Contacts of the helix formed by residues 174 - 188 (chain D) in PDB entry 5FI6
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 LEU 174 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162D LEU* 3.7 38.4 - - + -
167D LEU* 4.5 9.6 - - + -
168D ARG 4.2 5.6 - - - +
169D THR* 5.2 0.9 - - - +
171D ASP* 2.8 31.2 + - + +
173D ARG* 1.3 80.0 - - - +
175D LYS* 1.3 65.0 - - - +
176D GLU 3.3 3.0 + - - -
177D CYS* 3.3 5.2 + - + +
178D MET* 2.8 35.4 + - + +
206D ASN* 3.4 19.6 - - + +
209D LEU* 3.8 23.1 - - + -
210D LEU* 4.3 18.4 - - + -
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Residues in contact with LYS 175 (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 ASP 3.4 5.1 + - - +
172D PRO* 3.3 19.8 + - + +
173D ARG 3.5 0.8 - - - -
174D LEU* 1.3 75.4 - - - +
176D GLU* 1.3 57.6 + - + +
178D MET* 2.9 8.7 + - - +
179D ASP* 2.5 72.5 + - - +
182D ARG* 4.7 4.6 - - - +
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Residues in contact with GLU 176 (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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172D PRO 5.9 0.2 - - - +
173D ARG 4.8 2.4 - - - +
174D LEU 3.3 0.2 - - - -
175D LYS* 1.3 79.6 - - + +
177D CYS* 1.3 53.4 + - - +
179D ASP* 2.6 32.4 + - - +
180D MET* 2.7 25.1 + - + +
205D SER* 3.5 23.2 - - - +
206D ASN* 3.2 23.2 + - - +
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Residues in contact with CYS 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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158D PHE* 4.4 11.9 - - - -
174D LEU* 3.3 5.8 + - + +
176D GLU* 1.3 76.8 - - - +
178D MET* 1.3 79.8 + - - +
180D MET* 3.5 2.8 + - - +
181D LEU* 3.0 28.6 + - - +
202D CYS* 3.3 26.2 - - - +
203D VAL* 4.5 6.7 - - - -
205D SER* 3.8 1.8 + - - +
206D ASN* 3.2 26.9 + - + +
210D LEU* 4.3 19.7 - - + -
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Residues in contact with MET 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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158D PHE* 4.1 10.8 - - + -
159D ILE* 4.3 6.7 - - + -
162D LEU* 4.3 15.3 - - + -
169D THR* 3.3 38.4 - - - +
174D LEU* 2.8 25.6 + - + +
175D LYS* 3.4 9.2 - - - +
177D CYS* 1.3 104.2 - - - +
179D ASP* 1.3 61.0 + - - +
181D LEU* 3.6 25.4 - - + +
182D ARG* 2.9 41.2 + - + +
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Residues in contact with ASP 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D LYS* 2.5 61.7 + - - +
176D GLU* 2.6 17.8 + - - +
178D MET* 1.3 70.6 - - - +
180D MET* 1.3 64.4 + - + +
182D ARG* 2.2 49.3 + - - +
183D LEU* 3.1 31.6 + - + +
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Residues in contact with MET 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D GLU* 2.7 22.8 + - + +
177D CYS 3.9 0.7 - - - +
179D ASP* 1.3 75.0 - - + +
181D LEU* 1.3 59.9 + - - +
183D LEU* 3.6 20.3 + - + +
184D THR* 2.8 31.2 + - - +
201D LYS* 3.0 55.2 - - - +
202D CYS* 3.5 27.8 - - + +
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Residues in contact with LEU 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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155D VAL* 4.9 16.4 - - + -
158D PHE* 3.9 22.2 - - + -
159D ILE* 4.2 10.8 - - + -
177D CYS* 3.0 18.3 + - - +
178D MET* 3.6 35.4 - - + +
179D ASP 3.2 0.4 - - - -
180D MET* 1.3 75.9 - - - +
182D ARG* 1.3 60.0 + - + +
184D THR* 3.5 3.7 + - - +
185D LEU* 2.9 40.3 + - + +
194D LEU* 4.5 19.5 - - + -
202D CYS* 3.7 25.8 - - + -
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Residues in contact with ARG 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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175D LYS* 4.5 5.3 + - - +
178D MET* 2.9 35.1 + - + +
179D ASP* 2.2 49.7 + - - +
181D LEU* 1.3 77.3 - - + +
183D LEU* 1.3 64.5 + - + +
185D LEU* 3.4 13.7 + - - +
186D GLN* 3.4 21.0 + - - +
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Residues in contact with LEU 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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179D ASP* 3.1 20.2 + - + +
180D MET* 3.9 26.2 - - + +
182D ARG* 1.3 74.1 - - + +
184D THR* 1.3 66.5 + - - +
186D GLN* 2.9 23.7 + - - +
187D THR* 3.1 11.8 + - - -
201D LYS* 6.2 0.7 - - - +
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Residues in contact with THR 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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180D MET* 2.8 20.3 + - - +
181D LEU* 4.1 6.7 - - - -
183D LEU* 1.3 76.9 - - - +
185D LEU* 1.3 63.0 + - - +
187D THR* 3.0 38.5 + - + +
188D THR 3.6 2.6 + - - -
192D VAL* 3.7 18.7 - - + +
193D MET 5.5 0.2 - - - +
194D LEU* 5.2 5.6 - - + -
198D LEU* 4.5 24.5 - - + -
201D LYS* 5.2 9.0 + - + +
202D CYS* 4.0 12.5 - - - -
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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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155D VAL* 3.9 26.2 - - + -
181D LEU* 2.9 31.8 + - + +
182D ARG* 3.8 7.9 - - - +
183D LEU 3.1 0.6 - - - -
184D THR* 1.3 79.2 - - - +
186D GLN* 1.3 59.6 + - + +
188D THR 2.8 16.2 - - - +
189D SER* 4.9 1.7 + - - -
191D GLY 5.3 1.8 - - - +
192D VAL* 3.4 39.9 - - + +
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Residues in contact with GLN 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 ARG* 3.4 18.3 + - - +
183D LEU* 2.9 13.9 + - - +
185D LEU* 1.3 80.4 - - - +
187D THR* 1.3 63.1 + - - +
188D THR* 3.0 4.6 + - - -
189D SER* 5.4 2.2 + - - -
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Residues in contact with THR 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D LEU 3.1 10.5 + - - -
184D THR* 3.0 36.6 - - + +
186D GLN* 1.3 77.5 - - - +
188D THR* 1.3 71.1 + - - +
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Residues in contact with THR 188 (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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184D THR 3.6 0.4 + - - -
185D LEU* 2.8 21.9 - - - +
186D GLN 3.0 2.8 - - - -
187D THR* 1.3 94.0 + - - +
189D SER* 1.3 60.1 + - - +
190D ASP* 3.2 39.5 - - + +
192D VAL* 3.0 33.4 - - + +
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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