Contacts of the helix formed by residues 187 - 196 (chain A) in PDB entry 3UMO
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 ASN 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A LYS* 3.7 2.2 + - - +
186A PRO* 1.3 75.6 - - - +
188A GLN* 1.3 60.6 + - - +
189A LYS* 3.2 7.1 + - - +
190A GLU* 2.8 57.4 + - - +
191A LEU* 2.9 26.7 + - - +
223A VAL* 4.2 2.2 - - - -
224A SER* 3.4 21.3 - - - +
311A MG 3.8 0.4 - - - -
313A ATP 3.0 21.6 + - - +
312B ATP 2.8 38.4 + - - -
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Residues in contact with GLN 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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187A ASN* 1.3 76.0 - - - +
189A LYS* 1.3 64.7 + - + +
191A LEU* 3.3 4.3 + - - +
192A SER* 3.0 24.1 + - - -
199A LEU* 4.3 4.9 - - + +
205A VAL* 4.7 15.6 - - + +
223A VAL* 4.5 7.0 - - + -
224A SER 3.5 1.8 + - - +
225A LEU* 3.5 53.0 - - + +
228A GLN* 4.7 9.2 + - - +
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Residues in contact with LYS 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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187A ASN* 3.2 9.2 + - - +
188A GLN* 1.3 79.5 - - + +
190A GLU* 1.3 58.8 + - + +
192A SER* 3.3 7.3 + - - -
193A ALA* 3.0 28.4 + - - +
312B ATP 3.2 52.3 + - - +
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Residues in contact with GLU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ASP* 4.2 4.7 - - - +
167A SER 3.5 19.6 - - - +
168A SER* 3.7 26.2 - - - +
169A GLY 6.0 0.2 + - - -
172A LEU* 4.0 8.0 - - + +
185A LYS* 3.9 6.8 + - - +
186A PRO* 3.6 13.9 - - + +
187A ASN* 2.8 52.5 + - - +
189A LYS* 1.3 72.1 - - + +
191A LEU* 1.3 59.0 + - - +
193A ALA* 3.5 5.7 + - - +
194A LEU* 3.0 29.1 + - - +
310A MG 4.1 9.0 - - - -
313A ATP 4.6 0.7 + - - -
27B LYS* 5.3 0.7 + - - -
312B ATP 4.2 12.1 + - - +
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Residues in contact with LEU 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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186A PRO* 3.7 19.4 - - + +
187A ASN 2.9 17.8 + - - +
188A GLN 3.7 4.5 - - - +
189A LYS 3.3 0.2 - - - -
190A GLU* 1.3 72.5 - - - +
192A SER* 1.3 67.1 + - - +
194A LEU* 3.2 5.4 + - + +
195A VAL* 3.0 27.5 + - + +
199A LEU* 3.7 20.6 - - + -
205A VAL* 3.7 30.7 - - + +
208A ALA* 3.9 17.9 - - + -
209A ALA* 4.5 1.3 - - - +
212A ILE* 3.7 29.8 - - + -
221A VAL* 5.2 0.4 - - + -
223A VAL* 3.8 22.2 - - + -
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Residues in contact with SER 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 GLN 3.0 17.6 + - - -
189A LYS* 3.5 8.5 - - - -
191A LEU* 1.3 76.9 - - - +
193A ALA* 1.3 56.3 + - - +
195A VAL* 3.8 1.1 - - - +
196A ASN* 2.9 23.9 + - - -
197A ARG 2.7 34.9 + - - -
198A GLU* 4.0 14.7 + - - -
199A LEU* 3.9 15.9 - - - +
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Residues in contact with ALA 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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169A GLY* 5.3 15.5 - - - +
173A SER* 5.0 2.3 + - - -
189A LYS 3.0 15.4 + - - +
190A GLU* 3.9 6.3 - - - +
192A SER* 1.3 77.4 + - - +
194A LEU* 1.3 63.9 + - - +
196A ASN* 3.3 15.1 + - - +
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Residues in contact with LEU 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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169A GLY 6.0 0.9 - - - -
172A LEU* 4.1 15.3 - - + -
173A SER* 3.5 40.8 + - - +
176A LEU* 3.6 29.8 - - + -
184A VAL* 5.5 1.8 - - + -
186A PRO* 5.3 4.3 - - + -
190A GLU 3.0 17.3 + - - +
191A LEU* 3.5 9.2 - - + +
193A ALA* 1.3 80.0 - - - +
195A VAL* 1.3 61.4 + - + +
196A ASN* 3.4 2.1 + - - +
212A ILE* 3.6 30.3 - - + -
217A LYS* 6.0 7.0 - - + +
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Residues in contact with VAL 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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191A LEU* 3.0 29.2 + - + +
192A SER* 3.8 9.9 - - - +
194A LEU* 1.3 74.1 - - + +
196A ASN* 1.3 69.9 + - - +
197A ARG* 3.5 41.5 + - + +
199A LEU* 4.3 9.2 - - + -
208A ALA* 4.0 28.0 - - + +
211A GLU* 4.6 12.7 - - - +
212A ILE* 4.5 11.4 - - + -
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Residues in contact with ASN 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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192A SER 2.9 11.7 + - - -
193A ALA* 3.3 10.7 + - - +
194A LEU 3.2 5.4 - - - +
195A VAL* 1.3 81.2 - - - +
197A ARG* 1.3 59.3 + - - +
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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