Contacts of the helix formed by residues 188 - 205 (chain A) in PDB entry 1YA8
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 188 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A GLY 3.9 8.6 + - - -
177A PHE* 4.1 12.6 + - - +
187A GLY* 1.3 71.6 - - - +
189A TRP* 1.3 65.9 + - - +
190A GLY 3.0 3.4 - - - -
191A HIS* 2.9 28.2 + - + -
192A LEU* 3.1 12.9 + - + +
320A GLY 3.9 2.5 + - - +
321A THR* 3.4 11.0 - - - -
322A VAL* 2.9 52.7 + - - +
324A ASP* 3.3 27.5 + - - +
327A LEU* 4.0 13.7 - - + +
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Residues in contact with TRP 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 3.2 39.8 - + - +
66A THR* 3.5 14.4 - - - -
67A PRO* 3.6 27.1 - - + -
171A ARG* 3.7 21.0 + - - +
175A TRP 3.6 17.5 - - - -
176A GLY* 3.1 20.2 + - - +
177A PHE 3.9 2.7 - - - -
178A PHE 3.3 17.6 + - - -
185A SER* 3.7 16.2 - - - -
186A ARG* 3.9 14.1 - - + -
187A GLY* 3.2 34.6 - - - -
188A ASN* 1.3 71.4 - - - +
190A GLY* 1.3 57.0 - - - +
192A LEU* 3.2 16.2 + - + +
193A ASP* 2.9 33.5 + - - +
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Residues in contact with GLY 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A TYR* 3.5 5.4 - - - +
171A ARG 3.8 22.4 - - - -
176A GLY* 3.0 12.3 + - - -
177A PHE* 4.0 7.4 - - - -
188A ASN 3.0 1.0 - - - -
189A TRP* 1.3 76.9 - - - +
191A HIS* 1.3 62.2 + - - +
193A ASP* 3.1 12.4 + - - +
194A GLN* 3.0 27.8 + - - +
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Residues in contact with HIS 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LEU* 4.6 1.6 - - + -
177A PHE* 4.0 18.7 - + - -
188A ASN* 2.9 24.2 + - + +
190A GLY* 1.3 74.1 - - - +
192A LEU* 1.3 57.8 + - - +
194A GLN* 3.0 23.4 + - - +
195A VAL* 2.8 32.6 + - - +
225A GLU* 4.1 7.6 - - - -
226A SER* 3.7 24.7 + - - -
229A VAL* 4.3 9.8 - - + +
230A LEU* 4.5 3.6 - - + +
321A THR* 2.7 33.4 + - + +
327A LEU* 3.1 37.7 - - + -
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Residues in contact with LEU 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PRO* 4.2 21.8 - - + -
68A PRO* 3.5 16.3 - - + +
187A GLY 4.7 3.8 - - - +
188A ASN* 3.1 12.0 + - + +
189A TRP* 3.3 34.5 - - + +
191A HIS* 1.3 79.1 - - - +
193A ASP* 1.3 51.1 + - - +
195A VAL* 3.3 9.9 + - + +
196A ALA* 2.7 33.6 + - - +
235A LEU* 3.8 28.9 - - + -
324A ASP* 5.6 3.8 - - - +
326A MET* 6.1 7.2 - - + -
327A LEU* 4.3 13.0 - - + -
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Residues in contact with ASP 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A PHE* 3.4 10.6 - - + -
68A PRO* 3.1 13.6 - - - +
117A LEU* 3.5 19.1 - - + +
169A GLN 5.3 0.2 - - - -
170A TYR* 3.8 11.9 - - + -
171A ARG* 2.8 65.1 + - - +
189A TRP 2.9 13.9 + - - +
190A GLY* 3.1 7.9 + - - +
192A LEU* 1.3 73.2 - - - +
194A GLN* 1.3 65.9 + - - +
196A ALA* 3.1 9.5 + - - +
197A ALA* 2.9 20.6 + - - +
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Residues in contact with GLN 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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139A ILE* 3.4 15.2 - - + +
168A ILE* 4.1 19.3 - - + +
170A TYR* 3.4 40.6 - - + -
190A GLY 3.0 15.1 + - - +
191A HIS* 3.0 30.5 + - - +
193A ASP* 1.3 72.7 - - - +
195A VAL* 1.3 66.6 + - - +
197A ALA* 2.9 14.0 + - - +
198A LEU* 3.2 16.8 + - - +
226A SER* 3.0 30.2 + - - -
230A LEU* 4.6 17.2 - - + +
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Residues in contact with VAL 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 HIS 2.8 16.4 + - - +
192A LEU* 3.6 12.8 - - + +
194A GLN* 1.3 71.3 - - - +
196A ALA* 1.3 64.3 + - - +
198A LEU* 3.1 20.7 + - - +
199A ARG* 3.2 24.3 + - - +
230A LEU* 3.5 26.5 - - + -
235A LEU* 3.8 33.2 - - + +
236A ALA* 4.2 13.0 - - + -
239A LEU* 3.9 8.1 - - + -
327A LEU* 4.3 7.6 - - + -
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Residues in contact with ALA 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A PHE* 4.1 17.9 - - + +
56A ALA* 5.4 0.7 - - + -
68A PRO* 3.8 22.2 - - + +
192A LEU 2.7 17.4 + - - +
193A ASP* 3.1 13.9 - - - +
194A GLN 3.0 0.2 - - - -
195A VAL* 1.3 75.5 - - - +
197A ALA* 1.3 54.8 + - - +
199A ARG* 3.3 11.4 + - - +
200A TRP* 3.0 24.8 + - - +
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Residues in contact with ALA 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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55A PHE* 3.8 26.2 - - + -
119A LEU* 4.4 2.6 - - + +
137A VAL* 5.8 0.2 - - + -
168A ILE* 3.8 34.8 - - + -
193A ASP 2.9 12.6 + - - +
194A GLN 2.9 7.2 + - - +
196A ALA* 1.3 73.9 - - - +
198A LEU* 1.3 61.5 + - + +
200A TRP* 3.3 4.5 + - - +
201A VAL* 3.0 33.8 + - - +
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Residues in contact with LEU 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL* 4.2 24.9 - - + -
139A ILE* 6.1 1.8 - - + -
168A ILE* 6.0 2.0 - - + -
194A GLN 3.2 11.6 + - - +
195A VAL* 3.1 14.6 + - - +
197A ALA* 1.3 76.8 - - + +
199A ARG* 1.3 58.2 + - - +
201A VAL* 3.4 6.5 + - + +
202A GLN* 3.0 26.0 + - - +
215A VAL* 4.5 2.9 - - + -
217A ILE* 3.6 29.2 - - + -
230A LEU* 3.9 28.3 - - + -
236A ALA* 4.9 2.9 - - + -
239A LEU* 3.9 41.6 - - + +
240A PHE* 4.7 7.6 - - + -
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Residues in contact with ARG 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A VAL* 3.2 20.8 + - - +
196A ALA* 3.6 11.4 - - - +
197A ALA 3.2 0.2 - - - -
198A LEU* 1.3 74.7 - - - +
200A TRP* 1.3 65.5 + - - +
202A GLN* 3.2 11.1 + - - +
203A ASP* 3.1 28.9 + - - +
235A LEU* 3.5 27.1 + - - +
237A LYS 5.7 1.4 + - - -
239A LEU* 3.7 33.9 - - + +
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Residues in contact with TRP 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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28A THR* 4.5 13.4 + - + -
30A HIS* 4.8 17.6 - + - +
53A ILE* 3.6 24.8 - - + +
54A PRO 4.1 8.7 + - - -
55A PHE* 3.8 32.8 - - + +
74A TRP* 5.9 1.8 - + - -
119A LEU* 3.9 19.3 - - + -
121A ILE* 3.7 32.5 - - + -
196A ALA 3.0 13.1 + - - +
197A ALA 3.3 7.8 + - - +
199A ARG* 1.3 77.4 - - - +
201A VAL* 1.3 69.8 + - + +
203A ASP* 3.1 3.6 + - - -
204A ASN* 2.8 74.7 + - + +
205A ILE* 4.6 6.3 - - + -
208A PHE* 3.7 10.3 - + - -
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Residues in contact with VAL 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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119A LEU* 4.8 1.1 - - + -
135A VAL* 4.4 5.6 - - + -
137A VAL* 4.4 13.7 - - + -
166A VAL* 4.4 23.3 - - + -
197A ALA* 3.0 20.6 + - + +
198A LEU* 3.6 10.5 - - + +
199A ARG 3.2 0.2 - - - -
200A TRP* 1.3 89.8 - - + +
202A GLN* 1.3 66.7 + - - +
205A ILE* 2.8 57.1 + - + +
215A VAL* 3.9 23.1 - - + -
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Residues in contact with GLN 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 LEU 3.0 14.4 + - - +
199A ARG* 3.2 16.4 + - - +
201A VAL* 1.3 77.6 - - - +
203A ASP* 1.3 70.4 + - - +
212A PRO* 3.9 30.1 - - + +
215A VAL* 6.1 1.1 - - - -
238A ASN* 3.4 24.9 + - - +
239A LEU* 3.9 18.0 - - + +
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Residues in contact with ASP 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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29A VAL* 3.8 17.2 - - + +
199A ARG* 3.1 15.1 + - - +
200A TRP* 3.1 4.8 + - - +
201A VAL 3.0 0.4 - - - -
202A GLN* 1.3 99.4 - - - +
204A ASN* 1.3 69.5 + - - +
206A ALA* 5.5 1.5 - - - +
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Residues in contact with ASN 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A THR* 3.5 8.1 - - - -
29A VAL* 2.9 42.7 + - - +
30A HIS* 5.8 1.8 - - - -
200A TRP* 2.8 74.4 + - + +
203A ASP* 1.3 87.3 - - - +
205A ILE* 1.3 58.7 + - - +
206A ALA* 2.8 13.9 + - - -
207A SER* 2.9 23.4 + - - -
208A PHE* 3.7 5.6 - - + -
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Residues in contact with ILE 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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121A ILE* 4.4 11.9 - - + -
135A VAL* 3.8 26.7 - - + -
164A VAL* 3.8 22.4 - - + -
166A VAL* 3.9 17.7 - - + -
200A TRP* 4.6 4.0 - - + -
201A VAL* 2.8 44.6 + - + +
202A GLN 5.2 0.4 + - - -
204A ASN* 1.3 71.5 - - - +
206A ALA* 1.3 60.5 + - - +
207A SER 3.3 0.2 - - - -
208A PHE* 3.3 17.8 + - + -
210A GLY* 2.8 27.2 + - - -
212A PRO* 3.9 30.3 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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