Contacts of the helix formed by residues 196 - 208 (chain A) in PDB entry 3LEZ
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 ALA 196 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLY* 3.8 33.0 - - - +
62A VAL 3.9 2.2 - - - +
63A TYR* 3.8 17.3 - - + +
76A ARG 5.2 0.2 - - - +
77A GLU* 3.6 6.7 + - - +
79A GLU 4.4 3.2 + - - -
81A PHE* 5.2 1.2 - - - -
195A THR* 1.3 73.4 - - - +
197A LYS* 1.3 62.9 + - - +
200A ALA* 3.0 21.3 + - - +
274A ALA* 3.3 18.4 - - + +
276A MET* 3.6 18.2 - - + -
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Residues in contact with LYS 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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63A TYR* 3.7 54.1 + - + +
77A GLU* 3.1 24.1 + - + +
78A ASN* 4.1 17.9 - - - +
195A THR* 4.2 1.6 - - - +
196A ALA* 1.3 78.5 - - - +
198A ALA* 1.3 58.6 + - - +
200A ALA* 3.8 1.4 - - - +
201A THR* 2.8 42.3 + - - +
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Residues in contact with ALA 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ASP* 3.9 11.9 - - - +
172A THR* 3.5 23.3 - - - +
194A SER* 3.4 20.6 - - - +
195A THR* 3.1 14.8 + - - +
197A LYS* 1.3 78.6 - - - +
199A MET* 1.3 57.7 + - - +
201A THR* 3.9 4.6 - - - -
202A THR* 2.9 36.1 + - - -
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Residues in contact with MET 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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83A TYR* 4.1 10.8 - - + -
86A THR* 3.3 42.8 - - - +
87A PHE* 4.3 1.1 - - - +
90A LEU* 3.6 27.4 - - + +
170A ASP* 5.6 0.4 - - - +
173A ILE* 4.4 6.3 - - - -
194A SER* 3.7 25.1 - - - -
195A THR 2.9 20.8 + - - +
196A ALA 4.0 2.5 - - - +
198A ALA* 1.3 75.8 - - - +
200A ALA* 1.3 62.5 + - - +
202A THR* 4.1 2.9 - - - -
203A LEU* 3.0 26.4 + - - +
259A ILE* 3.9 27.4 - - + +
274A ALA* 4.3 3.1 - - + -
276A MET* 4.0 16.8 - - + -
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Residues in contact with ALA 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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63A TYR* 3.8 26.2 - - + +
65A ILE* 6.0 0.2 - - + -
196A ALA 3.0 18.3 + - - +
197A LYS 3.8 3.8 - - - +
199A MET* 1.3 77.7 - - - +
201A THR* 1.3 57.1 + - - +
203A LEU* 3.6 3.2 - - - +
204A GLN* 2.9 24.8 + - - +
259A ILE* 5.8 0.4 - - - -
272A VAL* 3.3 29.0 - - + +
273A ILE 4.8 1.6 - - - +
274A ALA* 3.8 16.9 - - + +
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Residues in contact with THR 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A TYR* 4.6 7.7 - - - -
169A GLY 6.0 2.0 - - - +
197A LYS* 2.8 34.6 + - - +
198A ALA* 3.9 5.6 - - - -
200A ALA* 1.3 76.2 - - - +
202A THR* 1.3 64.0 + - - +
204A GLN* 3.3 19.3 + - - +
205A GLN* 3.0 31.6 + - + +
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Residues in contact with THR 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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90A LEU* 3.9 27.1 - - + -
165A LEU* 4.2 11.2 - - + -
168A ILE* 4.2 8.3 - - + -
169A GLY 5.5 0.2 - - - -
170A ASP* 2.6 38.2 + - + +
198A ALA 2.9 12.5 + - - -
199A MET 4.2 1.8 - - - -
201A THR* 1.3 76.7 - - - +
203A LEU* 1.3 64.1 + - - +
205A GLN* 3.1 17.7 + - - +
206A TYR* 3.2 29.3 + - + -
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Residues in contact with LEU 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PRO* 4.3 20.4 - - + +
90A LEU* 3.9 14.7 - - + +
199A MET 3.0 18.6 + - - +
200A ALA* 3.6 4.7 - - - +
202A THR* 1.3 76.6 - - - +
204A GLN* 1.3 59.1 + - - +
206A TYR* 3.2 5.5 + - + +
207A VAL* 2.9 47.0 + - + +
220A LEU* 5.7 0.7 - - + -
224A LEU* 4.2 14.6 - - + -
259A ILE* 4.1 16.8 - - + -
260A GLY* 3.7 43.3 - - - +
261A ILE* 4.1 9.2 - - + -
272A VAL* 5.0 1.6 - - + -
273A ILE 5.0 1.3 - - - +
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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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63A TYR* 6.1 0.3 - - - -
65A ILE* 4.5 16.5 - - - +
67A THR* 4.2 19.8 - - - +
200A ALA 2.9 13.8 + - - +
201A THR* 3.3 26.5 + - - +
202A THR 3.2 0.2 - - - -
203A LEU* 1.3 77.2 - - - +
205A GLN* 1.3 60.0 + - - +
208A LEU* 2.9 36.4 + - + +
209A GLU* 3.1 28.9 + - + +
261A ILE* 4.8 2.9 - - - -
272A VAL* 4.0 26.7 - - + +
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Residues in contact with GLN 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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168A ILE* 4.2 30.2 + - + +
201A THR* 3.0 27.8 + - + +
202A THR* 3.1 11.2 + - - +
204A GLN* 1.3 78.2 - - - +
206A TYR* 1.3 61.9 + - - +
209A GLU* 3.4 43.8 + - - +
211A VAL* 3.5 36.5 - - + +
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Residues in contact with TYR 206 (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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89A PRO 5.4 0.2 - - - +
90A LEU* 3.8 23.8 - - + -
93A GLY* 3.3 31.2 - - - -
94A ALA* 3.4 13.1 - - - +
97A GLN* 2.8 29.9 + - + -
164A ILE* 4.5 0.5 - - - +
165A LEU* 3.4 25.3 - - + +
168A ILE* 3.5 19.6 - - + +
202A THR* 3.2 21.4 + - + -
203A LEU* 3.2 8.0 + - + +
205A GLN* 1.3 83.5 - - - +
207A VAL* 1.3 61.5 + - + +
209A GLU 4.6 1.2 - - - +
211A VAL* 3.5 20.0 - - + -
212A LEU* 3.5 28.9 + - + +
217A ARG* 3.6 10.4 - - - +
220A LEU* 3.9 16.6 - - + +
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Residues in contact with VAL 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LEU* 2.9 30.5 + - + +
206A TYR* 1.3 79.9 - - - +
208A LEU* 1.3 70.6 + - + +
217A ARG* 3.4 22.7 - - - +
220A LEU* 3.9 13.7 - - + -
221A THR* 3.6 20.8 + - + +
224A LEU* 3.7 28.3 - - + -
261A ILE* 4.0 24.5 - - + -
263A TRP* 4.4 10.8 - - + -
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Residues in contact with LEU 208 (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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67A THR* 4.4 9.2 - - + -
204A GLN* 2.9 19.2 + - + +
207A VAL* 1.3 97.3 - - + +
209A GLU* 1.3 72.1 + - + +
210A ASP* 5.1 1.0 - - - +
217A ARG* 4.8 5.8 + - - +
261A ILE* 4.3 7.4 - - + -
263A TRP* 4.3 13.9 - - + +
270A PRO* 3.6 35.4 - - + -
272A VAL* 3.6 31.2 - - + -
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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