Contacts of the helix formed by residues 190 - 204 (chain A) in PDB entry 1X3W
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 ARG 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A TRP* 3.8 24.9 - - + +
124A CYS 2.9 22.4 + - - +
125A ASN* 3.3 26.2 + - - +
161A GLU* 2.4 42.0 + - - -
163A TYR* 3.6 4.9 + - - -
174A PHE* 3.2 15.4 - - + -
176A ARG* 3.4 30.9 - - - +
189A GLY* 1.3 75.1 - - - -
191A CYS* 1.3 58.7 + - + +
192A GLY 3.4 1.3 - - - +
193A GLU* 2.8 7.4 + - - -
194A TRP* 2.7 35.8 + - - +
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Residues in contact with CYS 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A TRP* 3.5 10.2 - - + -
190A ARG* 1.3 78.2 - - + +
192A GLY* 1.3 69.7 + - - +
194A TRP* 3.1 6.8 + - - +
195A CYS* 2.8 23.0 + - - +
217A ASP 5.0 2.5 - - - -
218A HIS* 3.8 34.1 - - + +
219A VAL* 3.7 28.0 - - - -
237A CYS* 3.9 16.4 - - - -
2C FRU 5.2 4.7 - - - +
2E FRU 5.7 2.0 - - - -
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Residues in contact with GLY 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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176A ARG* 4.6 3.4 - - - +
190A ARG* 3.4 2.2 - - - +
191A CYS* 1.3 87.8 - - - +
193A GLU* 1.3 62.9 + - - +
195A CYS* 3.2 3.5 + - - +
196A ASN* 3.2 19.9 + - - +
211A TYR* 4.8 0.2 + - - -
219A VAL* 4.5 7.5 - - - +
1E GLC 3.5 29.8 + - - -
2E FRU 4.4 9.7 + - - -
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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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121A PHE* 4.5 3.1 - - + -
174A PHE* 4.3 4.0 - - - -
175A PRO 4.7 0.5 - - - +
176A ARG* 2.9 47.4 + - - -
177A TYR 4.1 3.8 + - - -
183A LEU* 3.3 29.2 - - + +
188A LYS 3.9 7.2 - - - +
189A GLY* 3.3 27.9 - - - -
190A ARG* 2.8 19.9 + - - -
192A GLY* 1.3 72.2 - - - +
194A TRP* 1.3 68.3 + - - +
195A CYS 3.0 1.3 + - - -
196A ASN* 3.7 0.2 - - - +
197A LEU* 3.2 26.3 + - - +
1E GLC 3.4 25.5 + - - +
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Residues in contact with TRP 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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116A PHE* 3.6 18.3 - + - -
117A LYS* 5.0 14.6 - - + +
121A PHE* 3.1 49.6 - + + -
122A LYS 2.8 42.2 - - - -
123A TRP* 3.2 23.6 - + + -
189A GLY 2.7 26.0 - - - -
190A ARG 2.7 18.5 + - - +
191A CYS* 3.2 9.9 - - - +
193A GLU* 1.3 80.1 - - - +
195A CYS* 1.3 62.6 + - - +
198A PHE* 3.5 10.7 + - - +
236A SER* 3.2 52.2 + - - -
237A CYS* 3.4 23.4 - - - +
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Residues in contact with CYS 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 CYS 2.8 14.5 + - - +
192A GLY 3.6 7.4 - - - +
194A TRP* 1.3 71.1 - - - +
196A ASN* 1.3 68.8 + - - +
198A PHE* 2.7 16.2 + - - +
199A THR* 2.8 27.3 + - - -
211A TYR* 3.6 20.2 - - + -
219A VAL* 3.8 16.4 - - + +
220A TRP* 3.6 36.3 - - - -
221A CYS* 4.3 2.9 - - - -
235A ASP* 6.1 0.7 - - - +
236A SER* 4.2 6.7 - - - -
237A CYS* 5.3 2.4 - - - -
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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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61A HIS* 5.6 2.8 - - - -
66A TYR* 2.4 60.2 + - - -
178A ASN 2.9 25.7 + - - +
180A PRO* 3.5 15.5 - - - +
183A LEU* 3.5 13.9 - - - +
192A GLY 3.2 6.2 + - - +
193A GLU 3.7 2.7 - - - +
195A CYS* 1.3 77.3 - - - +
197A LEU* 1.3 63.6 + - - +
199A THR* 3.3 3.9 + - - -
200A LEU* 3.3 3.3 + - - +
211A TYR* 4.1 4.3 - - - -
1E GLC 2.9 40.3 + - - +
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Residues in contact with LEU 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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75A VAL* 5.8 0.2 - - + -
116A PHE* 3.5 30.1 - - + -
120A PHE* 4.0 0.9 - - + -
121A PHE* 3.6 22.2 - - + -
180A PRO* 4.0 26.5 - - + +
183A LEU* 3.9 9.0 - - + +
184A LEU* 3.9 30.3 - - + -
193A GLU 3.2 13.5 + - - +
195A CYS 3.0 0.6 + - - -
196A ASN* 1.3 78.4 - - - +
198A PHE* 1.3 59.1 + - - +
200A LEU* 2.8 32.8 + - + +
201A ILE* 2.8 30.2 + - + -
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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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112A LEU* 3.6 33.9 - - + -
113A LEU* 3.5 42.4 - - + -
116A PHE* 3.4 34.5 - + + -
194A TRP 3.5 7.5 + - - +
195A CYS* 2.7 8.9 + - - +
197A LEU* 1.3 76.7 - - - +
199A THR* 1.3 61.5 + - - +
201A ILE* 3.2 18.2 + - + +
202A LEU* 3.0 47.2 + - + +
221A CYS* 4.2 9.6 - - - -
234A VAL* 4.3 6.5 - - + -
236A SER* 3.4 25.6 - - - +
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Residues in contact with THR 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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66A TYR* 4.0 24.0 - - + -
195A CYS* 2.8 32.9 + - - -
196A ASN 3.4 10.3 - - - -
198A PHE* 1.3 78.2 - - - +
200A LEU* 1.3 62.1 + - - +
202A LEU* 3.1 5.2 + - - +
203A LYS* 3.1 22.0 + - + +
209A VAL* 4.2 20.1 - - + +
210A ARG 5.0 0.2 - - - -
211A TYR* 3.6 22.1 - - + +
221A CYS* 3.7 15.3 - - + +
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Residues in contact with LEU 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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66A TYR* 3.4 27.1 - - + +
71A TRP* 3.1 49.8 - - + -
72A HIS* 5.4 2.5 - - + +
75A VAL* 3.5 23.8 - - + -
180A PRO* 4.3 13.5 - - + -
181A ILE* 4.9 2.2 - - + -
184A LEU* 5.4 3.8 - - + -
196A ASN 3.3 2.1 + - - +
197A LEU* 2.8 26.4 + - + +
199A THR* 1.3 70.9 - - - +
201A ILE* 1.3 60.9 + - - +
202A LEU 2.7 6.4 + - - -
203A LYS* 2.7 16.1 + - + +
204A SER* 2.5 33.0 + - - +
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Residues in contact with ILE 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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75A VAL* 4.4 9.9 - - + -
79A LEU* 3.7 31.9 - - + -
112A LEU* 3.8 20.1 - - + +
115A TYR* 6.4 0.2 - - + -
116A PHE* 3.2 39.0 - - + -
120A PHE* 5.5 0.2 - - + -
184A LEU* 5.9 0.7 - - + -
197A LEU* 2.8 40.2 + - + -
198A PHE* 3.3 26.9 - - + +
200A LEU* 1.3 72.6 - - - +
202A LEU* 1.3 58.9 + - + +
204A SER* 3.6 8.0 - - - -
205A PHE* 3.2 23.7 + - - -
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Residues in contact with LEU 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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109A VAL* 4.1 15.0 - - + -
112A LEU* 4.4 14.6 - - + -
198A PHE* 3.0 47.2 + - + +
199A THR 3.4 6.3 - - - +
200A LEU 2.7 4.6 + - - -
201A ILE* 1.3 72.4 - - - +
203A LYS* 1.3 64.8 + - - +
204A SER 3.0 1.6 - - - -
205A PHE* 3.0 15.8 + - + +
206A GLY 3.3 5.7 + - - -
207A LEU* 3.4 30.2 + - + +
209A VAL* 3.7 31.4 - - + -
221A CYS* 4.3 7.6 - - - -
223A TYR* 4.6 10.8 - - + -
234A VAL* 4.4 8.7 - - + -
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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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62A LEU 5.8 1.4 + - - -
63A CYS 6.1 0.2 - - - -
64A THR 5.1 0.2 + - - -
66A TYR* 4.1 19.7 - - + +
67A ASP* 3.5 33.5 + - - +
72A HIS* 3.4 21.3 + - + -
199A THR* 3.1 13.5 + - + +
200A LEU* 2.7 15.0 + - - +
202A LEU* 1.3 75.0 - - - +
204A SER* 1.3 54.4 + - - +
206A GLY* 2.6 27.8 + - - +
207A LEU 4.0 16.4 - - - +
208A ASP* 5.2 1.6 - - - +
209A VAL* 4.1 34.1 + - + +
262A GLY* 5.4 0.2 - - - -
263A LYS* 4.0 23.0 - - - +
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Residues in contact with SER 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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72A HIS* 3.1 19.7 + - - +
75A VAL* 3.4 25.1 - - - +
76A LEU* 3.2 36.6 - - - +
200A LEU* 2.5 31.1 + - - +
201A ILE* 3.6 7.6 - - - -
203A LYS* 1.3 72.5 - - - +
205A PHE* 1.3 59.0 + - - +
206A GLY 2.9 5.3 + - - -
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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