Contacts of the helix formed by residues 196 - 205 (chain A) in PDB entry 3LPJ
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 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A SER* 3.6 24.9 - - - +
99A PHE 6.1 0.7 - - - +
181A GLY 4.6 3.8 - - - +
183A ALA 3.9 10.3 - - - +
184A TYR 4.0 4.0 - - - -
185A ALA* 3.6 38.4 - - + +
188A ALA* 4.5 0.7 - - + -
194A LEU 3.4 6.3 - - - +
195A GLU* 1.4 89.1 - - + +
197A PHE* 1.3 65.7 + - - +
198A PHE* 4.5 3.4 - - + +
199A ASP* 3.2 30.2 + - - +
200A SER* 3.2 17.5 + - - -
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Residues in contact with PHE 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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79A MET* 3.9 19.3 - - + -
97A SER 5.0 0.6 + - - -
99A PHE* 4.4 22.8 - + + +
146A VAL* 3.8 20.2 - - + -
147A SER* 6.1 0.2 - - - -
148A ILE* 4.3 16.6 - - + -
156A VAL* 3.6 28.5 - - + -
158A ALA* 3.7 21.3 - - + -
159A ASN 5.8 1.5 + - - +
180A LEU* 3.6 36.1 - - + -
181A GLY 4.8 4.6 + - - +
182A LEU* 5.1 0.4 - - + -
195A GLU 3.8 0.6 + - - -
196A PRO* 1.3 73.1 - - - +
198A PHE* 1.3 68.4 + + + +
200A SER* 3.1 8.9 + - - -
201A LEU* 2.9 48.2 + - + +
237A ILE* 6.1 1.1 - - + -
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Residues in contact with PHE 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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182A LEU* 4.1 29.5 - - + +
183A ALA 6.1 0.2 - - - +
196A PRO* 3.4 2.6 - - + +
197A PHE* 1.3 85.3 - + - +
199A ASP* 1.3 62.3 + - - +
201A LEU* 3.3 26.4 + - + +
202A VAL* 3.0 41.8 + - + +
207A VAL* 5.0 0.2 - - + -
208A PRO 4.2 4.5 - - - -
209A ASN* 3.7 7.9 - - - -
210A LEU 3.6 32.8 - - - -
211A PHE* 3.9 12.3 - + - -
237A ILE* 3.9 22.2 - - + -
408A ARG* 3.4 37.9 - - - +
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Residues in contact with ASP 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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183A ALA 4.6 1.6 - - - +
184A TYR* 5.1 4.5 - - - -
185A ALA* 4.9 6.4 + - - +
195A GLU* 3.6 17.7 - - + +
196A PRO* 3.2 37.8 + - - +
198A PHE* 1.3 76.4 + - - +
200A SER* 1.3 58.9 + - - +
202A VAL* 3.4 4.5 + - - +
203A LYS* 3.0 30.3 + - - +
408A ARG* 3.3 25.6 + - - +
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Residues in contact with SER 200 (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 VAL* 4.9 2.7 - - - -
157A ARG 3.9 11.0 + - - -
158A ALA* 4.4 11.2 - - - -
159A ASN* 5.0 1.2 + - - -
195A GLU* 2.6 33.5 + - - +
196A PRO 3.2 7.9 + - - -
197A PHE* 3.1 11.3 + - - -
199A ASP* 1.3 76.4 - - - +
201A LEU* 1.3 65.3 + - - +
203A LYS* 3.3 2.1 + - - -
204A GLN* 2.9 45.1 + - - +
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Residues in contact with LEU 201 (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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148A ILE* 5.6 2.2 - - + -
152A PRO* 4.6 4.3 - - + -
154A VAL* 3.7 30.3 - - + -
156A VAL* 3.8 20.5 - - + +
197A PHE* 2.9 32.7 + - + +
198A PHE* 3.4 30.3 - - + +
200A SER* 1.3 78.1 - - - +
202A VAL* 1.3 53.6 + - + +
205A THR* 2.6 45.1 + - - +
207A VAL* 4.3 10.1 - - + -
237A ILE* 3.6 31.2 - - + -
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Residues in contact with VAL 202 (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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198A PHE* 3.0 44.9 + - + +
199A ASP* 3.9 4.5 - - - +
201A LEU* 1.3 77.7 - - + +
203A LYS* 1.3 62.0 + - - +
205A THR* 3.0 22.1 - - - +
207A VAL* 3.8 24.8 - - + +
208A PRO 4.2 0.9 - - - +
209A ASN* 3.7 29.2 - - + +
408A ARG* 6.1 0.2 - - - +
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Residues in contact with LYS 203 (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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195A GLU* 4.0 22.8 + - - +
199A ASP 3.0 18.6 + - - +
200A SER* 3.8 4.3 - - - +
202A VAL* 1.3 78.9 - - - +
204A GLN* 1.3 64.6 + - + +
205A THR 3.8 1.4 + - - +
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Residues in contact with GLN 204 (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 THR 4.8 1.0 - - - +
156A VAL* 3.6 15.6 - - + -
157A ARG* 2.8 52.2 + - - +
195A GLU* 4.6 3.6 + - - -
200A SER* 2.9 28.9 + - - +
203A LYS* 1.3 85.8 - - + +
205A THR* 1.3 59.1 + - + +
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Residues in contact with THR 205 (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 VAL* 3.8 27.1 - - + -
155A THR 4.8 2.5 - - - +
156A VAL* 3.7 22.9 - - + -
201A LEU 2.6 21.8 + - - +
202A VAL* 3.0 15.9 - - - +
203A LYS 4.5 1.7 - - - +
204A GLN* 1.3 84.2 - - + +
206A HIS* 1.3 71.0 + - - +
207A VAL* 3.1 25.7 + - - +
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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