Contacts of the helix formed by residues 148 - 162 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A THR* 1.3 68.5 - - - +
149A GLY* 1.3 61.6 + - - +
151A SER* 4.7 0.3 - - - -
152A GLN* 2.7 32.2 + - - +
294A ARG* 3.3 41.2 + - - +
321A ILE* 4.1 18.9 - - - +
323A GLY 4.8 1.8 - - - -
324A VAL* 3.6 9.3 - - - +
148B SER* 4.8 7.6 + - - -
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Residues in contact with GLY 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A THR* 2.8 26.8 + - - -
148A SER* 1.3 75.8 - - - +
150A VAL* 1.3 66.1 + - - -
151A SER 3.1 2.5 - - - -
152A GLN 3.2 5.0 + - - -
153A ALA 3.4 0.9 + - - -
286A LLP 3.5 11.7 - - - -
294A ARG* 3.4 17.2 - - - -
295A VAL 3.6 16.8 - - - +
296A GLY* 4.0 2.7 - - - -
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Residues in contact with VAL 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A THR* 4.4 0.4 - - - -
149A GLY* 1.3 68.6 - - - -
151A SER* 1.3 66.7 + - - +
153A ALA* 2.9 7.6 + - + +
154A ILE* 2.8 29.2 + - + +
253A ASP* 4.0 8.3 - - - +
255A ILE* 3.9 20.0 - - + -
281A LEU* 3.9 23.3 - - + -
282A GLY 3.4 34.8 - - - +
283A GLY* 5.0 0.7 - - - -
286A LLP 3.0 34.5 + - + +
295A VAL 5.7 0.2 - - - +
296A GLY* 4.2 3.3 - - - -
297A TRP 4.9 0.4 - - - +
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Residues in contact with SER 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A GLY 3.1 0.2 - - - -
150A VAL* 1.3 77.8 - - - +
152A GLN* 1.3 62.2 + - - +
154A ILE* 3.2 6.2 + - - +
155A VAL* 3.2 23.5 + - - +
175A PHE* 4.8 6.6 - - - -
177A HIS* 3.6 33.7 + - - -
286A LLP 2.5 29.3 + - - -
294A ARG* 3.7 10.7 + - - -
109B TYR* 6.0 0.2 - - - -
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Residues in contact with GLN 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ILE 4.6 0.9 - - - +
147A THR* 3.3 9.6 - - - -
148A SER* 2.7 50.3 + - - +
149A GLY 3.2 2.4 + - - -
150A VAL 3.2 0.2 - - - -
151A SER* 1.3 76.0 - - - +
153A ALA* 1.3 62.3 + - - +
155A VAL* 3.0 13.3 + - + +
156A LEU* 2.8 57.5 + - + +
317A LEU 5.0 1.4 + - - -
318A THR* 4.7 10.4 - - - +
321A ILE* 3.5 35.4 - - + +
323A GLY* 5.7 1.1 - - - +
324A VAL* 4.6 2.9 - - - +
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Residues in contact with ALA 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A THR* 3.5 32.0 - - + +
149A GLY 3.4 2.8 + - - -
150A VAL* 2.9 17.3 + - + +
152A GLN* 1.3 79.6 - - - +
154A ILE* 1.3 56.5 + - - +
156A LEU* 3.5 3.0 + - - +
157A ALA* 2.9 31.6 + - - +
281A LEU* 4.1 22.5 - - + +
297A TRP 4.2 8.3 - - - +
298A SER* 4.4 4.6 - - - -
314A MET* 5.4 0.5 - - - +
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Residues in contact with ILE 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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150A VAL* 2.8 26.9 + - + +
151A SER 3.5 7.0 - - - +
152A GLN 3.0 0.2 - - - -
153A ALA* 1.3 74.9 - - - +
155A VAL* 1.3 66.6 + - - +
157A ALA* 3.4 3.5 + - - +
158A LEU* 3.1 35.8 + - + +
175A PHE* 4.4 6.3 - - + -
177A HIS* 3.9 22.4 - - + -
178A TYR* 3.3 59.7 - - + +
181A VAL* 4.1 17.0 - - + -
253A ASP* 4.4 1.6 - - - +
281A LEU* 3.7 11.4 - - + -
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Residues in contact with VAL 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A SER 3.2 13.0 + - - +
152A GLN* 3.0 16.5 + - + +
154A ILE* 1.3 77.4 - - - +
156A LEU* 1.3 63.0 + - + +
159A THR* 2.8 46.1 + - + +
177A HIS* 4.6 3.1 - - - +
181A VAL* 4.2 27.1 - - + -
185A TYR* 3.9 23.6 - - + +
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Residues in contact with LEU 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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145A ILE* 4.7 3.6 - - + -
147A THR* 3.7 28.9 - - + -
152A GLN* 2.8 43.7 + - + +
153A ALA 3.9 3.4 - - - +
155A VAL* 1.3 78.4 - - + +
157A ALA* 1.3 64.7 + - - +
159A THR* 4.2 2.9 - - - -
160A ALA* 3.1 28.9 + - - +
298A SER* 6.1 0.2 - - - +
314A MET* 3.5 19.4 - - + +
317A LEU* 3.5 43.7 - - + +
318A THR* 3.9 16.4 - - + +
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Residues in contact with ALA 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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153A ALA 2.9 18.7 + - - +
154A ILE* 3.9 5.2 - - - +
156A LEU* 1.3 79.7 - - - +
158A LEU* 1.3 71.0 + - + +
161A LEU* 3.3 8.5 + - - +
251A ILE* 4.5 6.3 - - + -
279A LEU* 3.2 31.6 - - + -
281A LEU* 4.9 2.7 - - + -
310A TRP* 3.0 25.6 + - + +
314A MET* 3.7 12.1 - - - -
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Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ILE* 3.1 30.7 + - + +
155A VAL 4.2 0.9 - - - +
157A ALA* 1.3 81.4 - - + +
159A THR* 1.3 60.2 + - - +
161A LEU* 3.1 3.8 + - + -
162A CYS* 2.9 38.4 + - - +
168A ILE* 4.0 33.4 - - + -
178A TYR* 4.5 10.1 - - + +
181A VAL* 3.9 25.8 - - + -
182A CYS* 4.2 12.3 - - - -
187A ILE* 4.1 12.5 - - + +
219A VAL* 5.0 2.9 - - + -
251A ILE* 3.8 28.0 - - + -
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Residues in contact with THR 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 VAL* 2.8 30.9 + - + +
156A LEU* 4.2 0.2 - - - -
158A LEU* 1.3 80.4 - - + +
160A ALA* 1.3 51.9 + - - +
161A LEU 3.3 0.4 - - - -
162A CYS 3.9 6.6 - - - +
181A VAL* 4.7 1.8 - - + -
185A TYR* 3.6 51.5 - - + -
187A ILE* 4.9 2.2 - - + -
317A LEU* 3.5 15.7 - - - +
47B SER* 2.7 26.5 + - - -
49B HIS* 3.8 25.7 + - - +
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Residues in contact with ALA 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 LEU 3.1 21.2 + - - +
159A THR* 1.3 77.7 + - - +
161A LEU* 1.3 58.8 + - - +
310A TRP* 4.1 8.0 - - + +
313A GLY 3.8 7.2 - - - -
314A MET* 3.5 34.3 - - + +
317A LEU* 3.8 9.4 - - + -
46B SER* 3.2 12.6 - - - -
47B SER* 2.9 24.2 + - - -
50B ALA* 4.1 2.0 - - - -
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Residues in contact with LEU 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 ALA 3.3 15.9 + - - +
158A LEU* 3.1 4.4 + - + +
160A ALA* 1.3 81.7 - - - +
162A CYS* 1.3 66.3 + - - +
163A ASN* 4.3 1.9 + - - -
166A ASP* 4.4 2.6 - - - +
168A ILE* 5.3 0.2 - - + -
216A LYS* 3.4 44.1 + - + +
217A ALA* 3.8 17.3 - - + -
249A PRO* 4.3 3.8 - - + -
251A ILE* 4.8 2.5 - - + -
310A TRP* 3.5 31.9 - - + +
44B ILE* 3.5 32.5 - - + -
45B ALA 4.0 13.4 - - - +
46B SER 4.4 0.7 - - - -
47B SER* 4.1 6.2 + - - -
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Residues in contact with CYS 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 LEU* 2.9 20.5 + - - +
159A THR* 3.9 8.0 - - - +
161A LEU* 1.3 85.5 - - - +
163A ASN* 1.3 63.0 + - - +
166A ASP* 3.4 13.2 - - + +
168A ILE* 4.0 20.2 - - - -
187A ILE* 3.6 31.5 - - + +
216A LYS* 3.8 26.2 - - - -
47B SER* 3.3 14.8 - - - -
49B HIS* 5.7 0.7 - - - +
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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