Contacts of the helix formed by residues 151 - 171 (chain A) in PDB entry 4Q9U
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 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A THR 5.2 1.3 + - - +
149A PHE* 3.0 38.7 + - - +
150A HIS* 1.3 103.0 - - + +
152A THR* 1.3 70.3 + - - +
153A GLY 3.5 0.9 - - - -
154A GLN* 4.6 4.5 + - - +
155A GLU* 4.1 13.9 + - - +
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Residues in contact with THR 152 (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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149A PHE* 4.4 10.9 - - - +
151A LYS* 1.3 87.6 - - - +
153A GLY* 1.3 65.4 + - - +
154A GLN 3.2 2.7 - - - -
155A GLU* 3.0 27.7 + - + +
156A ILE* 2.9 43.5 + - + +
193A MET* 5.7 6.7 - - + -
197A GLY* 4.9 11.1 + - - -
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Residues in contact with GLY 153 (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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146A LEU* 4.6 21.4 - - - +
149A PHE* 3.8 27.9 + - - +
151A LYS 3.5 1.2 - - - -
152A THR* 1.3 76.7 - - - +
154A GLN* 1.3 62.6 + - - +
156A ILE* 3.4 10.3 - - - +
157A TYR* 3.0 24.9 + - - +
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Residues in contact with GLN 154 (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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149A PHE 5.2 0.8 + - - -
151A LYS 4.6 5.2 + - - +
152A THR 3.2 0.4 - - - -
153A GLY* 1.3 72.6 - - - +
155A GLU* 1.3 60.8 + - - +
157A TYR* 2.8 27.8 + - - -
158A LYS* 3.1 30.8 + - + +
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Residues in contact with GLU 155 (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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151A LYS 4.1 8.3 + - - +
152A THR* 3.2 37.7 + - + +
154A GLN* 1.3 80.7 - - - +
156A ILE* 1.3 62.6 + - + +
159A GLN* 3.7 20.5 + - - +
192A ARG 5.4 0.3 - - - +
193A MET* 5.2 6.1 - - - +
196A ARG* 4.3 22.6 + - - +
197A GLY* 4.3 18.6 + - - -
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Residues in contact with ILE 156 (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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142A PHE* 5.3 13.2 - - + -
146A LEU* 5.3 7.2 - - + -
152A THR* 2.9 29.6 + - + +
153A GLY* 3.4 17.0 - - - +
155A GLU* 1.3 80.6 - - + +
157A TYR* 1.3 78.1 + - + +
159A GLN* 3.3 25.8 + - - +
160A THR* 2.6 34.8 + - + +
189A VAL* 5.3 1.1 - - + -
193A MET* 4.4 24.2 - - + -
211A ILE* 5.9 6.1 - - + -
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Residues in contact with TYR 157 (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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142A PHE* 5.3 9.2 - + - -
143A ILE* 4.3 25.2 - - + +
146A LEU* 5.0 11.7 - - + -
153A GLY 3.0 19.6 + - - +
154A GLN* 2.8 17.3 + - - +
156A ILE* 1.3 78.1 - - + +
158A LYS* 1.3 70.4 + - + +
160A THR* 2.7 20.3 + - - -
161A LYS* 3.1 43.4 + - + +
214A TYR* 4.3 23.3 + + - -
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Residues in contact with LYS 158 (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 GLN* 3.1 26.0 + - + +
157A TYR* 1.3 86.2 - - + +
159A GLN* 1.3 63.6 + - - +
161A LYS* 3.2 4.8 + - + +
162A LEU* 3.0 58.0 + - + +
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Residues in contact with GLN 159 (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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155A GLU* 3.7 14.3 + - - +
156A ILE* 3.3 40.3 + - - +
158A LYS* 1.3 79.2 - - - +
160A THR* 1.3 64.2 + - - +
162A LEU* 3.6 16.6 + - - +
163A PHE* 3.2 19.8 - - + -
189A VAL* 3.3 24.7 - - + +
192A ARG* 2.6 54.0 + - - +
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Residues in contact with THR 160 (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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156A ILE* 2.6 24.1 + - + +
157A TYR* 2.7 14.1 + - - -
159A GLN* 1.3 81.8 - - - +
161A LYS* 1.3 63.9 + - - +
162A LEU 3.0 1.6 + - - -
163A PHE* 3.0 13.8 - - + -
164A LEU* 3.0 30.5 + - + +
185A PHE* 3.2 40.6 - - + -
189A VAL* 5.1 1.1 - - + -
211A ILE* 6.4 2.0 - - + -
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Residues in contact with LYS 161 (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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157A TYR* 3.1 42.7 + - + +
158A LYS* 3.2 4.0 + - + +
160A THR* 1.3 78.9 - - - +
162A LEU* 1.3 58.6 + - - +
164A LEU* 3.8 16.8 - - + -
165A GLU* 2.9 55.2 + - + +
214A TYR* 4.1 16.8 + - + +
218A ARG* 3.5 35.8 - - - +
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Residues in contact with LEU 162 (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 LYS* 3.0 55.9 + - + +
159A GLN* 3.7 13.2 - - - +
160A THR 3.0 2.0 + - - -
161A LYS* 1.3 75.1 - - - +
163A PHE* 1.3 63.6 + - + +
165A GLU* 3.0 31.1 + - - +
166A GLY* 3.1 7.4 + - - -
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Residues in contact with PHE 163 (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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159A GLN* 3.2 29.6 - - + -
160A THR* 3.0 24.0 - - + -
162A LEU* 1.3 76.6 - - + +
164A LEU* 1.3 71.3 - - + +
166A GLY* 2.8 21.7 + - - +
167A MET* 3.0 35.4 - - + +
170A LYS* 5.4 6.5 - - - +
181A CYS* 5.5 3.1 - - + -
185A PHE* 3.1 66.0 - + + -
192A ARG* 5.4 5.8 - - - -
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Residues in contact with LEU 164 (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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160A THR* 3.0 31.6 + - + +
161A LYS* 3.8 13.2 - - + -
163A PHE* 1.3 95.0 - - + +
165A GLU* 1.3 66.6 + - - +
167A MET* 2.8 37.2 + - + +
168A HIS* 3.7 3.8 + - - +
185A PHE* 4.4 4.7 - - + -
214A TYR* 4.8 16.4 - - + -
215A ILE* 3.4 37.0 - - + -
219A LEU* 4.9 10.8 - - + -
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Residues in contact with GLU 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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161A LYS* 2.9 46.5 + - + +
162A LEU* 3.1 25.4 - - - +
164A LEU* 1.3 75.1 - - - +
166A GLY* 1.3 61.8 + - - +
168A HIS* 3.5 18.4 + - - +
169A TYR* 4.0 5.7 + - - +
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Residues in contact with GLY 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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162A LEU 3.1 8.2 + - - -
163A PHE* 2.8 14.5 + - - -
165A GLU* 1.3 77.1 - - - +
167A MET* 1.3 54.6 + - - -
169A TYR* 3.0 16.0 + - - +
170A LYS* 2.9 42.2 + - - +
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Residues in contact with MET 167 (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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163A PHE* 3.0 46.8 + - + +
164A LEU* 2.8 35.8 + - + +
166A GLY* 1.3 67.2 - - - -
168A HIS* 1.3 58.6 + - - +
170A LYS* 3.6 32.9 - - + +
171A ARG* 3.0 26.0 + - - +
181A CYS* 4.6 23.6 - - + +
182A ALA* 6.3 0.7 - - - -
185A PHE* 5.4 1.6 - - - -
219A LEU* 4.8 17.7 - - + -
222A TYR* 4.4 4.2 - - - -
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Residues in contact with HIS 168 (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 LEU 3.7 3.7 + - - +
165A GLU* 3.5 12.2 + - - +
166A GLY 3.2 0.8 - - - -
167A MET* 1.3 77.7 - - - +
169A TYR* 1.3 83.0 + + - +
171A ARG* 3.3 27.1 - - - +
219A LEU* 5.8 1.9 - - + +
222A TYR* 2.9 37.8 + - + +
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Residues in contact with TYR 169 (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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165A GLU 4.0 2.9 + - - +
166A GLY* 3.0 14.6 + - - +
168A HIS* 1.3 101.0 - + - +
170A LYS* 1.3 61.6 + - + +
171A ARG* 3.2 3.1 + - - +
172A ASP* 4.2 10.4 + - - +
173A LEU* 4.8 3.8 - - - +
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Residues in contact with LYS 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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163A PHE* 4.5 6.4 + - - +
166A GLY* 2.9 27.0 + - - +
167A MET* 3.4 37.1 + - + +
168A HIS 3.3 0.2 - - - -
169A TYR* 1.3 76.1 - - + +
171A ARG* 1.3 50.9 + - - +
172A ASP 2.7 6.6 + - - -
173A LEU* 2.6 66.2 + - + +
178A GLN* 3.2 8.7 + - + -
181A CYS* 5.5 9.9 - - + -
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Residues in contact with ARG 171 (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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167A MET 3.0 8.8 + - - +
168A HIS* 3.3 24.4 + - - +
169A TYR 3.2 1.5 - - - +
170A LYS* 1.3 74.5 - - - +
172A ASP* 1.3 95.2 + - - +
173A LEU 4.2 0.2 - - - +
178A GLN* 2.9 21.4 + - - +
222A TYR* 3.7 39.9 - - + -
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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