Contacts of the helix formed by residues 183 - 192 (chain A) in PDB entry 5TOL
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 PRO 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A SER* 3.5 26.0 - - - +
86A PHE 5.9 0.7 - - - +
168A GLY 4.6 3.4 - - - +
169A LEU 5.9 0.2 - - - -
170A ALA 4.0 10.5 - - - +
171A TYR 4.0 4.0 - - - -
172A ALA* 3.6 35.7 - - + +
181A LEU 3.4 6.7 - - - +
182A GLU* 1.4 88.9 - - - +
184A PHE* 1.3 65.9 + - - +
185A PHE* 3.3 3.6 - - + +
186A ASP* 3.1 40.7 + - + +
187A SER* 3.2 9.4 + - - -
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Residues in contact with PHE 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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66A MET* 3.9 15.7 - - + -
84A SER 4.8 1.0 + - - -
86A PHE* 4.4 19.0 - + + +
133A VAL* 3.7 26.5 - - + -
135A ILE* 4.1 21.8 - - + -
143A VAL* 3.8 22.4 - - + -
145A ALA* 3.7 21.3 - - + -
146A ASN 5.9 1.3 + - - +
167A LEU* 3.6 36.1 - - + -
168A GLY 4.7 4.1 + - - +
169A LEU* 5.0 0.4 - - + -
182A GLU 3.8 1.0 + - - -
183A PRO* 1.3 72.1 - - - +
185A PHE* 1.3 68.9 + + + +
187A SER* 3.0 10.9 + - - -
188A LEU* 3.0 47.0 + - + -
222A MET* 6.5 0.2 - - + -
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Residues in contact with PHE 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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168A GLY 5.3 1.0 + - - -
169A LEU* 3.7 34.2 - - + +
170A ALA 6.1 0.2 - - - +
183A PRO* 3.3 2.7 - - + +
184A PHE* 1.3 81.5 - + - +
186A ASP* 1.3 65.8 + - - +
188A LEU* 3.2 13.7 + - + +
189A VAL* 3.0 42.0 + - + +
194A VAL* 5.0 0.7 - - + -
195A PRO 4.4 2.5 - - - -
196A ASN* 4.0 6.7 - - - -
197A LEU 3.6 29.6 - - - -
198A PHE* 3.8 21.3 - + + -
222A MET* 4.7 0.7 - - + -
224A ILE* 3.9 29.8 - - + -
395A ARG* 3.6 34.1 - - - +
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Residues in contact with ASP 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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170A ALA 4.5 3.6 - - - +
171A TYR* 4.8 4.7 - - - -
172A ALA* 4.6 5.9 + - - -
182A GLU* 3.9 16.6 - - + +
183A PRO* 3.1 37.4 + - + +
185A PHE* 1.3 79.0 - - - +
187A SER* 1.3 56.3 + - - +
189A VAL* 3.4 4.4 + - - +
190A LYS* 3.0 32.2 + - + +
395A ARG* 3.1 23.9 + - - +
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Residues in contact with SER 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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143A VAL* 4.6 3.8 - - - +
144A ARG 3.9 11.9 + - - -
145A ALA* 4.5 11.1 - - - -
146A ASN* 5.0 1.4 + - - -
182A GLU* 2.6 38.4 + - - +
183A PRO 3.2 4.9 + - - -
184A PHE* 3.0 12.2 + - - -
186A ASP* 1.3 77.5 - - - +
188A LEU* 1.3 62.0 + - - +
190A LYS* 4.5 1.8 - - - -
191A GLN* 3.1 43.9 + - - +
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Residues in contact with LEU 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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135A ILE* 5.3 3.1 - - + -
139A PRO* 4.8 2.7 - - + -
141A VAL* 3.6 30.7 - - + -
143A VAL* 3.7 18.4 - - + +
184A PHE* 3.0 34.1 + - + +
185A PHE* 3.2 23.3 + - + +
187A SER* 1.3 76.8 - - - +
189A VAL* 1.3 60.1 + - + +
192A THR* 2.6 41.7 + - - +
194A VAL* 4.2 12.1 - - + -
224A ILE* 3.8 29.2 - - + -
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Residues in contact with VAL 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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185A PHE* 3.0 29.7 + - + +
186A ASP* 4.0 3.8 - - - +
188A LEU* 1.3 78.2 - - + +
190A LYS* 1.3 58.2 + - + +
192A THR 3.0 23.7 - - - +
194A VAL* 3.9 17.8 - - + +
195A PRO 4.3 0.7 - - - +
196A ASN* 3.4 50.5 - - + +
395A ARG* 6.1 0.2 - - - +
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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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182A GLU* 4.1 24.1 + - - +
186A ASP* 3.0 19.6 + - + +
187A SER* 4.0 5.8 - - - +
189A VAL* 1.3 78.2 - - + +
191A GLN* 1.3 63.4 + - + +
192A THR 4.5 1.2 - - - +
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Residues in contact with GLN 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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142A THR 4.9 0.8 - - - +
143A VAL* 3.5 9.0 - - + -
144A ARG* 2.9 50.2 + - - +
182A GLU* 4.5 4.9 + - - -
187A SER* 3.1 30.9 + - - +
189A VAL 3.3 0.2 - - - -
190A LYS* 1.3 81.0 - - + +
192A THR* 1.3 69.8 + - + +
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Residues in contact with THR 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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141A VAL* 4.0 23.3 - - + -
142A THR 4.7 3.4 - - - +
143A VAL* 3.9 22.9 - - + -
188A LEU* 2.6 22.9 + - - +
189A VAL 3.0 15.3 - - - +
190A LYS 3.4 1.6 - - - +
191A GLN* 1.3 87.8 - - + +
193A HIS* 1.3 71.1 + - - +
194A VAL* 3.3 25.8 + - - +
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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