Contacts of the helix formed by residues 179 - 195 (chain A) in PDB entry 2VKZ
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 LYS 179 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A VAL* 3.0 31.2 + - + +
178A GLY* 1.3 68.7 - - - +
180A SER* 1.4 60.9 + - - +
181A THR* 3.2 3.8 - - - +
182A VAL* 3.1 34.0 + - + +
183A GLN 3.3 2.6 + - - -
1203C ASP* 3.6 40.2 + - - +
1207C GLN* 4.2 23.3 + - - +
1286C TRP* 6.2 2.5 - - - -
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Residues in contact with SER 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A GLY 2.9 9.6 + - - -
179A LYS* 1.4 69.2 - - - +
181A THR* 1.3 61.4 + - - +
182A VAL 3.2 0.7 - - - -
183A GLN* 3.7 23.4 - - - +
184A ASN* 3.0 38.4 + - - -
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Residues in contact with THR 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A LYS* 3.2 2.2 - - - -
180A SER* 1.3 81.4 + - - +
182A VAL* 1.5 55.6 + - + +
184A ASN* 3.3 10.6 + - - +
185A GLU* 3.0 58.3 + - + +
1272C ASN* 5.1 7.6 - - + -
1273C ASP* 4.4 19.0 + - + +
1276C GLN* 5.4 2.6 + - - -
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Residues in contact with VAL 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LYS* 3.9 31.4 - - + +
159A LEU* 3.9 20.0 - - + -
176A VAL* 4.0 7.2 - - + -
179A LYS* 3.1 30.0 + - + +
181A THR* 1.5 64.4 - - + +
183A GLN* 1.3 59.1 + - - +
185A GLU* 3.8 14.1 - - - +
186A ILE* 2.9 33.7 + - + +
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Residues in contact with GLN 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ILE* 4.3 18.2 - - + +
173A LYS* 5.2 14.1 - - - +
176A VAL* 3.9 14.3 - - + +
179A LYS 3.3 6.8 + - - +
180A SER* 3.8 26.8 - - - +
181A THR 3.4 0.2 - - - -
182A VAL* 1.3 77.2 - - - +
184A ASN* 1.3 62.3 + - - +
185A GLU 3.2 0.2 - - - -
186A ILE* 3.7 3.5 + - - +
187A LEU* 3.0 43.5 + - + +
202A GLU* 3.1 38.7 + - + +
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Residues in contact with ASN 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A SER* 3.0 29.5 + - - +
181A THR* 3.3 10.3 + - - +
183A GLN* 1.3 81.6 - - - +
185A GLU* 1.3 56.9 + - + +
187A LEU* 4.0 11.7 - - - +
188A GLY* 3.3 21.0 + - - -
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Residues in contact with GLU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LYS* 3.2 40.9 + - + +
181A THR* 3.0 47.8 + - + +
182A VAL* 4.1 14.1 - - - +
183A GLN 3.2 0.2 - - - -
184A ASN* 1.3 75.4 - - + +
186A ILE* 1.3 64.7 + - - +
187A LEU 3.1 1.6 - - - -
188A GLY* 3.4 0.7 + - - -
189A ASP* 3.0 32.0 + - - +
1272C ASN* 3.5 25.2 - - - +
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Residues in contact with ILE 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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154A LEU 5.6 0.7 - - - +
155A VAL* 3.4 37.0 - - + -
158A LYS* 3.9 21.5 - - + -
159A LEU* 3.8 28.7 - - + -
172A ILE* 3.7 29.4 - - + +
175A LEU* 5.9 1.1 - - + -
176A VAL* 4.0 12.3 - - + -
182A VAL 2.9 25.7 + - - +
183A GLN 4.2 2.7 - - - +
185A GLU* 1.3 76.0 - - - +
187A LEU* 1.3 59.1 + - - +
189A ASP* 4.0 5.4 - - - +
190A LEU* 3.0 36.1 + - + +
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Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ILE* 4.2 21.5 - - + -
183A GLN* 3.0 32.3 + - + +
184A ASN* 4.0 12.3 - - - +
185A GLU 3.1 0.2 - - - -
186A ILE* 1.3 79.3 - - - +
188A GLY* 1.3 60.5 + - - +
190A LEU* 3.6 6.9 + - + +
191A GLY* 3.5 15.4 + - - -
197A THR* 5.6 2.1 + - - +
201A PRO* 3.4 37.7 - - + -
202A GLU* 3.6 29.6 - - + +
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Residues in contact with GLY 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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184A ASN 3.3 13.7 + - - -
185A GLU 4.0 1.3 - - - -
187A LEU* 1.3 76.9 - - - +
189A ASP* 1.3 64.1 + - - +
191A GLY* 3.4 9.9 + - - -
192A LYS* 3.5 14.2 + - - +
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Residues in contact with ASP 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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154A LEU* 5.2 8.7 - - + +
158A LYS* 3.6 27.3 - - - +
185A GLU* 3.0 22.1 + - - +
186A ILE* 4.0 6.1 - - - +
188A GLY* 1.3 78.0 - - - +
190A LEU* 1.3 64.3 + - + +
191A GLY 3.3 0.9 + - - -
192A LYS* 3.4 4.3 + - - +
193A GLU* 3.3 19.8 + - - +
224A GLN* 3.7 42.8 + - + +
228A LEU* 5.7 0.7 - - - +
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Residues in contact with LEU 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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151A LEU* 3.4 35.0 - - + -
154A LEU* 4.0 28.3 - - + -
155A VAL* 4.8 3.4 - - + -
172A ILE* 4.3 14.1 - - + -
186A ILE* 3.0 32.1 + - + +
187A LEU* 3.9 8.5 - - + +
188A GLY 3.4 0.2 - - - -
189A ASP* 1.3 73.5 - - + +
191A GLY* 1.3 59.7 + - - +
193A GLU* 3.7 4.0 - - - -
194A PHE* 3.0 34.4 + - + +
195A GLY 3.9 2.6 + - - -
196A THR 6.0 0.2 - - - -
201A PRO* 6.1 2.0 - - + -
209A LEU* 5.1 5.2 - - + -
213A PHE* 4.5 19.7 - - + -
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Residues in contact with GLY 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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187A LEU 3.5 8.7 + - - -
188A GLY* 3.4 7.7 + - - -
189A ASP 3.1 1.0 - - - -
190A LEU* 1.3 74.1 - - - +
192A LYS* 1.3 57.0 + - - +
193A GLU 3.0 4.5 - - - -
195A GLY* 3.1 33.3 + - - +
196A THR 6.3 0.2 - - - -
197A THR* 4.8 13.2 - - - -
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Residues in contact with LYS 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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188A GLY 3.5 10.5 + - - +
189A ASP* 3.4 9.5 + - - +
191A GLY* 1.3 75.0 - - - +
193A GLU* 1.3 58.4 + - - +
223A LYS* 3.2 49.3 + - + +
224A GLN* 4.2 24.1 + - + +
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Residues in contact with GLU 193 (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 LEU* 3.1 32.7 - - + +
154A LEU* 3.5 25.1 - - + -
189A ASP 3.3 15.5 + - - +
190A LEU* 3.7 6.7 - - - +
191A GLY 3.0 0.6 - - - -
192A LYS* 1.3 80.5 - - - +
194A PHE* 1.3 82.5 + - + +
220A ALA* 6.0 1.2 - - - +
221A LEU 3.2 10.4 - - - +
222A GLY* 3.6 20.2 - - - -
223A LYS 4.5 0.2 - - - +
224A GLN* 3.2 7.8 + - - +
225A SER* 3.0 26.2 + - - -
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Residues in contact with PHE 194 (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 ALA* 4.5 3.6 - - + -
150A LEU* 3.6 40.2 - - + -
151A LEU* 4.2 14.6 - - + -
154A LEU* 4.6 2.0 - - + -
190A LEU* 3.0 29.2 + - + +
193A GLU* 1.3 92.1 - - + +
195A GLY* 1.3 58.2 + - - +
196A THR* 3.2 9.9 + - - -
213A PHE* 3.3 61.9 - + + +
216A THR* 5.2 5.4 + - - +
217A PHE* 4.0 35.0 - + + +
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Residues in contact with GLY 195 (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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190A LEU 3.9 1.6 + - - -
191A GLY* 3.1 24.1 + - - +
193A GLU 3.7 0.8 - - - -
194A PHE* 1.3 75.3 - - - +
196A THR* 1.3 59.9 + - - +
197A THR* 3.5 7.5 + - - -
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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