Contacts of the helix formed by residues 139 - 158 (chain A) in PDB entry 4KZK
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 139 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ILE* 1.3 66.8 - - - +
140A ALA* 1.3 59.2 + - - +
141A TYR 3.4 2.0 - - - -
142A ARG* 2.7 49.5 + - - +
143A ILE* 2.9 30.3 + - - +
313A LEU* 4.1 24.1 - - - +
314A THR 2.9 21.0 + - - +
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Residues in contact with ALA 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ILE* 2.9 18.4 + - + +
139A SER* 1.3 70.8 - - - +
141A TYR* 1.3 57.2 + - - +
143A ILE* 3.3 3.3 + - - +
144A GLY 2.9 24.6 + - - -
177A THR* 3.6 29.2 - - - +
180A GLU* 3.5 32.1 + - + +
181A ARG* 3.6 14.3 - - + -
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Residues in contact with TYR 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A SER 3.4 0.4 - - - -
140A ALA* 1.3 77.6 - - - +
142A ARG* 1.3 65.8 + - + +
144A GLY* 3.2 3.3 + - - -
145A ARG* 2.9 68.9 + - + +
180A GLU* 3.7 23.4 + - + +
183A THR* 4.1 10.5 - - + -
184A GLY* 3.5 24.4 - - - -
187A ASP* 2.6 30.2 + - - +
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Residues in contact with ARG 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A SER* 2.7 42.7 + - - +
141A TYR* 1.3 83.3 - - + +
143A ILE* 1.3 64.0 + - + +
145A ARG* 3.2 12.4 + - + +
146A GLN* 3.1 28.6 + - - +
313A LEU* 5.5 2.8 + - - +
315A SER* 2.9 30.7 + - - +
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Residues in contact with ILE 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ILE* 4.0 16.2 - - + -
139A SER* 2.9 27.4 + - - +
140A ALA 3.5 5.6 - - - +
142A ARG* 1.3 75.3 - - + +
144A GLY* 1.3 67.4 + - - +
146A GLN* 3.1 24.6 + - - +
147A VAL* 2.9 20.1 + - - +
261A ILE* 3.7 40.6 - - + -
283A ILE* 4.1 11.4 - - + +
285A LEU* 4.2 5.8 - - + -
314A THR 4.4 0.9 - - - +
315A SER* 4.1 8.5 - - - -
316A GLY* 3.6 27.4 - - - +
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Residues in contact with GLY 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ALA 2.9 12.2 + - - -
141A TYR 3.5 3.6 - - - -
143A ILE* 1.3 78.6 - - - +
145A ARG* 1.3 61.5 + - - +
147A VAL* 3.1 10.8 + - - +
148A GLY 3.0 18.5 + - - -
181A ARG* 3.2 28.2 - - - +
184A GLY* 4.0 0.4 - - - -
185A ALA* 3.1 16.1 - - - -
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Residues in contact with ARG 145 (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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141A TYR* 2.9 59.9 + - + +
142A ARG* 3.2 11.9 + - + +
144A GLY* 1.3 74.8 - - - +
146A GLN* 1.3 57.9 + - + +
148A GLY 3.3 1.0 + - - -
149A ASP* 2.9 41.4 + - - +
184A GLY 3.2 19.9 - - - -
187A ASP* 3.6 11.3 + - - +
188A ALA* 3.4 24.6 - - - +
191A ALA* 4.3 13.9 - - - +
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Residues in contact with GLN 146 (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 ARG* 3.1 15.5 + - - +
143A ILE* 3.1 37.9 + - - +
145A ARG* 1.3 74.5 - - + +
147A VAL* 1.3 64.9 + - - +
149A ASP* 3.8 8.0 - - - +
150A ALA* 3.0 24.9 + - - +
283A ILE* 3.7 17.1 - - + +
316A GLY 2.9 28.0 + - - +
317A THR* 4.0 8.3 - - - +
318A LEU* 4.8 3.6 - - + +
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Residues in contact with VAL 147 (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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143A ILE 2.9 18.0 + - - +
144A GLY* 3.1 9.1 + - - +
146A GLN* 1.3 77.0 - - - +
148A GLY* 1.3 62.6 + - - +
150A ALA* 3.3 2.3 + - - +
151A ILE* 3.0 31.6 + - + +
181A ARG 5.7 0.2 - - - +
185A ALA* 4.0 8.1 - - + -
232A PHE* 3.8 19.7 - - + -
259A VAL* 3.7 29.7 - - + +
260A GLY 3.9 5.2 - - - +
261A ILE* 3.7 25.4 - - + -
283A ILE* 3.6 19.1 - - + -
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Residues in contact with GLY 148 (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 GLY 3.0 11.3 + - - -
145A ARG 3.7 2.2 - - - -
147A VAL* 1.3 77.6 - - - +
149A ASP* 1.3 57.3 + - - +
151A ILE* 3.3 2.5 + - - -
152A ALA* 2.9 31.0 + - - +
185A ALA* 3.8 23.1 - - - -
188A ALA* 3.8 8.7 - - - -
189A LEU* 3.6 15.3 - - - +
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Residues in contact with ASP 149 (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 ARG* 2.9 27.6 + - - +
146A GLN* 3.8 8.0 - - - +
148A GLY* 1.3 75.7 - - - +
150A ALA* 1.3 57.4 - - - +
152A ALA* 3.3 6.7 + - - +
153A ALA* 2.9 31.4 + - - +
188A ALA* 3.5 19.5 - - - +
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Residues in contact with ALA 150 (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 GLN 3.0 18.1 + - - +
147A VAL 3.6 5.2 - - - +
149A ASP* 1.3 78.4 - - - +
151A ILE* 1.3 61.9 + - - +
153A ALA* 3.4 5.6 + - - +
154A GLU* 3.2 23.4 + - - +
259A VAL* 4.3 13.2 - - + -
280A PHE* 4.4 5.6 - - + -
318A LEU* 3.7 41.5 - - + -
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Residues in contact with ILE 151 (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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147A VAL* 3.0 26.4 + - + +
148A GLY 3.6 6.3 - - - +
149A ASP 3.3 0.2 - - - -
150A ALA* 1.3 75.6 - - - +
152A ALA* 1.3 63.4 + - - +
154A GLU* 3.2 4.2 + - - +
155A ALA* 2.9 21.7 + - - +
189A LEU* 3.7 15.0 - - + -
194A PHE* 4.8 1.1 - - + -
230A VAL* 3.3 35.7 - - + -
231A ALA 3.8 13.7 - - - +
232A PHE* 3.8 29.8 - - + -
257A ILE* 4.2 18.8 - - + +
259A VAL* 3.5 18.4 - - + -
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Residues in contact with ALA 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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148A GLY 2.9 17.7 + - - +
149A ASP* 3.7 7.4 - - - +
151A ILE* 1.3 76.2 - - - +
153A ALA* 1.3 58.7 + - - +
155A ALA* 3.4 2.5 + - - +
156A LYS* 2.9 30.9 + - - +
188A ALA 5.2 0.4 - - - +
189A LEU* 4.1 1.5 - - + +
192A ALA* 3.6 30.7 - - + -
194A PHE* 4.1 18.3 - - + -
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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
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149A ASP 2.9 17.2 + - - +
150A ALA* 3.8 6.3 - - - +
151A ILE 3.2 0.2 - - - -
152A ALA* 1.3 78.7 - - - +
154A GLU* 1.3 56.2 + - - +
156A LYS* 3.4 10.2 + - - +
157A ARG* 3.0 27.0 + - - +
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Residues in contact with GLU 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 ALA 3.2 8.5 + - - +
151A ILE 3.2 4.1 + - - +
153A ALA* 1.3 75.0 - - - +
155A ALA* 1.3 66.8 + - - +
157A ARG* 2.7 51.2 + - - +
158A ARG* 2.9 44.6 + - - +
257A ILE* 3.7 21.3 - - + -
280A PHE* 3.4 48.5 - - + -
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Residues in contact with ALA 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 ILE 2.9 17.0 + - - +
152A ALA 3.7 4.5 - - - +
154A GLU* 1.3 77.6 - - - +
156A LYS* 1.3 61.8 + - - +
158A ARG* 3.2 3.1 + - - +
159A GLY 3.2 3.8 + - - -
160A TRP* 3.1 55.0 + - + +
162A PRO* 6.0 1.3 - - + -
194A PHE* 4.0 21.5 - - + -
230A VAL* 5.2 0.4 - - + -
257A ILE* 3.5 12.0 - - + +
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Residues in contact with LYS 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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152A ALA 2.9 17.2 + - - +
153A ALA* 3.6 9.6 - - - +
154A GLU 3.2 0.2 - - - -
155A ALA* 1.3 73.3 - - - +
157A ARG* 1.3 65.3 + - - +
159A GLY* 3.0 14.9 + - - +
160A TRP 4.9 5.4 - - - +
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Residues in contact with ARG 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 3.0 15.4 + - - +
154A GLU* 2.7 47.6 + - - +
156A LYS* 1.3 76.8 - - - +
158A ARG* 1.3 75.1 + - - +
159A GLY 3.4 0.5 + - - -
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Residues in contact with ARG 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A GLU* 2.9 43.8 + - - +
155A ALA 3.6 3.8 - - - +
156A LYS 3.1 0.6 - - - -
157A ARG* 1.3 87.3 - - - +
159A GLY* 1.3 60.4 + - - +
160A TRP* 3.5 34.2 + - + +
253A THR* 3.0 31.7 + - - -
254A ASP* 3.5 17.9 + - - +
256A MET 3.9 2.8 + - - -
257A ILE* 3.7 23.8 - - - +
280A PHE* 4.3 11.7 - - - +
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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
------------------------------------------------------------
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