Contacts of the helix formed by residues 183 - 200 (chain A) in PDB entry 1YH3
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 183 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A PRO 3.0 10.3 - - - +
101A ILE* 4.0 2.7 - - - -
174A PRO* 3.8 29.1 + - + +
176A TRP* 4.0 7.5 + - - -
180A CYS* 3.0 21.2 - - - +
181A SER 3.0 6.9 + - - +
182A ASN* 1.3 76.6 - - - +
184A PRO* 1.3 79.3 - - + +
185A VAL* 3.1 13.6 + - - +
186A SER* 2.8 46.8 + - - +
187A VAL* 2.9 23.4 + - - +
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Residues in contact with PRO 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 3.9 15.0 - - + +
98A PRO* 3.3 19.3 - - + +
101A ILE* 3.7 23.3 - - + -
106A TYR* 2.7 23.4 + - - +
159A TRP* 3.5 29.6 - - + +
160A CYS* 3.9 25.6 - - + -
161A GLY 4.6 0.7 - - - +
174A PRO* 4.9 0.4 - - + -
183A ASN* 1.3 90.9 - - + +
185A VAL* 1.3 62.1 + - - +
188A PHE* 3.2 14.9 + - - +
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Residues in contact with VAL 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU 4.5 6.7 - - - +
158A THR* 3.8 18.4 - - + +
159A TRP* 3.5 49.8 - - + +
173A CYS* 6.2 0.4 - - + -
183A ASN* 3.1 9.6 - - - +
184A PRO* 1.3 75.3 - - - +
186A SER* 1.3 70.3 + - - +
188A PHE* 3.2 2.3 + - - +
189A TRP* 3.1 51.2 + - + +
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Residues in contact with SER 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A TRP* 3.7 32.4 - - - +
181A SER 3.6 12.6 - - - -
183A ASN* 2.8 30.8 + - - +
185A VAL* 1.3 78.2 - - - +
187A VAL* 1.3 58.7 + - - +
189A TRP* 3.4 5.0 + - - +
190A LYS* 3.0 31.7 + - - +
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Residues in contact with VAL 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ILE* 3.4 27.8 - - + +
102A THR 3.5 33.0 - - - +
103A GLU 3.6 4.3 - - - +
106A TYR* 3.9 11.2 - - + -
181A SER 4.3 1.6 - - - +
182A ASN* 3.6 24.5 - - + +
183A ASN 2.9 20.8 + - - +
186A SER* 1.3 75.4 - - - +
188A PHE* 1.3 64.5 + - - +
190A LYS* 3.4 8.6 + - + +
191A THR* 2.8 33.8 + - - +
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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
----------------------------------------------------------
89A PHE* 4.6 6.3 - + - -
106A TYR* 3.7 33.8 - + + -
109A LEU* 4.0 20.4 - - + -
110A MET* 5.5 0.9 - - + -
150A LEU* 3.4 28.5 - - + -
153A LEU* 6.0 0.2 - - + -
154A ALA* 3.5 20.2 - - + -
159A TRP* 3.6 22.0 - + + -
184A PRO 3.2 19.8 + - - +
185A VAL 3.2 3.6 + - - +
187A VAL* 1.3 78.4 - - - +
189A TRP* 1.3 84.0 + + - +
191A THR* 3.2 3.7 + - - -
192A VAL* 2.9 59.5 + - + +
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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
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145A LEU* 3.6 32.1 - - + -
146A GLU* 4.4 13.5 - - + -
151A GLY* 3.7 31.2 - - - -
154A ALA* 3.7 27.4 + - + -
155A ASP* 4.0 8.3 - - - -
156A ASP 4.9 2.0 - - - -
157A LEU 5.1 1.8 + - - -
159A TRP* 4.4 4.9 - - - -
185A VAL* 3.1 42.9 + - + +
186A SER* 4.0 5.2 - - - +
188A PHE* 1.3 96.3 - + - +
190A LYS* 1.3 60.1 + - - +
192A VAL* 3.8 6.1 - - + -
193A SER* 2.9 36.2 + - - -
221A THR* 5.7 7.4 - - + +
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Residues in contact with LYS 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A TRP* 5.8 12.8 - - + -
186A SER 3.0 18.3 + - - +
187A VAL* 3.8 9.2 - - + +
189A TRP* 1.3 75.2 - - - +
191A THR* 1.3 64.2 + - - +
193A SER* 3.6 4.9 + - - -
194A ARG* 3.2 28.2 + - + +
221A THR* 5.7 1.1 - - - -
224A SER 5.9 0.8 + - - -
225A VAL* 4.1 27.0 - - + +
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Residues in contact with THR 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLU* 3.5 55.0 + - + +
106A TYR* 4.9 4.6 - - + -
110A MET* 3.6 26.5 - - - -
187A VAL* 2.8 24.4 + - - +
188A PHE* 3.6 5.2 - - - -
190A LYS* 1.3 81.4 - - - +
192A VAL* 1.3 63.6 + - - +
194A ARG* 3.5 5.7 + - - +
195A ARG* 3.3 25.5 + - - +
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Residues in contact with VAL 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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110A MET* 3.4 30.3 - - + -
145A LEU* 3.7 17.4 - - + +
150A LEU* 4.5 11.7 - - + -
151A GLY* 5.6 1.6 - - - -
188A PHE* 2.9 49.9 + - + +
189A TRP* 3.8 28.3 - - + +
191A THR* 1.3 77.1 - - - +
193A SER* 1.3 61.7 + - - +
195A ARG* 3.9 5.5 - - - +
196A PHE* 3.0 28.9 + - - +
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Residues in contact with SER 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU* 3.8 18.4 - - - -
189A TRP* 2.9 23.2 + - - -
190A LYS* 3.6 1.0 + - - -
192A VAL* 1.3 76.3 - - - +
194A ARG* 1.3 67.9 + - - +
196A PHE* 3.8 3.0 - - - +
197A ALA* 3.0 24.4 + - - +
221A THR* 3.5 15.7 - - - +
225A VAL* 3.4 17.6 - - - +
226A GLU* 3.6 24.3 - - - +
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Residues in contact with ARG 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLU* 2.4 44.2 + - - -
190A LYS* 3.2 22.3 + - + +
191A THR* 3.8 7.8 - - - +
192A VAL 3.4 0.2 - - - -
193A SER* 1.3 76.8 + - - +
195A ARG* 1.3 75.7 + - - +
197A ALA* 3.3 2.1 + - - +
198A GLU* 2.9 52.4 + - - +
225A VAL* 3.7 12.7 - - + +
229A ASN* 3.3 36.7 - - - +
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Residues in contact with ARG 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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103A GLU* 4.6 1.3 - - - -
107A GLN* 4.5 14.6 + - - +
110A MET* 3.9 48.9 + - - +
111A LYS* 6.1 0.2 - - - +
114A THR* 5.6 4.9 + - - +
150A LEU* 5.7 2.0 - - - +
191A THR* 3.3 21.1 + - - +
192A VAL* 3.9 4.9 - - - +
193A SER 3.2 0.6 - - - -
194A ARG* 1.3 102.7 - - - +
196A PHE* 1.3 62.2 + - - +
198A GLU* 3.3 14.6 + - - +
199A ALA* 3.1 23.0 + - - +
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Residues in contact with PHE 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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117A VAL* 4.2 11.2 - - + -
122A ILE* 3.6 42.4 - - + +
123A LEU 4.5 0.4 - - - -
124A LEU* 4.0 19.3 - - + -
143A PHE* 3.8 11.4 - - + -
144A THR* 3.5 19.3 - - - -
145A LEU* 3.4 36.3 - - + -
148A THR* 3.4 30.5 - - + -
192A VAL 3.0 17.8 + - - +
193A SER* 3.8 4.3 - - - +
195A ARG* 1.3 75.2 - - - +
197A ALA* 1.3 66.2 + - - +
199A ALA* 3.2 17.0 + - + +
200A ALA* 3.5 7.1 + - - +
226A GLU* 5.3 2.5 - - - -
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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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124A LEU* 5.2 6.0 - - + +
193A SER 3.0 17.7 + - - +
194A ARG 3.7 3.1 - - - +
196A PHE* 1.3 80.5 - - - +
198A GLU* 1.3 63.9 + - - +
200A ALA* 3.1 20.3 + - - +
226A GLU* 3.7 37.9 - - + +
229A ASN* 3.6 14.8 - - + +
230A LEU* 3.8 15.7 - - + +
231A GLN 4.7 0.5 + - - -
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Residues in contact with GLU 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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194A ARG* 2.9 45.9 + - - +
195A ARG* 3.6 15.9 - - - +
196A PHE 3.2 0.4 - - - -
197A ALA* 1.3 77.1 - - - +
199A ALA* 1.3 56.4 + - - +
200A ALA 3.3 0.2 - - - -
229A ASN* 3.4 34.0 - - + +
231A GLN* 3.5 18.9 + - + +
234A LYS* 3.2 25.5 + - - -
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Residues in contact with ALA 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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116A THR* 6.1 5.2 - - + -
119A CYS* 3.3 19.9 - - + +
122A ILE* 4.7 5.6 - - + -
195A ARG 3.1 14.4 + - - +
196A PHE* 3.7 10.8 - - + +
197A ALA 3.1 1.0 - - - -
198A GLU* 1.3 75.5 - - - +
200A ALA* 1.3 65.8 + - - +
234A LYS* 3.4 9.6 + - - +
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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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119A CYS 3.7 7.0 - - - +
122A ILE* 3.9 26.2 - - + -
196A PHE 3.5 5.1 + - - +
197A ALA* 3.1 16.2 + - - +
198A GLU 3.3 0.5 - - - +
199A ALA* 1.3 81.5 - - - +
201A CYS* 1.3 58.3 + - - +
204A VAL* 3.8 22.0 - - + -
230A LEU* 4.2 9.2 - - + -
231A GLN 5.1 0.2 + - - -
234A LYS* 3.3 18.5 + - - -
235A VAL* 3.6 10.7 - - - +
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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
------------------------------------------------------------
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