Contacts of the helix formed by residues 175 - 192 (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 LEU 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A LYS* 4.3 9.0 - - - +
98A VAL* 3.8 34.1 - - + +
120A ASP* 3.7 24.9 - - + +
121A GLN 5.7 0.4 - - - +
172A TYR* 3.2 28.1 + - + +
173A ASP 3.1 2.4 - - - -
174A GLN* 1.3 79.1 - - + +
176A PRO* 1.4 77.1 - - + +
177A THR* 3.7 25.4 - - + +
178A ALA* 2.9 21.1 + - + +
179A ARG* 3.0 11.4 + - - +
600A GAL 4.3 2.2 - - - +
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Residues in contact with PRO 176 (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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98A VAL* 4.9 8.5 - - + -
123A VAL* 5.5 9.9 - - + -
127A GLY 5.8 2.7 - - - +
173A ASP 5.1 1.1 - - - +
174A GLN 3.6 8.7 - - - +
175A LEU* 1.4 89.4 - - + +
177A THR* 1.3 64.7 + - - +
179A ARG* 3.2 11.9 + - + +
180A GLU* 2.9 42.5 + - + +
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Residues in contact with THR 177 (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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119A ASP 4.2 10.7 + - - +
120A ASP* 3.8 14.4 - - - +
121A GLN 6.2 0.2 - - - -
138A ILE* 4.3 5.4 + - - +
140A ALA* 3.6 12.5 - - - +
175A LEU* 3.7 24.6 - - + +
176A PRO* 1.3 78.1 - - - +
178A ALA* 1.3 65.8 + - - +
180A GLU* 4.3 9.4 - - - -
181A ARG* 2.9 65.0 + - - +
600A GAL 4.2 0.7 - - - +
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Residues in contact with ALA 178 (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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172A TYR* 3.5 26.7 - - + +
173A ASP* 5.2 0.4 - - - -
175A LEU* 2.9 22.7 + - + +
177A THR* 1.3 79.9 - - - +
179A ARG* 1.3 64.9 + - - +
181A ARG* 3.4 6.7 + - - +
182A THR* 3.2 26.9 + - + +
234A SER* 3.8 27.3 - - - -
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Residues in contact with ARG 179 (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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169A ARG* 5.4 0.4 - - - +
172A TYR 4.3 1.2 + - - -
173A ASP* 3.8 46.4 - - - +
175A LEU 3.0 10.1 + - - +
176A PRO* 3.6 12.1 + - + +
178A ALA* 1.3 75.9 - - - +
180A GLU* 1.3 79.7 + - - +
182A THR* 3.3 3.1 + - - -
183A THR* 2.8 59.9 + - - +
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Residues in contact with GLU 180 (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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140A ALA* 3.5 27.6 + - + +
141A TYR* 3.7 26.2 + - + +
176A PRO* 2.9 33.6 + - - +
177A THR* 4.3 3.1 - - - -
179A ARG* 1.3 98.4 + - - +
181A ARG* 1.3 55.9 + - - +
183A THR* 3.8 5.8 - - - -
184A GLY 2.9 24.9 + - - -
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Residues in contact with ARG 181 (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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119A ASP 4.8 2.4 + - - -
138A ILE* 3.5 19.6 - - + +
140A ALA* 3.6 22.2 - - + +
143A ILE* 5.2 0.2 - - + -
144A GLY* 3.2 22.7 - - - -
147A VAL* 5.6 0.2 - - - +
177A THR* 2.9 50.2 + - - +
178A ALA* 3.6 4.9 - - - +
180A GLU* 1.3 76.7 - - - +
182A THR* 1.3 61.1 + - - +
185A ALA* 3.2 8.5 + - - +
233A GLY 4.3 7.2 - - - +
234A SER* 2.8 44.5 + - - +
261A ILE* 3.8 25.6 - - + +
600A GAL 2.9 57.8 + - - -
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Residues in contact with THR 182 (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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169A ARG* 2.9 37.6 + - + -
170A LEU 3.4 23.6 - - - +
171A ALA* 5.1 1.3 - - - -
172A TYR 5.8 0.9 - - - +
173A ASP* 4.0 0.5 + - - -
178A ALA 3.2 12.0 + - - +
179A ARG* 3.3 9.2 + - - -
181A ARG* 1.3 74.1 - - - +
183A THR* 1.3 62.0 + - - +
185A ALA* 3.3 2.1 + - - +
186A VAL* 2.9 33.9 + - - +
232A PHE* 3.8 11.2 - - + -
233A GLY* 3.4 26.2 - - - +
234A SER* 4.4 1.1 - - - +
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Residues in contact with THR 183 (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* 4.1 8.5 - - + -
169A ARG* 5.2 3.0 + - - +
179A ARG* 2.8 47.2 + - - +
180A GLU* 3.8 6.1 - - - -
182A THR* 1.3 75.3 + - - +
184A GLY* 1.3 59.9 + - - +
186A VAL* 3.3 5.9 + - - +
187A ASP* 2.9 52.9 + - - +
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Residues in contact with GLY 184 (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* 3.5 37.1 - - - -
144A GLY 3.4 8.1 - - - -
145A ARG* 3.2 11.5 - - - -
180A GLU 2.9 13.3 + - - -
183A THR* 1.3 75.5 - - - +
185A ALA* 1.3 57.1 + - - +
187A ASP 3.3 0.3 + - - -
188A ALA* 2.9 27.2 + - - +
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Residues in contact with ALA 185 (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 3.1 19.8 + - - +
147A VAL* 4.0 13.0 - - + -
148A GLY* 3.8 5.7 - - - +
181A ARG 3.2 10.8 + - - +
182A THR 3.6 2.2 - - - +
184A GLY* 1.3 77.1 - - - +
186A VAL* 1.3 63.8 + - - +
188A ALA 3.4 0.2 + - - -
189A LEU* 3.0 29.7 + - - +
232A PHE* 3.5 36.8 - - + -
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Residues in contact with VAL 186 (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 VAL* 5.0 2.2 - - + -
169A ARG* 3.6 26.0 - - - -
182A THR 2.9 21.1 + - - +
183A THR* 3.8 5.6 - - - +
185A ALA* 1.3 76.1 - - - +
187A ASP* 1.3 61.8 + - - +
189A LEU* 3.1 6.6 + - - +
190A LYS* 2.9 47.7 + - + +
199A VAL* 4.2 30.1 - - + -
232A PHE* 3.7 16.4 - - + -
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Residues in contact with ASP 187 (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* 2.6 37.1 + - - +
145A ARG* 3.6 11.6 + - - +
183A THR* 2.9 29.9 + - - +
184A GLY 3.7 2.0 - - - +
186A VAL* 1.3 79.0 - - - +
188A ALA* 1.3 61.8 + - - +
190A LYS* 3.4 22.3 + - - +
191A ALA* 3.0 23.9 + - - +
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Residues in contact with ALA 188 (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* 3.4 44.1 - - - +
148A GLY* 3.8 9.1 - - - +
149A ASP* 3.5 17.8 - - - +
152A ALA* 5.2 0.2 - - - +
184A GLY 2.9 15.4 + - - +
185A ALA 3.8 4.0 - - - +
187A ASP* 1.3 77.9 - - - +
189A LEU* 1.3 61.2 + - - +
191A ALA* 3.4 5.3 + - - +
192A ALA* 3.2 21.7 + - - +
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Residues in contact with LEU 189 (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* 3.6 25.1 - - - +
151A ILE* 3.7 19.1 - - + -
152A ALA* 4.1 1.6 - - + +
167A VAL* 4.0 14.8 - - + -
185A ALA 3.0 19.7 + - - +
186A VAL* 3.1 4.9 + - - +
188A ALA* 1.3 73.9 - - - +
190A LYS* 1.3 65.6 + - + +
192A ALA* 3.0 11.0 + - - -
193A GLY 3.2 0.7 + - - -
194A PHE* 3.0 58.8 + - + -
230A VAL* 4.2 6.7 - - + -
232A PHE* 3.5 35.0 - - + -
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Residues in contact with LYS 190 (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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186A VAL* 2.9 36.6 + - + +
187A ASP* 3.9 19.5 + - - +
189A LEU* 1.3 76.3 - - + +
191A ALA* 1.3 57.2 + - - +
193A GLY* 3.1 17.7 + - - -
194A PHE* 3.5 20.5 - - + +
195A ALA 5.0 0.4 - - - -
196A ALA* 4.0 30.3 - - + +
199A VAL* 5.0 4.0 - - + -
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Residues in contact with ALA 191 (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* 4.3 14.8 - - - +
187A ASP 3.0 18.4 + - - +
188A ALA* 3.6 7.2 - - - +
189A LEU 3.2 0.2 - - - -
190A LYS* 1.3 74.7 - - - +
192A ALA* 1.3 56.6 + - - +
193A GLY 3.4 1.5 + - - -
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Residues in contact with ALA 192 (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* 3.6 29.4 - - + -
162A PRO* 3.9 15.1 - - - +
188A ALA 3.2 11.3 + - - +
189A LEU 3.0 11.0 + - - +
191A ALA* 1.3 77.1 - - - +
193A GLY* 1.3 59.7 + - - +
194A PHE* 3.5 4.1 + - + -
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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