Contacts of the helix formed by residues 180 - 193 (chain A) in PDB entry 3FGU
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 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A ASP 4.8 0.4 + - - -
161A LYS* 3.6 34.7 - - + +
162A GLY 3.1 23.9 + - - +
163A ILE* 3.8 9.9 - - + +
179A ASN* 1.3 70.5 - - - +
181A VAL* 1.3 62.4 + - - +
182A VAL* 3.2 16.5 + - - +
183A GLY* 3.0 20.1 + - - +
184A LEU* 3.0 28.0 + - - +
186A ARG* 5.0 6.5 - - - +
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Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A PHE* 4.3 7.2 - - + -
148A PHE* 3.6 27.1 - - + -
150A PHE* 3.6 34.5 - - + -
154A VAL* 4.5 2.0 - - + -
162A GLY 3.2 5.1 + - - +
164A LEU* 3.8 28.7 - - + +
179A ASN 4.0 1.8 - - - +
180A ASN* 1.3 72.1 + - - +
182A VAL* 1.3 66.5 + - - +
184A LEU* 3.3 15.1 + - + +
185A LEU* 3.1 21.3 + - - +
202A MET* 3.7 20.2 - - - -
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Residues in contact with VAL 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A PHE* 5.4 4.3 - - + -
160A ASP* 3.2 28.3 - - - +
180A ASN* 3.2 6.8 + - - +
181A VAL* 1.3 77.1 - - - +
183A GLY* 1.3 57.1 + - - +
185A LEU* 3.4 6.5 + - - +
186A ARG* 2.8 65.0 + - - +
199A VAL* 3.8 24.5 - - + -
202A MET* 3.8 32.1 - - + +
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Residues in contact with GLY 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ASN* 3.0 23.8 + - - +
182A VAL* 1.3 78.0 - - - +
184A LEU* 1.3 59.0 + - - +
186A ARG* 3.7 9.0 - - - +
187A ASP* 2.8 40.3 + - - +
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Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ALA* 4.6 9.9 - - + -
123A PHE* 3.9 33.6 - - + +
175A GLY 4.2 13.7 - - - +
176A ALA* 3.9 29.4 - - + +
179A ASN* 4.2 16.8 - - + +
180A ASN 3.0 18.5 + - - +
181A VAL* 3.3 17.2 + - + +
183A GLY* 1.3 75.0 - - - +
185A LEU* 1.3 61.3 + - - +
187A ASP* 3.5 10.5 + - - +
188A ALA* 3.1 23.9 + - - +
191A ARG* 4.6 6.6 + - - +
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Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LEU* 3.6 24.0 - - + -
123A PHE* 4.0 16.5 - - + +
126A ILE* 3.9 28.0 - - + -
127A SER* 4.5 3.8 - - - +
130A ILE* 4.4 4.7 - - + -
146A LEU* 4.7 4.0 - - + -
148A PHE* 3.9 19.5 - - + -
181A VAL 3.1 13.5 + - - +
182A VAL* 3.6 7.4 - - - +
184A LEU* 1.3 74.9 - - - +
186A ARG* 1.3 65.7 + - - +
188A ALA* 3.3 3.1 + - - -
189A ILE* 3.1 47.1 + - + +
199A VAL* 4.2 23.8 - - + -
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Residues in contact with ARG 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ASP* 4.5 13.5 + - - +
180A ASN* 5.0 7.5 - - - +
182A VAL* 2.8 43.8 + - - +
183A GLY* 3.7 7.9 - - - +
185A LEU* 1.3 72.7 - - - +
187A ASP* 1.3 64.7 + - - +
189A ILE* 4.5 3.1 - - - -
190A LYS* 2.8 51.9 + - + +
197A MET 5.8 2.0 - - - +
199A VAL* 3.3 43.4 + - + +
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Residues in contact with ASP 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A GLY* 2.8 31.1 + - - +
184A LEU* 3.6 10.6 - - - +
185A LEU 3.2 0.2 - - - -
186A ARG* 1.3 75.7 - - - +
188A ALA* 1.3 57.6 + - - +
190A LYS* 3.3 10.5 + - - +
191A ARG* 3.0 51.2 + - - +
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Residues in contact with ALA 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A PHE* 3.4 35.0 - - + +
124A ASP* 3.9 4.8 - - - +
127A SER* 3.4 18.4 + - - +
184A LEU 3.1 8.5 + - - +
185A LEU* 3.3 2.9 + - - +
187A ASP* 1.3 73.8 - - - +
189A ILE* 1.3 64.9 + - - +
191A ARG* 3.3 26.5 + - - +
192A ARG* 3.2 21.5 + - - +
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Residues in contact with ILE 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A SER* 3.4 13.4 + - - +
130A ILE* 4.6 5.6 - - + -
146A LEU* 4.7 4.3 - - + -
185A LEU* 3.1 37.7 + - + +
186A ARG* 4.7 3.6 - - - -
188A ALA* 1.3 76.5 - - - +
190A LYS* 1.3 68.8 + - - +
192A ARG* 3.3 3.6 + - - +
193A GLY* 2.8 32.2 + - - -
195A PHE* 3.5 58.4 + - + +
196A GLU* 4.8 4.3 - - - -
197A MET* 4.5 16.4 - - + +
199A VAL* 4.9 4.5 - - + -
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Residues in contact with LYS 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ARG* 2.8 53.9 + - + +
187A ASP* 3.5 9.9 - - - +
189A ILE* 1.3 100.2 - - - +
191A ARG* 1.3 65.4 + - - +
192A ARG 3.4 0.2 + - - -
193A GLY* 3.4 13.2 + - - +
196A GLU* 6.1 3.7 - - - +
197A MET 5.3 6.6 + - - +
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Residues in contact with ARG 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLU* 3.9 38.8 + - - +
123A PHE* 5.5 0.4 - - - +
124A ASP* 2.8 30.1 + - - +
184A LEU* 4.6 7.1 + - - +
187A ASP* 3.0 36.0 + - - +
188A ALA* 3.3 30.8 - - - +
189A ILE 3.3 0.4 - - - -
190A LYS* 1.3 77.5 - - - +
192A ARG* 1.3 63.1 + - - +
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Residues in contact with ARG 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ASP 5.2 0.8 + - - -
127A SER* 4.0 15.0 - - - -
128A GLU* 3.6 36.1 + - - +
131A SER* 3.0 27.6 + - - -
140A LYS* 5.4 0.2 - - - +
188A ALA 3.2 10.2 + - - +
189A ILE* 3.7 8.1 - - - +
191A ARG* 1.3 80.9 - - - +
193A GLY* 1.3 64.6 + - - +
194A ASP* 3.2 39.2 + - - +
195A PHE* 4.4 2.9 - - + -
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Residues in contact with GLY 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A ILE 2.8 20.6 + - - -
190A LYS* 3.4 12.5 + - - -
192A ARG* 1.3 74.8 - - - +
194A ASP* 1.3 57.3 + - - +
195A PHE 3.7 6.3 - - - -
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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