Contacts of the helix formed by residues 164 - 188 (chain A) in PDB entry 4IB4
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 164 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A GLN 3.9 4.2 + - - +
163A ALA* 1.3 74.7 - - - +
165A GLN* 1.3 55.4 + - - +
166A TYR 4.8 0.7 - - - +
167A ASN* 3.4 29.6 - - + +
168A SER* 2.8 39.7 + - - -
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Residues in contact with GLN 165 (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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88A ALA* 5.3 1.2 - - - +
164A ASN* 1.3 69.5 - - - +
166A TYR* 1.4 62.6 + - - +
168A SER* 3.9 5.2 - - - -
169A ARG* 3.3 22.2 + - - +
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Residues in contact with TYR 166 (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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164A ASN* 3.5 0.8 - - - +
165A GLN* 1.4 76.5 - - - +
167A ASN* 1.3 67.9 + - - +
169A ARG* 3.5 14.4 + - - +
170A ALA* 3.5 12.3 + - - +
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Residues in contact with ASN 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ASN* 3.4 26.3 + - + +
165A GLN 3.4 0.2 - - - -
166A TYR* 1.3 79.3 - - - +
168A SER* 1.4 55.6 + - - +
170A ALA* 3.4 8.5 + - - +
171A THR* 2.7 36.8 + - - +
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Residues in contact with SER 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ALA* 3.5 17.6 - - - +
163A ALA* 4.9 7.3 - - - +
164A ASN 2.8 30.4 + - - -
165A GLN* 3.9 4.5 - - - -
167A ASN* 1.4 69.0 - - - +
169A ARG* 1.4 60.3 + - - +
171A THR* 3.6 8.0 - - - -
172A ALA* 2.9 31.5 + - - +
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Residues in contact with ARG 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ALA* 3.9 10.0 - - + +
91A TYR* 4.7 21.7 + - + -
165A GLN 3.3 12.7 + - - +
166A TYR* 3.7 11.2 - - - +
167A ASN 3.3 0.2 - - - -
168A SER* 1.4 77.1 - - - +
170A ALA* 1.4 61.1 + - - +
172A ALA* 3.4 3.4 + - - +
173A PHE* 3.1 61.3 + - + -
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Residues in contact with ALA 170 (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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166A TYR 3.5 8.3 + - - +
167A ASN* 3.4 11.3 + - - +
169A ARG* 1.4 77.9 - - - +
171A THR* 1.4 56.0 + - - +
173A PHE* 3.3 10.3 + - - +
174A ILE* 3.0 43.0 + - + +
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Residues in contact with THR 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ASP* 5.6 3.4 - - - +
167A ASN* 2.7 24.8 + - - +
168A SER* 3.6 9.1 - - - -
170A ALA* 1.4 75.8 - - - +
172A ALA* 1.4 59.7 + - - +
174A ILE* 3.5 12.2 + - - +
175A LYS* 3.2 44.2 + - + +
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Residues in contact with ALA 172 (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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88A ALA* 3.5 30.5 - - + +
91A TYR* 5.0 3.8 - - + -
92A PHE* 4.0 22.3 - - + -
168A SER 2.9 18.3 + - - +
169A ARG 3.7 4.7 - - - +
171A THR* 1.4 72.8 - - - +
173A PHE* 1.4 62.9 + - + +
175A LYS* 3.3 4.7 + - - +
176A ILE* 3.0 33.9 + - + +
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Residues in contact with PHE 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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91A TYR* 4.2 35.4 - + + -
169A ARG* 3.1 52.4 + - + +
170A ALA* 3.6 7.4 - - - +
172A ALA* 1.4 76.3 - - + +
174A ILE* 1.4 53.4 + - + +
176A ILE* 3.5 12.1 + - + +
177A THR* 2.7 38.4 + - - +
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Residues in contact with ILE 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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170A ALA* 3.0 33.6 + - + +
171A THR* 3.6 10.5 - - - +
172A ALA 3.3 0.2 - - - -
173A PHE* 1.4 75.7 - - + +
175A LYS* 1.4 60.6 + - + +
177A THR* 3.3 7.9 + - - -
178A VAL* 3.1 39.5 + - + +
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Residues in contact with LYS 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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92A PHE* 3.7 29.2 - - + -
148A ALA* 5.3 8.1 - - + +
151A VAL* 4.7 6.5 - - - +
152A ASP* 3.6 21.9 + - - +
155A ILE* 3.7 26.9 - - - +
171A THR* 3.2 31.7 + - + +
172A ALA 3.3 7.2 + - - +
174A ILE* 1.4 74.9 - - + +
176A ILE* 1.4 64.2 + - - +
178A VAL* 3.5 8.0 + - - +
179A VAL* 3.1 29.1 + - - +
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Residues in contact with ILE 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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91A TYR* 4.3 8.7 - - + +
92A PHE* 3.6 41.5 - - + -
95A SER* 3.5 24.9 - - - +
145A HIS* 3.6 21.3 - - + +
172A ALA* 3.0 23.5 + - + +
173A PHE* 3.7 15.3 - - + +
175A LYS* 1.4 72.4 - - - +
177A THR* 1.4 65.9 + - - +
179A VAL* 3.2 8.0 + - + +
180A TRP* 3.1 35.1 + - + -
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Residues in contact with THR 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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173A PHE* 2.7 23.1 + - - +
174A ILE* 3.5 7.1 - - - -
176A ILE* 1.4 77.8 - - - +
178A VAL* 1.4 56.5 + - + +
180A TRP* 3.2 8.8 + - - +
181A LEU* 2.9 51.6 + - + +
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Residues in contact with VAL 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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174A ILE* 3.1 26.0 + - + +
175A LYS* 3.7 10.5 - - - +
176A ILE 3.3 0.2 - - - -
177A THR* 1.4 74.6 - - + +
179A VAL* 1.3 58.3 + - + +
181A LEU* 3.2 12.8 + - + +
182A ILE* 2.9 47.7 + - + +
2011A PEG 5.4 4.7 - - - +
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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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92A PHE* 6.0 0.4 - - + -
141A ALA* 3.9 5.8 - - - +
144A TRP* 3.7 42.1 - - + +
145A HIS* 3.5 37.0 - - + +
148A ALA* 3.9 16.4 - - + -
175A LYS 3.1 17.6 + - - +
176A ILE* 3.2 9.6 + - - +
178A VAL* 1.3 74.8 - - + +
180A TRP* 1.3 59.0 + - - +
182A ILE* 3.4 11.8 + - + +
183A SER* 2.9 30.8 + - - -
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Residues in contact with TRP 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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95A SER* 2.9 31.4 + - - -
98A VAL* 5.3 5.6 - - + -
99A ALA* 3.7 34.5 - - + -
102A LEU* 5.1 3.1 - - + -
137A LEU* 4.3 17.7 - - + -
138A PHE* 3.7 31.4 - + - -
141A ALA* 4.0 14.1 - - + -
145A HIS* 3.7 11.6 - + - -
176A ILE* 3.1 33.3 + - + +
177A THR* 3.2 9.8 + - - +
179A VAL* 1.3 73.7 - - - +
181A LEU* 1.3 58.9 + - + +
183A SER* 3.3 4.1 + - - -
184A ILE* 3.0 40.0 + - + +
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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 THR* 2.9 39.4 + - + +
178A VAL* 3.7 11.0 - - + +
180A TRP* 1.3 73.7 - - + +
182A ILE* 1.4 65.1 + - - +
184A ILE* 3.4 21.2 + - + +
185A GLY 3.2 17.7 + - - -
2009A OLA 3.9 13.2 - - + +
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Residues in contact with ILE 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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144A TRP* 3.6 57.4 - - + +
178A VAL* 2.9 40.0 + - + +
179A VAL* 3.5 9.0 - - + +
181A LEU* 1.4 75.1 - - - +
183A SER* 1.4 61.0 + - - +
185A GLY* 3.4 2.9 + - - -
186A ILE* 3.2 32.2 + - + +
2009A OLA 4.1 13.6 - - + +
2011A PEG 3.7 37.2 - - - +
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Residues in contact with SER 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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137A LEU* 3.6 29.3 - - - +
140A THR* 3.7 15.0 - - - +
141A ALA* 3.2 30.4 + - - +
144A TRP* 4.9 0.7 - - - +
179A VAL* 2.9 14.3 + - - +
180A TRP* 3.5 10.5 - - - -
182A ILE* 1.4 73.9 - - - +
184A ILE* 1.4 63.3 + - - +
186A ILE* 3.5 2.4 + - - +
187A ALA* 3.1 25.5 + - - +
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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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133A PHE* 4.3 8.9 - - + -
137A LEU* 3.8 19.7 - - + -
180A TRP* 3.0 33.2 + - + +
181A LEU* 3.4 22.8 + - + +
183A SER* 1.4 73.5 - - - +
185A GLY* 1.3 55.3 + - - +
187A ALA* 3.1 3.2 + - - +
188A ILE* 2.7 57.0 + - + +
2005A OLB 5.3 4.7 - - + -
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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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181A LEU 3.2 11.5 + - - -
182A ILE 3.4 4.2 + - - -
183A SER 3.4 0.2 - - - -
184A ILE* 1.3 77.2 - - - +
186A ILE* 1.3 57.5 + - - +
188A ILE* 3.6 20.3 - - - +
189A PRO* 3.8 2.3 - - - +
2009A OLA 3.6 37.1 - - - +
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Residues in contact with ILE 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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136A VAL* 4.3 7.2 - - + -
140A THR* 3.7 34.5 - - + +
144A TRP* 3.9 7.4 - - + +
182A ILE* 3.2 23.1 + - + +
183A SER 3.5 4.2 + - - +
184A ILE 3.3 0.2 - - - -
185A GLY* 1.3 76.1 - - - +
187A ALA* 1.4 58.4 + - - +
188A ILE 3.6 0.2 - - - -
189A PRO* 3.1 4.0 - - - +
217A PHE* 3.1 29.1 - - - -
221A GLY* 4.1 15.9 - - - +
224A ALA* 3.6 33.7 - - + +
225A ALA* 4.0 11.0 - - + -
2001A ERM 4.7 1.6 - - + +
2009A OLA 4.1 25.5 - - + +
2011A PEG 4.8 3.8 - - - -
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Residues in contact with ALA 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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133A PHE* 3.4 33.4 - - + +
136A VAL* 3.8 12.8 - - + -
137A LEU* 3.6 27.8 - - - +
183A SER 3.1 16.4 + - - +
184A ILE 3.1 1.8 + - - +
186A ILE* 1.4 74.4 - - - +
188A ILE* 1.4 62.2 + - - +
189A PRO* 3.2 4.0 - - - -
190A VAL* 3.3 18.4 + - - +
191A PRO* 3.5 2.3 - - - +
217A PHE* 5.0 0.2 - - - -
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Residues in contact with ILE 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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133A PHE* 3.9 19.0 - - + -
184A ILE* 2.7 27.6 + - + +
185A GLY* 3.6 22.4 - - - +
187A ALA* 1.4 70.4 - - - +
189A PRO* 1.4 70.1 - - + +
190A VAL 3.2 0.9 + - - -
191A PRO* 3.3 11.2 - - + +
192A ILE* 3.4 36.0 - - + +
2005A OLB 4.1 36.3 - - + -
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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
------------------------------------------------------------
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