Contacts of the helix formed by residues 177 - 187 (chain B) in PDB entry 1FX7
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 ASP 177 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173B HIS 4.0 1.0 + - - -
174B VAL 3.2 10.0 + - - +
175B GLN 3.2 2.4 - - - -
176B GLY* 1.3 74.9 - - - +
178B ILE* 1.3 56.1 + - - +
179B ASP* 3.3 11.8 + - - +
180B LEU* 3.1 36.3 + - + +
181B ILE* 2.8 30.1 + - - +
183B ARG* 5.4 1.1 + - - -
221B MET* 4.4 19.4 - - + +
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Residues in contact with ILE 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B GLU* 3.4 29.8 - - + +
96B GLU* 5.2 4.3 - - + -
98B HIS* 6.1 1.1 - - + -
99B ALA* 5.3 14.4 - - + +
175B GLN 4.1 12.8 - - - +
176B GLY* 3.6 6.5 + - - +
177B ASP* 1.3 68.8 + - - +
179B ASP* 1.3 66.5 + - - +
181B ILE* 3.1 5.5 - - + +
182B THR* 2.9 45.1 + - - +
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Residues in contact with ASP 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ASP* 3.3 8.1 + - - +
178B ILE* 1.3 81.9 - - - +
180B LEU* 1.3 61.8 + - - +
182B THR* 3.3 6.2 + - - -
183B ARG* 3.1 53.4 + - - +
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Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B VAL* 3.9 12.6 - - + -
177B ASP* 3.1 29.4 + - + +
179B ASP* 1.3 75.1 - - - +
181B ILE* 1.3 65.3 + - - +
183B ARG* 3.1 21.3 + - + +
184B LEU* 2.9 44.1 + - + +
215B VAL* 4.1 20.6 - - + -
216B THR 4.4 7.9 - - - +
217B LEU* 4.0 13.5 - - + -
218B PRO* 4.4 8.3 - - + -
221B MET* 3.6 31.6 - - + -
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Residues in contact with ILE 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TRP* 4.5 7.4 - - + -
95B GLU* 3.8 26.6 - - + +
128B PHE* 4.1 24.9 - - + -
170B LEU* 4.0 27.1 - - + -
174B VAL* 3.9 23.1 + - + +
175B GLN* 3.9 20.2 - - + +
177B ASP 2.8 20.1 + - - +
178B ILE* 3.1 25.8 - - - +
180B LEU* 1.3 72.7 - - - +
182B THR* 1.3 56.2 + - - +
184B LEU* 3.4 4.4 + - + +
185B LYS* 2.9 29.8 + - - +
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Residues in contact with THR 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B GLU* 3.6 29.6 - - + +
178B ILE* 2.9 22.5 + - - +
179B ASP* 3.6 6.5 - - - -
181B ILE* 1.3 76.4 - - - +
183B ARG* 1.3 63.1 + - + +
185B LYS* 3.3 8.6 + - - +
186B ASP* 2.9 39.5 + - - +
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Residues in contact with ARG 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B ASP* 5.2 1.2 + - - -
179B ASP* 3.1 38.4 + - - +
180B LEU* 3.1 39.3 + - - +
182B THR* 1.3 76.4 - - + +
184B LEU* 1.3 56.4 + - - +
186B ASP* 3.3 8.1 + - - +
187B ALA* 3.0 30.5 + - - +
215B VAL* 4.4 20.8 - - + +
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Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B TRP* 6.0 0.2 - - + -
170B LEU* 3.9 24.7 - - + -
174B VAL* 4.0 22.7 - - + -
180B LEU* 2.9 25.0 + - + +
181B ILE* 3.8 6.7 - - + +
183B ARG* 1.3 72.1 - - - +
185B LYS* 1.3 66.0 + - - +
187B ALA* 3.2 2.9 + - - -
188B GLY 3.1 4.3 + - - -
189B VAL* 2.8 62.5 + - + +
207B ILE* 4.4 7.9 - - + -
215B VAL* 4.1 18.4 - - + -
217B LEU* 4.0 25.8 - - + -
225B VAL* 5.2 2.0 - - + -
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Residues in contact with LYS 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B PRO* 5.5 1.8 - - - +
94B TRP* 3.7 41.0 - - + +
95B GLU* 2.9 33.2 + - + +
181B ILE 2.9 17.8 + - - +
182B THR* 3.6 7.4 - - - +
184B LEU* 1.3 75.9 - - - +
186B ASP* 1.3 77.1 + - - +
188B GLY* 3.0 14.9 + - - -
189B VAL 4.5 0.2 + - - -
190B VAL* 4.3 17.6 - - + +
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Residues in contact with ASP 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B THR* 2.9 33.6 + - - +
183B ARG* 3.7 6.6 - - - +
185B LYS* 1.3 91.3 - - - +
187B ALA* 1.3 59.8 + - - +
188B GLY 3.4 1.2 + - - -
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Residues in contact with ALA 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B ARG 3.0 16.5 + - - +
184B LEU 3.7 4.0 - - - +
185B LYS 3.2 0.4 - - - -
186B ASP* 1.3 75.0 - - - +
188B GLY* 1.3 61.3 + - - +
189B VAL* 3.3 14.6 + - + +
195B VAL* 5.3 4.0 - - - +
207B ILE* 4.9 3.6 - - + +
209B ILE* 4.0 31.0 - - + +
215B VAL* 4.3 8.5 - - + -
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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