Contacts of the helix formed by residues 171 - 186 (chain A) in PDB entry 4FLL
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 THR 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A GLY 4.5 2.7 - - - +
170A VAL* 1.3 79.5 - - - +
172A THR* 1.3 66.6 + - - +
173A GLU* 3.5 5.9 + - - +
174A GLU* 2.9 54.1 + - - +
175A ILE* 3.2 11.6 + - - +
216A ASP 3.6 11.9 - - - -
217A ARG* 3.3 23.1 - - + +
218A ARG 3.3 6.1 - - - -
219A PRO* 3.9 13.2 - - + -
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Residues in contact with THR 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A THR* 1.3 75.1 - - - +
173A GLU* 1.3 59.8 + - - +
175A ILE* 3.2 14.0 + - + +
176A ASP* 3.0 18.0 + - - +
204A THR* 3.3 33.7 + - + +
206A VAL* 4.5 11.2 - - + -
214A ILE 4.5 0.3 + - - -
215A PRO* 3.5 10.1 - - - +
216A ASP* 2.9 33.3 + - - -
218A ARG* 3.5 9.0 + - + +
220A LEU* 4.0 26.0 - - + -
226A VAL* 4.7 2.0 - - + -
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Residues in contact with GLU 173 (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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102A LEU* 3.5 8.1 - - - +
103A MET* 2.7 61.0 + - + +
106A ARG* 4.3 4.3 + - - -
171A THR* 3.8 4.3 - - - +
172A THR* 1.3 79.8 + - - +
174A GLU* 1.3 58.2 + - - +
176A ASP* 3.6 2.6 - - - +
177A HIS* 2.8 28.1 + - - +
200A LYS* 2.8 23.9 + - - +
215A PRO* 3.6 6.5 - - - +
216A ASP* 2.9 37.1 + - - +
217A ARG* 3.7 20.4 + - - +
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Residues in contact with GLU 174 (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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103A MET* 5.9 6.1 - - + -
165A MET* 3.6 13.6 - - + +
169A GLY 4.3 2.1 - - - +
170A VAL* 3.7 16.8 - - + +
171A THR* 2.9 48.0 + - - +
173A GLU* 1.3 76.0 - - + +
175A ILE* 1.3 62.9 + - - +
177A HIS* 3.4 7.5 + - - +
178A ALA* 3.1 17.7 + - - +
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Residues in contact with ILE 175 (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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162A ALA* 4.0 27.6 - - + +
165A MET* 4.0 18.4 - - + +
166A ILE* 3.7 24.9 - - + -
170A VAL* 4.0 13.5 - - + -
171A THR 3.2 13.9 + - - +
172A THR* 3.2 17.2 + - + +
174A GLU* 1.3 73.6 - - - +
176A ASP* 1.3 65.0 + - - +
178A ALA* 3.1 4.5 + - - +
179A VAL* 2.9 29.2 + - + +
202A CYS* 4.9 0.2 - - - -
204A THR* 4.6 7.0 - - + -
220A LEU* 4.1 17.5 - - + -
226A VAL* 5.6 1.3 - - + -
228A VAL* 4.4 17.3 - - + -
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Residues in contact with ASP 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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106A ARG* 3.8 17.2 + - - +
172A THR 3.0 5.8 + - - +
173A GLU* 3.3 5.5 + - - +
175A ILE* 1.3 76.7 - - - +
177A HIS* 1.3 61.2 + - - +
179A VAL* 3.2 1.8 + - - +
180A HIS* 2.9 26.9 + - - +
200A LYS* 3.5 26.5 + - - +
201A SER* 2.8 34.7 + - - -
202A CYS* 3.2 21.6 + - - -
215A PRO* 3.6 24.9 - - + +
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Residues in contact with HIS 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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103A MET* 6.3 0.2 - - - +
106A ARG* 3.4 50.5 + - - +
173A GLU 2.8 14.4 + - - +
174A GLU* 3.6 8.1 - - - +
175A ILE 3.2 0.2 - - - -
176A ASP* 1.3 76.9 + - - +
178A ALA* 1.3 63.8 + - - +
180A HIS* 3.2 3.9 + + + +
181A LEU* 3.0 50.3 + - + +
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Residues in contact with ALA 178 (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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161A VAL* 4.6 11.6 - - + +
165A MET* 3.4 35.4 - - + -
174A GLU 3.1 7.8 + - - +
175A ILE 3.1 2.2 + - - +
177A HIS* 1.3 80.2 - - - +
179A VAL* 1.3 56.7 + - + +
181A LEU* 3.3 9.1 + - - +
182A ALA* 2.9 30.8 + - - +
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Residues in contact with VAL 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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158A VAL* 3.9 12.7 - - + +
161A VAL* 5.6 1.1 - - + -
162A ALA* 4.0 23.1 - - + +
175A ILE* 2.9 21.8 + - + +
176A ASP* 3.6 7.2 - - - +
178A ALA* 1.3 73.4 - - + +
180A HIS* 1.3 68.2 + - - +
182A ALA* 3.2 7.0 + - - +
183A CYS* 2.9 32.6 + - - -
201A SER* 4.1 10.3 - - - +
202A CYS* 4.0 19.1 - - + -
230A ILE* 3.6 34.5 - - + -
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Residues in contact with HIS 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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106A ARG* 3.5 40.6 - - + +
107A PRO 2.9 22.8 + - - -
108A VAL* 3.6 26.2 - - + -
176A ASP 2.9 17.1 + - - +
177A HIS* 3.5 5.4 - + - +
179A VAL* 1.3 78.3 - - - +
181A LEU* 1.3 70.8 + - + +
183A CYS* 3.3 6.0 + - - +
184A ILE* 3.2 47.4 + - + +
190A PRO* 3.8 6.0 - - + +
193A LEU* 3.9 3.1 - - + -
201A SER* 2.8 31.9 + - - +
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Residues in contact with LEU 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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177A HIS* 3.0 49.4 + - + +
178A ALA* 3.8 7.2 - - - +
180A HIS* 1.3 81.7 - - + +
182A ALA* 1.3 55.3 + - - +
184A ILE* 3.3 18.0 + - + +
185A ALA* 2.9 28.9 + - - +
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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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158A VAL* 4.0 14.8 - - + -
161A VAL* 4.3 17.3 - - + -
178A ALA 2.9 19.1 + - - +
179A VAL* 3.6 8.3 - - - +
181A LEU* 1.3 73.0 - - - +
183A CYS* 1.4 63.8 + - - +
185A ALA* 3.5 3.5 + - - -
186A ARG* 2.9 48.4 + - - +
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Residues in contact with CYS 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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158A VAL* 4.3 11.4 - - - -
179A VAL* 2.9 27.0 + - - -
180A HIS 3.3 6.3 + - - +
182A ALA* 1.4 74.1 - - - +
184A ILE* 1.3 66.1 - - - +
186A ARG* 3.1 9.8 + - - -
188A CYS* 2.8 44.4 + - + +
190A PRO* 3.9 27.8 - - + -
201A SER 5.5 0.2 - - - -
231A THR 5.0 0.7 - - - -
232A LEU* 3.5 31.6 - - - -
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Residues in contact with ILE 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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107A PRO 4.1 1.6 - - - +
108A VAL* 4.2 9.2 - - + -
109A PRO* 3.6 24.9 - - + -
111A TYR* 3.8 22.6 + - - +
112A ILE* 3.8 24.4 - - + +
180A HIS* 3.2 44.0 + - + +
181A LEU* 3.3 17.9 + - + +
183A CYS* 1.3 78.4 - - + +
185A ALA* 1.3 57.3 + - - +
187A ASN* 2.9 23.6 + - - -
188A CYS 4.0 2.7 - - - +
190A PRO* 5.5 1.6 - - + -
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Residues in contact with ALA 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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181A LEU 2.9 17.4 + - - +
182A ALA* 3.7 10.3 - - - +
184A ILE* 1.3 75.8 - - - +
186A ARG* 1.3 66.9 + - + +
187A ASN* 3.3 8.8 + - - -
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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
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154A LEU* 4.1 27.0 - - + +
157A GLU* 2.8 40.0 + - - +
158A VAL* 3.7 17.9 - - - -
161A VAL* 4.4 14.4 - - - +
182A ALA* 2.9 42.1 + - - +
183A CYS* 3.1 6.3 + - - +
185A ALA* 1.3 85.3 - - + +
187A ASN* 1.3 71.0 + - - +
188A CYS* 3.1 19.0 + - - -
232A LEU* 4.9 0.4 - - + -
234A ARG* 4.2 7.1 + - - -
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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