Contacts of the helix formed by residues 175 - 187 (chain A) in PDB entry 1FXL
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 LYS 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A SER* 5.8 1.6 - - - -
121A SER* 3.4 29.7 + - - +
122A ILE* 4.3 8.2 - - + +
125A ALA* 3.7 3.9 - - - +
173A PHE* 3.7 6.1 - - - +
174A ASP* 1.3 99.6 + - - +
176A ARG* 1.3 65.9 + - - +
177A ILE* 4.1 11.7 - - + +
178A GLU* 2.8 46.9 + - + +
179A ALA 3.4 7.6 + - - -
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Residues in contact with ARG 176 (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 ALA* 2.7 35.5 + - - +
121A SER* 2.8 15.8 + - - +
123A ARG* 3.0 33.1 + - - +
124A ASP* 3.6 27.5 + - - +
125A ALA* 3.7 12.8 - - - +
175A LYS* 1.3 72.0 - - - +
177A ILE* 1.3 67.4 + - + +
179A ALA* 3.0 4.5 + - - +
180A GLU* 3.0 40.9 + - + +
202A PHE* 4.5 5.8 - - + -
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Residues in contact with ILE 177 (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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121A SER* 5.9 5.2 - - - +
175A LYS* 3.1 8.5 - - + -
176A ARG* 1.3 82.6 - - + +
178A GLU* 1.3 61.7 + - + +
180A GLU* 3.2 14.1 + - + +
181A GLU* 3.1 33.6 + - + +
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Residues in contact with GLU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A TYR* 3.3 23.4 - - - +
149A GLY* 3.3 21.8 - - - -
150A ARG* 3.3 11.4 + - - +
173A PHE* 3.8 10.4 - - + +
174A ASP* 3.3 15.7 + - - +
175A LYS* 2.8 49.1 + - + +
177A ILE* 1.3 78.2 - - + +
179A ALA* 1.3 57.3 + - - +
181A GLU* 3.4 7.3 + - - +
182A ALA* 3.0 27.0 + - - +
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Residues in contact with ALA 179 (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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125A ALA* 3.9 26.7 - - - +
127A LEU* 3.9 9.3 - - + +
173A PHE* 3.6 18.1 - - + -
175A LYS 3.4 2.9 + - - +
176A ARG 3.0 10.1 + - - +
178A GLU* 1.3 76.4 - - - +
180A GLU* 1.3 65.6 + - - +
182A ALA* 3.3 2.1 + - - +
183A ILE* 3.1 28.6 + - - +
202A PHE* 3.9 19.1 - - + -
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Residues in contact with GLU 180 (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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176A ARG* 3.0 31.1 + - - +
177A ILE* 3.2 16.5 + - + +
179A ALA* 1.3 76.9 - - - +
181A GLU* 1.3 65.8 + - + +
183A ILE* 3.2 2.8 + - - +
184A LYS* 3.1 47.8 + - + +
202A PHE* 3.1 32.8 - - + -
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Residues in contact with GLU 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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148A TYR* 3.5 26.0 - - + +
177A ILE* 3.1 28.0 + - + +
178A GLU* 3.7 10.3 - - - +
180A GLU* 1.3 81.7 - - - +
182A ALA* 1.3 55.8 + - - +
184A LYS* 3.6 11.8 + - - +
185A GLY 2.9 22.9 + - - -
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Residues in contact with ALA 182 (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 LEU* 4.0 7.9 - - + -
145A PHE* 4.0 7.4 - - + -
148A TYR* 3.7 19.9 - - + -
173A PHE* 3.6 28.9 - - + -
178A GLU 3.0 17.3 + - - +
179A ALA 3.6 4.0 - - - +
180A GLU 3.2 0.4 - - - -
181A GLU* 1.3 73.9 - - - +
183A ILE* 1.3 61.4 + - - +
186A LEU* 2.8 34.5 + - - +
200A VAL* 4.4 2.6 - - - +
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Residues in contact with ILE 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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127A LEU* 3.7 20.9 - - + -
179A ALA 3.1 13.5 + - - +
180A GLU* 3.2 7.8 + - - +
182A ALA* 1.3 73.9 - - - +
184A LYS* 1.3 74.7 + - + +
187A ASN* 2.8 42.9 + - + +
200A VAL* 3.5 29.8 - - + +
201A LYS* 4.2 2.2 - - - -
202A PHE* 3.5 45.8 - - + +
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Residues in contact with LYS 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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180A GLU* 3.1 44.4 + - + +
181A GLU* 3.9 13.2 - - - +
183A ILE* 1.3 93.9 - - + +
185A GLY* 1.3 62.0 + - - +
187A ASN 4.6 5.4 + - - +
189A GLN* 5.3 3.1 + - - +
202A PHE* 5.7 0.2 - - - -
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Residues in contact with GLY 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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148A TYR* 3.4 25.8 + - - -
181A GLU 2.9 17.1 + - - -
184A LYS* 1.3 79.8 - - - +
186A LEU* 1.3 59.6 + - - +
189A GLN* 3.2 17.7 - - - +
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Residues in contact with LEU 186 (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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144A LEU* 4.1 29.8 - - + +
145A PHE* 3.4 44.9 - - + -
147A GLN* 4.7 2.7 - - - +
148A TYR* 3.6 32.1 - - + +
182A ALA 2.8 15.6 + - - +
185A GLY* 1.3 78.8 - - - +
187A ASN* 1.3 65.4 + - - +
188A GLY 3.1 0.9 + - - -
189A GLN* 3.0 26.0 + - + +
191A PRO* 6.1 1.8 - - + -
198A ILE* 3.6 16.6 - - + +
200A VAL* 4.0 11.9 - - + -
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Residues in contact with ASN 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 ILE* 2.8 31.0 + - + +
184A LYS 4.8 3.5 - - - +
186A LEU* 1.3 70.2 - - - +
188A GLY* 1.3 63.5 + - - +
189A GLN* 3.2 11.0 + - - +
198A ILE 4.0 0.4 - - - -
199A THR* 3.5 13.2 - - - +
200A VAL* 3.0 47.3 + - + +
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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