Contacts of the helix formed by residues 184 - 195 (chain A) in PDB entry 5LZK
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 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A ASP* 3.3 27.9 + - - +
156A ILE* 3.5 31.3 - - + +
157A PHE 5.7 0.5 + - - -
181A ASP* 3.0 23.9 + - - +
182A GLU 3.1 1.0 - - - -
183A SER* 1.3 80.9 + - - +
185A PHE* 1.3 62.6 + - - +
186A ASN 3.2 3.1 - - - -
187A HIS* 3.2 37.9 + - + +
188A PHE* 4.0 2.4 + - - +
226A LYS* 3.4 25.2 + - - +
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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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180A LEU* 3.9 16.6 - - + -
181A ASP 3.3 6.7 + - - +
182A GLU 3.1 16.4 + - - +
183A SER 3.6 0.4 - - - -
184A ASN* 1.3 77.4 - - - +
186A ASN* 1.3 69.8 + - - +
188A PHE* 3.0 31.3 + + - +
189A LEU* 3.1 26.0 + - + -
207A VAL* 3.8 25.6 - - + -
209A THR* 3.6 24.9 - - + -
283A PRO* 3.6 30.1 - - + -
285A SER* 3.7 22.4 - - - -
286A PHE* 4.0 17.5 - + - -
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Residues in contact with ASN 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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182A GLU 5.0 0.2 + - - -
183A SER 5.2 0.8 + - - -
184A ASN 3.2 1.4 + - - -
185A PHE* 1.3 81.0 - - - +
187A HIS* 1.3 63.0 + - + +
189A LEU* 3.8 9.8 - - - +
190A ASN* 2.8 44.8 + - - +
285A SER* 3.7 18.5 + - - -
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Residues in contact with HIS 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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156A ILE* 4.7 13.2 - - + -
157A PHE 5.7 0.4 - - - +
158A THR* 3.6 29.6 - - + +
183A SER 5.2 2.2 + - - -
184A ASN* 3.5 42.2 + - + +
185A PHE 3.1 1.0 - - - -
186A ASN* 1.3 83.3 - - + +
188A PHE* 1.3 60.9 + - - +
190A ASN* 3.8 13.0 + - - +
191A MET* 3.1 17.3 + - - +
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Residues in contact with PHE 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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157A PHE* 3.3 55.9 + + + +
163A PHE* 4.0 21.5 - + - -
178A ILE* 4.8 6.3 - - + -
180A LEU* 3.5 24.2 - - + -
184A ASN 4.0 1.5 + - - +
185A PHE* 3.0 22.6 + + - +
187A HIS* 1.3 75.1 - - - +
189A LEU* 1.3 70.9 + - - +
191A MET* 3.2 8.1 + - + +
192A THR* 3.0 50.0 + - + +
199A VAL* 4.3 15.9 - - + -
207A VAL* 4.0 28.7 - - + -
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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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185A PHE* 3.1 21.4 + - + +
186A ASN* 3.8 12.6 - - - +
188A PHE* 1.3 83.4 - - + +
190A ASN* 1.3 63.1 + - - +
192A THR* 2.9 26.6 + - - +
193A GLU* 3.1 34.6 + - + +
199A VAL* 4.8 5.4 - - + -
200A GLN* 5.0 4.9 - - - +
285A SER* 3.6 33.2 - - - +
286A PHE* 3.8 28.7 - - + -
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Residues in contact with ASN 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 ASN* 2.8 34.8 + - - +
187A HIS* 3.8 14.1 + - - +
189A LEU* 1.3 79.4 - - - +
191A MET* 1.3 60.8 + - - +
193A GLU* 3.5 13.3 + - - +
194A LYS* 3.1 38.6 + - - +
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Residues in contact with MET 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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157A PHE* 3.8 20.6 - - + +
158A THR* 3.5 35.2 - - + +
159A ASP 4.2 1.6 - - - +
160A VAL* 3.8 22.4 - - + -
163A PHE* 3.8 38.1 - - + -
187A HIS 3.1 15.1 + - - +
188A PHE* 3.2 18.1 + - + +
190A ASN* 1.3 74.6 - - - +
192A THR* 1.3 71.4 + - + +
194A LYS* 3.3 11.6 + - - +
195A GLN* 3.1 25.5 + - - +
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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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163A PHE* 3.6 33.2 - - + -
188A PHE* 3.0 41.4 + - + +
189A LEU* 2.9 28.4 + - - +
191A MET* 1.3 83.2 - - - +
193A GLU* 1.3 59.7 + - - +
195A GLN* 3.3 8.6 + - - +
197A CYS* 3.0 40.2 + - - +
199A VAL* 4.2 8.9 - - + +
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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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189A LEU* 3.1 38.1 + - + +
190A ASN* 3.8 14.3 - - - +
191A MET 3.2 0.2 - - - -
192A THR* 1.3 81.2 + - - +
194A LYS* 1.3 65.1 + - + +
195A GLN 3.0 1.6 - - - -
196A GLY* 2.9 15.1 + - - +
197A CYS 4.3 7.9 - - - +
198A SER* 6.3 0.4 - - - -
200A GLN* 5.7 1.9 + - - -
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Residues in contact with LYS 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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190A ASN* 3.1 29.8 + - - +
191A MET* 3.3 10.7 + - - +
193A GLU* 1.3 76.0 - - + +
195A GLN* 1.3 68.7 + - - +
196A GLY* 3.1 1.1 + - - -
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Residues in contact with GLN 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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160A VAL* 3.7 39.5 + - + +
163A PHE* 5.2 7.2 - - + -
191A MET* 3.1 20.3 + - - +
192A THR* 3.6 10.5 - - - +
193A GLU 3.0 1.2 - - - -
194A LYS* 1.3 83.3 - - - +
196A GLY* 1.3 61.4 + - - +
197A CYS* 3.3 6.9 + - + +
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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