Contacts of the helix formed by residues 159 - 178 (chain A) in PDB entry 1Y8B
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 ASP 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A ALA* 3.3 38.7 - - - +
154A MET* 5.0 1.1 - - - +
155A VAL* 4.5 9.9 - - + +
157A GLY 4.2 0.8 + - - -
158A TYR* 1.3 73.4 - - - +
160A PRO* 1.3 56.5 - - - +
161A GLN* 2.4 50.6 + - - +
162A ARG* 3.3 40.6 + - - +
163A GLY 4.4 0.3 + - - -
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Residues in contact with PRO 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A TYR* 5.9 2.0 - - - +
158A TYR* 3.2 24.2 - - + +
159A ASP* 1.3 85.2 - - - +
161A GLN* 1.3 64.8 + - - +
162A ARG 3.4 0.4 - - - -
163A GLY* 3.0 15.9 + - - +
164A GLU* 3.3 8.3 + - - +
247A ARG* 5.2 23.8 - - + +
248A ILE* 4.1 8.4 - - + +
250A LYS* 5.1 13.4 + - - +
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Residues in contact with GLN 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ALA* 5.0 1.8 - - + -
159A ASP* 2.4 43.6 + - - +
160A PRO* 1.3 72.1 - - + +
162A ARG* 1.3 66.3 + - + +
164A GLU* 2.7 24.3 + - - +
165A GLN* 3.2 9.5 + - - +
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Residues in contact with ARG 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A TYR* 5.7 1.6 + - + -
143A TYR* 3.1 50.4 + - + +
148A ILE* 4.4 18.6 - - + -
150A GLN* 5.0 11.7 - - + -
152A GLY 4.5 2.4 + - - -
153A ALA* 3.2 38.0 - - + +
154A MET* 4.1 7.5 - - - +
157A GLY 5.1 2.2 + - - -
158A TYR* 4.9 4.0 - - - +
159A ASP* 3.3 36.3 + - - +
161A GLN* 1.3 74.2 - - + +
163A GLY* 1.3 57.4 + - - +
164A GLU 2.8 0.5 + - - -
165A GLN* 2.9 9.1 + - - +
166A VAL* 2.3 54.5 + - + +
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Residues in contact with GLY 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A TYR* 3.9 28.6 + - - -
159A ASP 4.4 0.4 + - - -
160A PRO* 3.0 14.2 + - - +
161A GLN 3.0 0.2 + - - -
162A ARG* 1.3 79.1 - - - +
164A GLU* 1.3 60.5 + - - +
166A VAL* 3.9 1.9 - - - +
167A ILE* 3.4 26.9 + - - +
248A ILE* 3.7 17.6 - - - +
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Residues in contact with GLU 164 (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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160A PRO 3.3 6.6 + - - +
161A GLN* 2.7 24.3 + - - +
163A GLY* 1.3 70.7 - - - -
165A GLN* 1.3 61.4 + - - +
167A ILE* 2.8 29.9 - - + +
168A ALA* 3.7 4.5 + - - +
248A ILE* 3.8 16.9 - - + +
250A LYS* 5.0 11.8 - - - -
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Residues in contact with GLN 165 (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* 3.7 20.2 - - + +
149A PRO* 2.7 40.0 + - - +
150A GLN* 4.6 4.6 - - - +
161A GLN 3.2 6.3 + - - +
162A ARG* 2.9 10.0 + - - +
164A GLU* 1.3 75.3 - - - +
166A VAL* 1.3 65.2 + - - +
167A ILE 3.3 0.2 - - - -
168A ALA* 3.3 18.7 + - + +
169A TRP* 3.7 22.3 + - + +
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Residues in contact with VAL 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A TYR* 3.9 22.7 - - + +
142A LEU* 3.9 30.6 - - + +
143A TYR* 4.8 12.6 - - + -
148A ILE* 3.8 23.1 - - + -
162A ARG* 2.3 60.0 + - + +
163A GLY* 3.9 6.5 - - - +
165A GLN* 1.3 69.8 - - - +
167A ILE* 1.3 63.4 + - + +
168A ALA 3.3 0.2 + - - -
169A TRP* 3.4 6.0 + - - +
170A VAL* 3.3 20.6 + - + +
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Residues in contact with ILE 167 (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 TYR* 5.7 9.0 - - + -
163A GLY 3.4 12.5 + - - +
164A GLU* 2.8 29.8 - - + +
166A VAL* 1.3 79.5 - - + +
168A ALA* 1.3 61.9 + - - +
170A VAL* 3.7 8.7 - - + -
171A ARG* 2.8 77.1 + - - +
248A ILE* 3.8 31.6 - - + -
252A ASP* 4.3 4.3 - - - +
256A ILE 5.1 0.4 - - - +
257A ASN 6.5 0.7 - - - -
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Residues in contact with ALA 168 (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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164A GLU 4.3 2.0 - - - +
165A GLN* 3.3 20.8 + - + +
166A VAL 3.1 0.8 - - - -
167A ILE* 1.3 84.3 - - + +
169A TRP* 1.3 79.5 + - + +
171A ARG* 4.4 3.2 - - - +
172A ARG* 3.3 18.7 + - - +
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Residues in contact with TRP 169 (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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142A LEU* 5.5 2.0 - - + -
147A ILE* 4.2 23.9 + - + -
148A ILE* 5.7 2.7 - - + -
149A PRO* 3.6 33.5 - - + +
165A GLN* 3.7 22.1 + - + +
166A VAL* 3.4 8.5 + - - +
167A ILE 3.2 0.4 - - - -
168A ALA* 1.3 96.8 - - + +
170A VAL* 1.3 66.1 + - + +
172A ARG* 3.2 6.4 + - + +
173A PHE* 2.8 53.8 + + + -
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Residues in contact with VAL 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 4.1 21.3 - - + -
139A TYR* 5.4 2.9 - - - -
142A LEU* 3.8 36.1 - - + -
166A VAL* 3.3 20.3 + - + +
167A ILE* 3.9 7.6 - - + +
169A TRP* 1.3 73.0 - - - +
171A ARG* 1.3 60.2 + - + +
172A ARG 2.5 16.4 + - - -
173A PHE* 2.6 20.2 + - + +
174A LEU* 3.0 34.3 + - + +
259A VAL* 4.6 10.3 - - + -
546A LEU* 5.6 0.4 - - + -
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Residues in contact with ARG 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 2.8 67.5 + - + +
168A ALA* 4.6 3.6 - - - +
170A VAL* 1.3 73.5 - - - +
172A ARG* 1.3 60.8 + - - +
174A LEU* 4.1 14.1 - - - +
175A ASP* 3.8 6.6 + - - +
184A SER* 4.9 2.3 + - - -
185A TYR* 3.7 31.2 - - + +
186A GLN* 4.9 14.2 + - + +
252A ASP* 3.0 24.8 + - - -
253A PRO* 5.5 0.8 - - - +
254A ALA* 4.3 16.8 - - - +
256A ILE* 2.6 56.1 + - - +
257A ASN 5.4 0.2 - - - -
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Residues in contact with ARG 172 (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 ALA 3.3 15.4 + - - +
169A TRP* 3.2 13.0 + - + +
170A VAL 2.5 5.5 + - - -
171A ARG* 1.3 76.0 - - - +
173A PHE* 1.3 57.9 + - + +
175A ASP* 3.2 22.1 + - - +
176A GLU* 2.3 43.8 + - - +
184A SER* 5.4 5.7 + - - -
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Residues in contact with PHE 173 (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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142A LEU* 5.6 0.2 - - + -
147A ILE* 4.7 6.7 - - + -
169A TRP* 2.8 55.9 + + + -
170A VAL* 2.6 13.4 + - + +
172A ARG* 1.3 72.8 - - + +
174A LEU* 1.3 61.6 + - + +
175A ASP 2.9 4.9 - - - -
176A GLU* 2.7 26.8 + - + +
177A SER* 3.2 12.0 + - - -
546A LEU* 3.6 55.1 - - + +
547A HIS* 3.5 36.3 - + - -
549A HIS* 4.9 2.3 - - - +
550A GLN* 5.6 6.7 - - + -
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Residues in contact with LEU 174 (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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138A LEU* 5.3 2.2 - - + -
170A VAL* 3.0 35.6 + - + +
171A ARG* 4.3 14.8 - - - +
173A PHE* 1.3 80.0 - - + +
175A ASP* 1.3 61.4 + - - +
177A SER* 4.1 7.9 - - - -
178A LEU* 3.1 26.2 + - + +
185A TYR* 3.3 37.3 - - + -
238A ILE* 4.2 23.6 - - + -
240A LEU* 4.9 7.6 - - + -
256A ILE* 5.4 3.6 - - + -
259A VAL* 4.4 20.6 - - + -
546A LEU* 5.2 9.6 - - + -
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Residues in contact with ASP 175 (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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171A ARG 3.8 8.0 + - - +
172A ARG* 3.2 30.5 + - - +
173A PHE 2.9 0.4 - - - -
174A LEU* 1.3 79.8 - - - +
176A GLU* 1.3 69.5 + - - +
178A LEU 4.2 2.9 - - - -
179A PRO* 3.1 38.5 - - - +
180A LEU 4.7 0.9 + - - -
183A GLY 4.3 4.2 - - - +
184A SER* 3.8 32.6 - - - +
185A TYR* 4.1 6.2 + - - +
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Residues in contact with GLU 176 (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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172A ARG* 2.3 44.9 + - - +
173A PHE* 2.7 17.0 - - + +
175A ASP* 1.3 87.6 - - - +
177A SER* 1.3 70.1 + - - +
178A LEU 3.3 0.2 + - - -
179A PRO* 3.4 11.6 - - - +
546A LEU 5.6 0.2 - - - +
549A HIS* 3.6 27.5 - - + +
550A GLN* 4.0 24.7 - - + +
552A ASN* 5.8 0.9 + - - -
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Residues in contact with SER 177 (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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173A PHE 3.2 11.0 + - - -
174A LEU* 4.3 6.1 - - - -
176A GLU* 1.3 82.1 - - - +
178A LEU* 1.3 79.1 + - - +
179A PRO* 3.3 4.9 - - - +
211A ARG* 4.8 0.5 - - - -
233A ASN* 3.0 26.3 + - - +
238A ILE* 4.7 6.4 - - - +
546A LEU* 6.3 1.3 - - - -
549A HIS* 3.4 48.4 + - - +
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Residues in contact with LEU 178 (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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174A LEU* 3.1 11.9 + - - +
175A ASP 3.5 2.2 - - - -
177A SER* 1.3 109.0 - - - +
179A PRO* 1.3 63.0 - - - +
180A LEU* 5.1 0.4 - - - -
185A TYR* 2.9 49.4 - - + +
210A LEU* 4.6 4.5 - - + -
215A GLN* 3.5 32.1 - - - +
231A LEU* 4.0 31.6 - - + -
232A LYS 5.2 0.2 - - - +
233A ASN* 4.5 6.5 - - + +
238A ILE* 3.8 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
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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