.3 74.7 - - - +
189D GLY* 1.3 50.6 + - - +
190D VAL 3.6 0.9 - - - -
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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