Contacts of the helix formed by residues 185 - 199 (chain A) in PDB entry 1VOM
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 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A ILE* 3.6 39.0 - - + +
178A THR* 3.8 14.8 - - - +
179A GLY* 2.9 19.3 + - - +
180A GLU 2.8 20.0 + - - -
183A ALA 3.8 0.4 - - - -
184A GLY* 1.3 77.8 - - - +
186A THR* 1.3 59.4 + - - +
188A ASN* 3.3 1.6 + - - +
189A THR* 2.8 33.3 + - - -
454A ASP* 3.3 11.9 - - - +
455A ILE* 3.2 34.5 - - + +
457A GLY* 3.4 7.4 - - - +
655A CYS* 3.8 1.3 - - + -
998A VO4 2.7 26.4 + - - -
999A ADP 2.7 24.9 + - - +
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Residues in contact with THR 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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185A LYS* 1.3 79.4 - - - +
187A GLU* 1.3 62.3 + - - +
189A THR* 3.4 1.7 + - + -
190A LYS* 3.1 38.1 + - + +
219A ASN* 5.4 0.4 - - - +
223A GLU* 3.5 27.1 - - - +
227A ASN* 5.0 2.7 - - - +
235A ASN* 5.0 1.8 - - - +
237A SER* 2.8 7.3 + - - +
241A LYS* 4.5 4.5 - - - +
454A ASP* 2.6 27.8 + - - +
997A MG 2.0 30.7 - - - -
999A ADP 2.9 16.0 + - - +
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Residues in contact with GLU 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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184A GLY 3.3 0.6 + - - +
185A LYS 3.3 0.4 - - - -
186A THR* 1.3 72.3 - - - +
188A ASN* 1.3 64.3 + - - +
190A LYS* 3.2 33.9 + - - +
191A LYS* 3.0 43.7 + - - +
235A ASN* 4.6 5.2 + - - -
999A ADP 2.8 93.1 + - + +
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Residues in contact with ASN 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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115A ILE* 6.1 0.2 - - - +
116A TYR* 2.7 36.2 + - - -
125A ALA* 4.5 7.3 - - - +
155A ILE* 3.7 14.6 - - + +
177A ILE* 4.1 19.7 - - + -
183A ALA 5.4 0.2 + - - -
184A GLY* 2.8 32.0 + - - +
185A LYS 3.8 2.5 - - - +
187A GLU* 1.3 76.7 - - - +
189A THR* 1.3 61.6 + - - +
191A LYS* 2.9 16.9 + - - +
192A VAL* 2.9 15.6 + - - +
653A VAL* 4.9 0.9 - - + -
655A CYS* 3.8 11.7 - - - -
999A ADP 4.4 14.0 + - - -
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Residues in contact with THR 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ILE* 3.5 19.2 - - - +
185A LYS 2.8 26.2 + - - -
186A THR* 3.5 5.4 - - + -
188A ASN* 1.3 71.7 - - - +
190A LYS* 1.3 65.1 + - + +
192A VAL* 3.0 4.7 + - - +
193A ILE* 3.0 30.6 + - + +
219A ASN* 6.0 0.9 - - - +
241A LYS* 4.6 4.0 - - - -
243A ILE* 3.7 30.5 - - + -
452A VAL* 3.7 14.2 - - + +
453A LEU 4.3 0.2 + - - -
454A ASP* 3.3 28.4 - - + +
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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 THR* 3.1 25.5 + - + +
187A GLU* 3.2 41.1 + - - +
189A THR* 1.3 82.8 - - + +
191A LYS* 1.3 72.4 + - - +
193A ILE* 3.4 7.6 + - - +
194A GLN* 3.0 23.9 + - - +
216A LEU* 5.9 0.2 - - - +
219A ASN* 3.7 26.8 - - + +
223A GLU* 3.4 31.8 + - - -
235A ASN* 4.5 1.8 - - - +
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Residues in contact with LYS 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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135A TYR* 3.6 51.8 - - + +
155A ILE* 3.6 21.1 - - + -
156A PHE* 3.6 9.0 - - + -
187A GLU* 3.0 35.2 + - + +
188A ASN* 2.9 9.7 + - - +
190A LYS* 1.3 85.5 - - - +
192A VAL* 1.3 63.5 + - - +
194A GLN* 3.4 18.5 + - - +
195A TYR* 3.0 26.0 + - - +
999A ADP 5.7 2.2 - - - +
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Residues in contact with VAL 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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155A ILE* 3.7 19.7 - - + -
159A SER* 3.4 25.6 - - - +
175A LEU* 4.0 17.0 - - + -
177A ILE* 4.2 13.9 - - + -
188A ASN 2.9 16.5 + - - +
189A THR* 3.4 8.7 - - - +
191A LYS* 1.3 78.5 - - - +
193A ILE* 1.3 61.9 + - - +
195A TYR* 3.4 2.3 + - - +
196A LEU* 3.0 35.8 + - + +
452A VAL* 3.8 28.3 - - + -
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Residues in contact with ILE 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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189A THR* 3.0 27.1 + - + +
190A LYS* 3.8 6.7 - - - +
192A VAL* 1.3 75.2 - - + +
194A GLN* 1.3 56.7 + - - +
196A LEU* 3.1 4.4 + - - +
197A ALA* 2.7 37.9 + - + +
215A ILE* 3.9 30.5 - - + +
216A LEU* 3.9 13.9 - - + -
243A ILE* 4.6 13.7 - - + -
245A ILE* 3.9 22.9 - - + -
452A VAL* 3.7 33.2 - - + -
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Residues in contact with GLN 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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135A TYR* 3.1 26.8 + - - +
136A THR 4.8 2.6 - - - -
137A GLN* 5.0 5.4 + - - +
140A VAL* 3.8 15.3 - - + +
156A PHE* 3.9 11.7 - - - -
190A LYS 3.0 17.6 + - - +
191A LYS* 3.6 25.2 + - - +
192A VAL 3.4 0.2 - - - -
193A ILE* 1.3 74.9 - - - +
195A TYR* 1.3 59.1 + - - +
197A ALA* 3.4 2.3 + - - +
198A SER* 2.9 31.5 + - - -
216A LEU* 4.3 16.9 - - + +
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Residues in contact with TYR 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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140A VAL* 3.7 31.2 - - + -
143A PHE* 3.4 16.1 - - + -
144A LYS* 3.4 4.2 + - - -
156A PHE* 3.6 50.0 - + + -
159A SER* 3.6 21.8 - - - -
160A ASP* 2.4 44.9 + - + +
191A LYS 3.0 17.6 + - - +
192A VAL 3.6 4.7 - - - +
194A GLN* 1.3 77.4 - - - +
196A LEU* 1.3 58.5 + - + +
198A SER* 3.1 4.0 + - - -
199A VAL* 2.7 65.9 + - + +
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Residues in contact with LEU 196 (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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159A SER* 4.1 18.6 - - - +
163A TYR* 4.3 15.7 - - + -
175A LEU* 5.5 0.4 - - + -
192A VAL* 3.0 33.8 + - + +
193A ILE* 3.8 3.1 - - - +
195A TYR* 1.3 85.7 - - + +
197A ALA* 1.3 55.4 - - - +
199A VAL* 4.2 3.1 - - + -
200A ALA* 2.8 38.8 + - - +
245A ILE* 4.1 32.1 - - + -
247A PHE* 4.3 9.2 - - + -
253A ILE* 3.7 2.9 - - - +
450A ILE* 4.1 39.7 - - + -
452A VAL* 5.0 0.2 - - + -
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Residues in contact with ALA 197 (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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193A ILE* 2.7 22.8 + - + +
194A GLN 3.6 4.0 - - - +
196A LEU* 1.3 73.0 - - - +
198A SER* 1.3 57.7 + - - +
201A GLY* 3.0 27.2 - - - -
212A GLU* 4.2 20.9 - - + +
215A ILE* 5.7 2.7 - - + -
216A LEU* 4.1 24.7 - - + -
253A ILE* 3.6 16.3 - - + +
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Residues in contact with SER 198 (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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137A GLN* 3.2 31.3 + - - -
140A VAL* 3.7 16.0 - - - +
144A LYS* 4.5 8.2 + - - -
194A GLN* 2.9 20.3 + - - -
195A TYR 3.4 3.8 - - - -
197A ALA* 1.3 78.3 - - - +
199A VAL* 1.3 66.0 + - - +
200A ALA 3.3 0.9 + - - -
201A GLY* 3.7 6.9 + - - +
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Residues in contact with VAL 199 (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 VAL* 4.3 8.3 - - + -
144A LYS* 4.2 26.2 - - + +
163A TYR* 4.3 31.3 + - + -
164A ARG* 4.8 8.6 + - - +
195A TYR* 2.7 65.0 + - + +
196A LEU* 3.8 9.0 - - + +
198A SER* 1.3 75.7 - - - +
200A ALA* 1.3 60.5 + - + +
201A GLY 5.2 0.2 - - - -
252A PHE* 6.0 0.2 - - - -
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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