Contacts of the helix formed by residues 179 - 190 (chain A) in PDB entry 2YWD
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 PRO 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ALA* 4.2 8.5 - - + +
23A ARG* 4.0 29.4 - - + +
24A LEU* 3.8 24.6 - - + +
177A GLU 3.1 11.9 - - - +
178A ASP* 1.3 84.9 - - - +
180A ARG* 1.3 62.9 + - + +
181A LEU 3.3 3.1 - - - -
182A HIS* 3.1 12.7 + - + +
183A ARG* 2.9 27.4 + - - +
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Residues in contact with ARG 180 (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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128A LEU* 3.3 54.3 + - + +
129A GLY* 4.6 1.4 - - - -
130A SER 2.6 31.3 + - - +
131A PHE* 4.2 4.0 - - - -
178A ASP* 2.8 34.8 + - - +
179A PRO* 1.3 81.7 - - + +
181A LEU* 1.3 57.3 + - - +
183A ARG* 3.8 7.6 - - - +
184A TYR* 3.0 26.3 + - - +
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Residues in contact with LEU 181 (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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78A PHE* 4.0 19.8 - - + -
125A VAL* 4.9 1.8 - - + -
128A LEU* 3.8 15.7 - - + +
131A PHE* 3.9 25.8 - - + -
160A LEU* 3.9 26.0 - - + -
167A LEU* 4.5 5.8 - - + -
171A PHE* 3.6 36.8 - - + -
173A PRO* 3.8 14.6 - - + -
179A PRO 3.3 0.8 - - - -
180A ARG* 1.3 74.7 - - - +
182A HIS* 1.3 66.1 + - - +
184A TYR* 3.3 20.8 + - + +
185A PHE* 3.1 21.0 + - - +
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Residues in contact with HIS 182 (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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17A HIS* 3.0 29.2 + + - -
20A ALA* 3.8 25.9 - - + +
21A LEU* 3.9 17.0 - - + -
24A LEU* 3.7 15.9 - - + -
44A ILE* 3.8 23.6 - - + -
78A PHE* 4.8 5.8 - + - -
173A PRO* 3.9 18.9 - - + +
174A GLU* 3.9 20.0 - - - -
178A ASP 4.7 2.6 + - - -
179A PRO* 3.1 17.3 + - + +
181A LEU* 1.3 79.2 - - - +
183A ARG* 1.3 56.8 + - - +
185A PHE* 3.1 9.6 + + + +
186A LEU* 2.9 30.1 + - - +
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Residues in contact with ARG 183 (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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24A LEU* 3.3 57.9 + - + +
26A ILE* 5.8 1.4 - - - +
179A PRO 2.9 14.8 + - - +
180A ARG* 3.8 9.0 - - + +
181A LEU 3.3 0.2 - - - -
182A HIS* 1.3 73.5 - - - +
184A TYR* 1.3 67.2 + - - +
186A LEU* 3.1 21.6 + - - +
187A GLU* 2.8 55.0 + - + +
191A VAL* 5.0 9.1 + - - +
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Residues in contact with TYR 184 (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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125A VAL* 6.2 1.8 - - + -
126A GLU 4.8 12.7 + - - -
127A GLY* 6.0 2.5 - - - -
128A LEU* 4.8 15.9 - - + -
149A GLU* 5.1 0.5 + - - -
151A LEU* 3.4 39.4 - - + +
160A LEU* 5.7 0.4 - - + -
162A ARG* 3.1 26.3 + - - -
167A LEU* 4.1 16.4 - - + -
180A ARG 3.0 15.8 + - - +
181A LEU* 3.4 22.0 - - + +
182A HIS 3.2 0.2 - - - -
183A ARG* 1.3 75.4 - - - +
185A PHE* 1.3 63.6 + - - +
187A GLU* 3.4 8.5 + - + +
188A LEU* 3.2 36.5 + - + +
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Residues in contact with PHE 185 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A VAL* 5.6 0.4 - - + -
42A ALA* 3.6 23.1 - - + -
43A LEU 3.8 2.2 - - - -
44A ILE* 3.8 19.3 - - + -
76A ALA* 3.6 31.2 - - + -
77A LEU 3.4 26.0 - - - -
78A PHE* 3.6 44.6 - + + -
167A LEU* 4.0 9.9 - - + -
181A LEU 3.1 12.5 + - - +
182A HIS* 3.3 9.0 - - - +
183A ARG 3.1 0.2 - - - -
184A TYR* 1.3 77.1 - - - +
186A LEU* 1.3 76.8 + - + +
188A LEU* 3.1 23.5 - - + +
189A ALA* 3.0 19.1 + - - +
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Residues in contact with LEU 186 (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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5A VAL* 3.9 28.9 - - + -
21A LEU* 4.4 7.4 - - + -
24A LEU* 3.5 25.1 - - + -
26A ILE* 4.0 26.7 - - + -
42A ALA* 4.4 3.4 - - + -
182A HIS 2.9 16.7 + - - +
183A ARG* 3.1 23.5 + - - +
185A PHE* 1.3 92.7 - - + +
187A GLU* 1.3 61.2 + - - +
189A ALA* 3.2 3.8 + - - -
190A GLY 3.0 4.7 + - - -
191A VAL* 2.9 45.3 + - + +
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Residues in contact with GLU 187 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A ARG* 2.8 44.9 + - + +
184A TYR* 3.6 9.0 - - + +
186A LEU* 1.3 77.4 - - - +
188A LEU* 1.3 58.0 + - - +
190A GLY* 3.1 17.5 + - - -
191A VAL 4.3 11.8 - - - +
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Residues in contact with LEU 188 (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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76A ALA* 4.1 8.1 - - + -
162A ARG* 3.7 44.3 + - - +
164A GLY 4.5 1.1 - - - +
165A LYS* 3.7 53.2 + - + +
167A LEU* 4.6 9.4 - - + -
184A TYR* 3.2 29.8 + - + +
185A PHE* 3.1 29.6 + - + +
187A GLU* 1.3 78.7 - - - +
189A ALA* 1.3 61.3 + - - +
190A GLY 3.2 2.0 + - - -
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Residues in contact with ALA 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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41A LYS* 3.9 16.8 - - - +
42A ALA* 3.8 21.5 - - + -
76A ALA* 3.4 31.4 - - + -
165A LYS* 5.0 7.9 - - - +
185A PHE* 3.0 15.8 + - + +
186A LEU 3.6 6.1 - - - +
187A GLU 3.1 0.2 - - - -
188A LEU* 1.3 76.7 - - - +
190A GLY* 1.3 62.0 + - - +
191A VAL* 4.1 4.7 - - + -
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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
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41A LYS* 3.9 16.8 + - - +
186A LEU 3.0 2.4 + - - -
187A GLU 3.1 12.1 + - - -
188A LEU 3.2 1.2 - - - -
189A ALA* 1.3 80.7 - - - +
191A VAL* 1.3 65.5 + - - +
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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