Contacts of the helix formed by residues 150 - 167 (chain B) in PDB entry 4U9W
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 GLY 150 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B TYR* 3.3 12.4 + - - -
51B ASN* 5.0 0.7 - - - -
148B ARG 3.6 0.2 - - - -
149B LYS* 1.3 77.4 - - - +
151B LEU* 1.3 64.5 + - - +
152B GLY 3.3 2.5 - - - -
153B LYS* 3.4 6.7 + - - +
154B PHE* 3.0 23.7 + - - +
301B COA 2.7 23.8 + - - -
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Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TYR* 3.8 31.8 + - + -
53B LEU* 3.7 28.9 - - + -
55B VAL* 4.4 10.5 - - + -
57B ILE* 4.5 7.2 - - + -
111B ALA* 4.2 8.7 - - + -
119B VAL* 4.6 5.8 - - + -
120B ALA* 3.7 30.3 - - + -
142B LEU* 4.1 8.5 - - + -
146B VAL* 4.4 12.6 - - + +
149B LYS 3.4 2.8 + - - -
150B GLY* 1.3 78.7 - - - +
152B GLY* 1.3 58.1 + - - +
154B PHE* 3.2 5.5 + - + +
155B LEU* 2.9 41.0 + - + +
301B COA 3.7 1.2 + - - -
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Residues in contact with GLY 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B VAL* 4.8 1.6 - - - +
142B LEU* 3.8 14.9 - - - +
151B LEU* 1.3 73.3 - - - +
153B LYS* 1.3 60.8 + - - +
155B LEU* 3.2 6.9 + - - +
156B ILE* 3.2 25.8 + - - +
185B PHE* 3.5 7.8 - - - -
301B COA 2.8 38.0 + - - -
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Residues in contact with LYS 153 (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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150B GLY* 3.8 7.4 - - - +
152B GLY* 1.3 73.8 - - - +
154B PHE* 1.3 57.6 + - - +
156B ILE* 3.2 4.9 + - - +
157B GLN* 2.9 54.5 + - - +
185B PHE* 3.5 9.5 - - + -
189B ALA* 5.0 9.9 + - + +
190B LEU* 3.8 28.8 - - + +
301B COA 2.9 30.1 + - - +
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Residues in contact with PHE 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A LYS 4.1 8.3 - - - -
220A PHE* 4.2 4.7 - - + -
44B VAL 4.8 1.6 - - - -
45B PHE* 3.8 34.1 - + - -
47B LYS 3.7 18.6 - - - -
48B TYR* 3.4 27.1 - + + -
50B ARG* 3.6 25.8 - - - -
57B ILE* 3.5 32.1 - - + -
150B GLY 3.0 19.1 + - - +
151B LEU* 3.4 6.7 - - + +
153B LYS* 1.3 77.8 - - - +
155B LEU* 1.3 63.0 + - - +
157B GLN* 3.1 18.7 + - + +
158B ILE* 3.0 35.3 + - + +
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ILE* 4.3 28.5 - - + -
109B LEU* 3.6 30.6 - - + +
111B ALA* 5.0 4.7 - - + +
120B ALA* 4.0 26.7 - - + -
121B PHE* 4.3 14.6 - - - +
122B SER* 4.7 3.4 - - - +
140B VAL* 4.2 23.8 - - + -
142B LEU* 4.3 5.4 - - + -
151B LEU* 2.9 24.5 + - + +
152B GLY 3.2 7.8 + - - +
154B PHE* 1.3 76.2 - - - +
156B ILE* 1.3 59.2 + - + +
158B ILE* 3.2 8.0 + - + +
159B LEU* 3.1 28.6 + - - +
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Residues in contact with ILE 156 (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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122B SER* 5.4 0.2 - - - +
137B CYS* 4.3 5.2 - - + -
140B VAL* 4.2 23.3 - - + -
152B GLY 3.4 12.6 - - - +
153B LYS 3.2 3.9 + - - +
155B LEU* 1.3 74.1 - - + +
157B GLN* 1.3 61.5 + - - +
159B LEU* 3.3 25.6 + - + +
160B GLN* 2.9 27.3 + - - +
171B VAL* 5.3 1.6 - - + -
173B LEU* 5.7 0.2 - - + -
185B PHE* 4.1 4.3 - - + -
186B PHE* 4.0 19.1 - - + -
190B LEU* 3.5 34.8 - - + -
192B PHE* 3.9 23.8 - - + -
216B ARG* 3.9 7.2 - - - +
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Residues in contact with GLN 157 (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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219A LYS* 4.3 36.8 - - + +
304A GOL 5.1 2.5 - - - +
45B PHE* 5.5 4.7 - - + -
50B ARG* 5.9 0.5 + - - -
153B LYS* 2.9 44.5 + - - +
154B PHE* 3.1 22.0 + - + +
156B ILE* 1.3 78.1 - - - +
158B ILE* 1.3 57.2 + - + +
160B GLN* 3.2 7.5 + - + +
161B LEU* 2.8 30.1 + - - +
190B LEU* 6.6 0.2 - - + -
216B ARG* 4.4 12.9 - - - +
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Residues in contact with ILE 158 (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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39B LEU* 3.9 21.8 - - + -
45B PHE* 3.5 44.6 - - + +
57B ILE* 4.2 17.3 - - + -
109B LEU* 3.7 23.1 - - + -
154B PHE* 3.0 34.1 + - + +
155B LEU* 3.2 9.4 + - - +
157B GLN* 1.3 74.8 - - - +
159B LEU* 1.3 54.8 + - - +
161B LEU* 3.2 7.2 + - + +
162B MET* 2.8 45.9 + - + +
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Residues in contact with LEU 159 (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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109B LEU* 4.0 10.8 - - + -
122B SER* 3.5 20.4 - - - +
124B PHE* 3.5 35.0 - - + -
135B LEU* 3.3 22.8 - - + +
137B CYS* 3.6 28.9 - - + -
155B LEU 3.1 16.0 + - - +
156B ILE* 3.5 19.7 - - + +
158B ILE* 1.3 75.5 - - - +
160B GLN* 1.3 57.8 + - - +
162B MET* 3.2 17.3 + - + -
163B ALA* 2.8 28.2 + - - +
171B VAL* 3.9 11.2 - - + -
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Residues in contact with GLN 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GOL 3.6 18.4 - - - +
156B ILE 2.9 7.3 + - - +
157B GLN* 3.2 10.3 + - + +
159B LEU* 1.3 76.9 - - - +
161B LEU* 1.3 64.3 + - - +
163B ALA* 3.3 2.1 + - - +
164B ASN* 3.0 32.0 + - - +
171B VAL* 3.5 26.2 - - - +
192B PHE* 4.0 3.6 - - - -
216B ARG* 2.6 76.5 + - - +
217B ARG 3.4 15.9 + - - +
218B THR* 4.4 7.3 - - - +
219B LYS* 5.6 4.2 - - - +
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Residues in contact with LEU 161 (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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161A LEU* 3.9 16.2 - - + -
164A ASN* 4.2 12.6 - - + +
219A LYS* 5.6 1.8 - - + -
304A GOL 3.8 21.7 - - - -
39B LEU* 4.7 6.3 - - + -
42B PHE* 3.7 42.0 - - + -
45B PHE* 3.5 44.4 - - + -
157B GLN 2.8 19.7 + - - +
158B ILE* 3.6 6.7 - - - +
160B GLN* 1.3 74.4 - - - +
162B MET* 1.3 57.3 + - + +
164B ASN* 3.2 4.3 + - - +
165B SER* 3.0 27.2 + - - -
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Residues in contact with MET 162 (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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38B PRO* 3.6 42.4 - - + +
39B LEU* 4.3 15.9 - - + -
42B PHE* 5.7 1.1 - - + -
59B CYS* 4.0 12.3 - - - -
109B LEU* 3.9 5.4 - - + -
124B PHE* 3.6 18.2 - - + -
126B PHE* 4.6 5.4 - - + -
135B LEU* 4.0 7.6 - - + -
158B ILE* 2.8 29.6 + - + +
159B LEU* 3.5 33.4 - - + +
161B LEU* 1.3 76.1 - - + +
163B ALA* 1.3 61.7 + - - +
165B SER* 3.2 8.0 + - - +
166B THR* 2.7 31.3 + - + +
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Residues in contact with ALA 163 (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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135B LEU* 3.7 17.4 - - + +
159B LEU 2.8 19.8 + - - +
160B GLN 3.7 2.5 - - - +
162B MET* 1.3 73.4 - - - +
164B ASN* 1.3 57.5 + - - +
166B THR* 3.8 5.2 - - - -
167B GLN 3.1 6.4 + - - -
168B MET* 2.8 37.8 + - + +
170B LYS 4.3 2.0 - - - +
171B VAL* 3.7 20.0 - - + -
218B THR* 3.6 19.5 - - + -
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Residues in contact with ASN 164 (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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45A PHE* 3.1 19.5 - - - -
157A GLN* 3.9 12.6 + - - +
161A LEU* 4.4 13.5 - - + -
304A GOL 3.4 25.2 + - - -
160B GLN* 3.0 27.5 + - - +
161B LEU 3.5 7.6 - - - +
163B ALA* 1.3 75.6 - - - +
165B SER* 1.3 64.7 + - - +
167B GLN* 3.0 12.0 + - - -
218B THR* 3.4 20.7 - - - +
219B LYS* 2.9 30.7 + - - +
220B PHE* 3.8 9.3 - - + -
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Residues in contact with SER 165 (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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42A PHE* 4.4 11.6 - - - +
44A VAL* 3.7 10.0 - - - +
45A PHE* 3.5 21.2 - - - -
161A LEU* 4.2 9.4 - - - +
38B PRO 4.6 5.7 + - - -
42B PHE* 4.0 29.8 - - - -
161B LEU 3.0 14.3 + - - -
162B MET* 3.2 17.2 + - - +
164B ASN* 1.3 76.3 - - - +
166B THR* 1.3 64.6 + - - +
167B GLN 3.4 0.2 - - - -
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Residues in contact with THR 166 (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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44A VAL* 5.0 6.9 - - - +
28B LYS* 4.7 8.8 - - - +
32B ALA* 4.0 16.6 - - + -
35B LEU* 3.8 28.3 - - + -
38B PRO* 5.4 2.5 - - + -
126B PHE* 3.4 26.7 - - + -
162B MET* 2.7 21.6 + - - +
163B ALA 3.5 0.7 + - - -
165B SER* 1.3 84.0 - - - +
167B GLN* 1.3 70.0 + - - +
168B MET* 3.4 21.2 - - - +
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Residues in contact with GLN 167 (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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44A VAL* 3.1 44.2 + - + +
45A PHE* 3.7 34.1 - - + -
47A LYS 4.8 1.3 + - - +
154A PHE* 3.8 10.5 - - - -
28B LYS* 3.5 35.1 + - + +
133B GLU* 3.7 14.0 - - - +
163B ALA 3.1 0.6 + - - -
164B ASN 3.0 7.3 + - - -
166B THR* 1.3 83.2 - - - +
168B MET* 1.3 67.2 + - - +
169B LYS* 5.0 0.9 - - - +
220B PHE* 3.4 34.5 - - + -
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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
------------------------------------------------------------
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