Contacts of the helix formed by residues 148 - 162 (chain B) in PDB entry 4IX8
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 SER 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A SER* 4.8 8.4 + - - -
321A ILE* 3.5 28.8 - - - +
323A GLY 4.1 5.2 + - - -
147B THR* 1.3 68.7 - - - +
149B GLY* 1.3 61.4 + - - +
152B GLN* 2.7 30.4 + - - +
294B ARG* 3.3 40.8 + - - +
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Residues in contact with GLY 149 (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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147B THR* 2.7 30.0 + - - -
148B SER* 1.3 75.1 - - - +
150B VAL* 1.3 63.9 + - - -
151B SER 3.1 1.6 - - - -
152B GLN 3.2 6.1 + - - -
286B LLP 3.6 7.6 - - - -
294B ARG* 3.4 21.7 - - - -
295B VAL 3.8 16.6 - - - -
296B GLY* 4.1 2.5 - - - -
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Residues in contact with VAL 150 (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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147B THR* 4.2 0.7 - - - -
149B GLY* 1.3 69.4 - - - -
151B SER* 1.3 66.0 + - - +
153B ALA* 2.8 18.1 + - + -
154B ILE* 3.0 21.7 + - + +
253B ASP* 4.2 4.9 - - - +
255B ILE* 3.9 22.7 - - + -
281B LEU* 3.8 25.8 - - + -
282B GLY* 3.4 34.3 - - - +
283B GLY* 4.5 0.7 - - - +
286B LLP 3.0 35.4 + - + +
295B VAL 5.5 0.2 - - - +
296B GLY* 4.6 2.9 - - - -
297B TRP 4.9 0.7 - - - +
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Residues in contact with SER 151 (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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320A LEU 3.7 4.3 - - - +
321A ILE 3.7 21.1 - - - -
322A ALA* 3.9 8.8 - - - +
149B GLY 3.1 0.2 - - - -
150B VAL* 1.3 77.8 - - - +
152B GLN* 1.3 61.3 + - - +
154B ILE* 3.4 7.6 + - - +
155B VAL* 3.3 22.5 + - - +
175B PHE* 5.2 4.0 - - - -
177B HIS* 3.6 30.5 + - - -
286B LLP 2.6 28.5 + - - -
294B ARG* 3.6 3.1 + - - -
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Residues in contact with GLN 152 (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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321A ILE* 3.7 27.4 - - + +
146B ILE 4.6 1.0 - - - +
147B THR* 3.3 9.8 - - - -
148B SER* 2.7 51.7 + - - +
149B GLY 3.2 2.2 + - - -
150B VAL 3.1 0.6 - - - -
151B SER* 1.3 76.7 - - - +
153B ALA* 1.3 60.2 + - - +
155B VAL* 3.1 6.9 + - + +
156B LEU* 2.8 56.2 + - + +
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Residues in contact with ALA 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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147B THR* 3.4 31.3 - - + +
149B GLY 3.4 2.6 + - - -
150B VAL* 2.8 16.9 + - + +
152B GLN* 1.3 79.1 - - - +
154B ILE* 1.3 57.3 + - - +
156B LEU* 3.5 3.5 + - - +
157B ALA* 3.0 30.8 + - - +
279B LEU* 5.1 0.2 - - - +
281B LEU* 4.3 16.9 - - + +
297B TRP 4.2 14.1 - - - +
298B SER* 4.4 5.6 - - - -
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Residues in contact with ILE 154 (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 VAL* 3.0 25.8 + - + +
151B SER* 3.5 7.6 - - - +
153B ALA* 1.3 75.1 - - - +
155B VAL* 1.3 65.4 + - - +
157B ALA* 3.7 3.2 - - - +
158B LEU* 3.0 37.7 + - + +
175B PHE* 4.4 7.0 - - + -
177B HIS* 4.0 21.3 - - + -
178B TYR* 3.4 50.7 - - + +
181B VAL* 4.2 14.8 - - + -
253B ASP* 4.3 1.8 - - - +
281B LEU* 3.6 22.9 - - + -
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Residues in contact with VAL 155 (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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320A LEU* 3.4 37.5 - - + +
321A ILE* 4.9 4.7 - - + -
151B SER 3.3 5.4 + - - +
152B GLN* 3.1 14.5 + - + +
154B ILE* 1.3 78.3 - - - +
156B LEU* 1.3 59.5 + - + +
159B THR* 2.6 48.7 + - + +
181B VAL* 4.0 25.1 - - + -
185B TYR* 3.8 21.1 - - + +
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Residues in contact with LEU 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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145B ILE* 4.8 12.6 - - + -
146B ILE 5.6 0.4 - - - +
147B THR* 3.8 20.2 - - + -
152B GLN* 2.8 53.3 + - + +
153B ALA* 3.9 3.6 - - - +
155B VAL* 1.3 77.8 - - + +
157B ALA* 1.3 63.7 + - - +
159B THR* 4.1 4.3 - - - +
160B ALA* 3.0 30.3 + - - +
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Residues in contact with ALA 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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153B ALA 3.0 19.8 + - - +
154B ILE* 3.7 5.6 - - - +
156B LEU* 1.3 77.6 - - - +
158B LEU* 1.3 72.3 + - + +
160B ALA* 4.2 1.8 - - - +
161B LEU* 3.3 23.6 + - - +
251B ILE* 4.6 10.3 - - + -
279B LEU* 3.4 31.9 - - + -
281B LEU* 5.0 3.4 - - + -
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Residues in contact with LEU 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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154B ILE* 3.0 38.2 + - + +
155B VAL 4.2 1.1 - - - +
157B ALA* 1.3 81.4 - - + +
159B THR* 1.3 59.8 + - - +
161B LEU* 3.2 4.3 + - + -
162B CYS* 3.0 35.7 + - - +
168B ILE* 4.1 33.7 - - + -
178B TYR* 4.5 9.6 - - + +
181B VAL* 3.9 21.5 - - + -
182B CYS* 4.2 13.0 - - - -
187B ILE* 4.5 11.0 - - + -
219B VAL* 5.0 2.9 - - + -
251B ILE* 4.0 26.5 - - + -
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Residues in contact with THR 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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47A SER* 2.8 22.2 + - - -
49A HIS* 4.0 27.4 + - - +
50A ALA 4.7 0.3 + - - -
155B VAL* 2.6 33.3 + - + +
156B LEU* 4.0 5.0 + - - +
158B LEU* 1.3 74.7 - - + +
160B ALA* 1.3 61.7 + - - +
161B LEU 3.2 0.2 - - - -
162B CYS 4.0 5.3 - - - +
181B VAL* 4.8 4.7 - - + -
185B TYR* 3.6 52.5 - - + -
187B ILE* 4.9 3.4 - - + -
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Residues in contact with ALA 160 (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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46A SER* 3.2 14.3 - - - -
47A SER* 2.9 24.8 + - - -
50A ALA* 4.1 12.6 - - + -
156B LEU* 3.0 20.9 + - + +
157B ALA* 4.3 2.7 - - - +
159B THR* 1.3 78.3 + - - +
161B LEU* 1.3 56.9 + - - +
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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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44A ILE* 3.5 32.3 - - + -
45A ALA 3.9 15.5 - - - +
46A SER* 4.2 1.3 - - - +
47A SER* 4.0 6.7 + - - -
157B ALA 3.3 17.9 - - - +
158B LEU* 3.2 3.8 + - + +
159B THR 3.2 0.4 - - - -
160B ALA* 1.3 80.4 - - - +
162B CYS* 1.3 72.6 + - - +
163B ASN* 4.3 1.6 + - - -
166B ASP* 4.6 1.7 - - - +
168B ILE* 5.3 0.2 - - + -
216B LYS* 3.5 36.4 - - + +
217B ALA* 3.8 16.8 - - + -
249B PRO* 4.4 7.0 - - + -
251B ILE* 4.8 8.1 - - + -
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Residues in contact with CYS 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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47A SER* 3.3 13.9 - - - -
49A HIS* 5.9 0.3 - - - +
158B LEU* 3.0 19.9 + - - +
159B THR* 4.0 7.6 - - - +
161B LEU* 1.3 87.5 - - - +
163B ASN* 1.3 63.4 + - - +
166B ASP* 3.4 12.1 - - + +
168B ILE* 3.9 21.1 - - - -
187B ILE* 3.7 29.4 - - + +
216B LYS* 3.8 24.0 - - - -
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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