Contacts of the helix formed by residues 140 - 150 (chain A) in PDB entry 2YG9
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 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.8 30.1 - - + +
20A PRO* 3.5 24.0 - - + +
21A ALA* 5.5 0.9 - - - -
22A VAL* 3.5 12.5 - - + +
138A GLY 3.8 6.7 - - - +
139A GLN* 1.3 86.7 - - - +
141A ASP* 1.3 66.8 + - - +
142A GLU 4.4 0.7 - - - +
143A LEU* 3.0 41.2 + - + +
144A VAL* 3.2 8.7 + - - +
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Residues in contact with ASP 141 (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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20A PRO 5.2 0.6 + - - -
22A VAL* 5.0 5.4 - - - +
23A LEU 5.4 1.6 + - - -
140A PRO* 1.3 70.4 - - - +
142A GLU* 1.3 62.2 + - + +
144A VAL* 3.2 4.8 + - - +
145A ILE* 2.8 38.0 + - + +
163A LEU* 3.7 18.8 - - + +
169A ARG* 2.8 36.7 + - - +
171A ASP* 4.1 13.7 + - - +
172A VAL* 3.9 18.1 - - - +
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Residues in contact with GLU 142 (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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19A LEU* 3.9 31.4 - - + +
20A PRO* 5.9 1.1 - - + -
140A PRO* 3.2 1.6 - - - +
141A ASP* 1.3 84.6 - - + +
143A LEU* 1.3 59.6 + - - +
145A ILE* 3.6 13.1 - - - +
146A ALA* 2.9 29.3 + - - +
156A ARG* 2.4 44.7 + - - -
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Residues in contact with LEU 143 (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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19A LEU* 3.4 29.4 - - + +
139A GLN* 4.3 24.9 + - - +
140A PRO* 3.0 32.7 + - + +
142A GLU* 1.3 75.7 - - - +
144A VAL* 1.3 65.2 + - - +
146A ALA* 3.5 6.6 + - + +
147A GLU* 3.2 28.4 + - - +
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Residues in contact with VAL 144 (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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131A ILE* 6.5 0.4 - - + -
136A LEU* 4.3 26.9 - - + -
139A GLN* 3.4 35.2 - - + +
140A PRO 3.2 8.3 + - - +
141A ASP* 3.6 6.3 - - - +
143A LEU* 1.3 71.5 - - - +
145A ILE* 1.3 66.6 + - - +
147A GLU* 3.3 5.8 + - - +
148A LEU* 3.0 36.2 + - + +
162A PHE* 5.0 0.4 - - + -
163A LEU* 3.6 25.4 - - + -
167A LEU* 4.4 8.5 - - + -
169A ARG* 3.9 13.2 - - - +
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Residues in contact with ILE 145 (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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141A ASP* 2.8 26.0 + - + +
142A GLU* 3.6 25.4 - - - +
144A VAL* 1.3 76.5 - - - +
146A ALA* 1.3 65.0 + - - +
148A LEU* 3.2 3.1 + - - +
149A VAL* 2.9 38.7 + - + +
156A ARG* 3.8 34.3 - - + +
159A ALA* 4.1 20.6 - - + -
160A GLU* 4.0 16.6 - - + +
163A LEU* 3.6 24.7 - - + -
172A VAL* 5.9 1.3 - - + -
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Residues in contact with ALA 146 (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 GLU 2.9 18.9 + - - +
143A LEU* 3.9 7.9 - - + +
144A VAL 3.3 0.6 - - - -
145A ILE* 1.3 77.1 - - - +
147A GLU* 1.3 69.8 + - - +
149A VAL* 3.6 8.3 + - - +
150A GLN* 3.4 27.4 + - - +
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Residues in contact with GLU 147 (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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130A GLN* 3.7 28.4 - - - +
131A ILE* 3.8 31.2 - - + +
139A GLN* 5.5 7.0 - - - +
143A LEU* 3.2 17.2 + - + +
144A VAL* 3.9 4.9 - - - +
145A ILE 3.2 1.0 - - - -
146A ALA* 1.3 85.3 - - - +
148A LEU* 1.3 62.2 + - + +
150A GLN* 3.5 22.9 + - - +
151A LEU* 4.1 3.1 + - - +
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Residues in contact with LEU 148 (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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65A LEU* 3.8 33.0 - - + -
131A ILE* 4.3 12.1 - - + -
133A PHE* 4.4 8.5 - - + -
144A VAL* 3.0 33.1 + - + +
145A ILE 3.7 2.9 - - - +
147A GLU* 1.3 74.2 - - + +
149A VAL* 1.3 60.0 + - - +
151A LEU* 2.9 38.5 + - + +
154A ILE* 3.4 16.5 - - + +
159A ALA* 3.9 27.1 - - + +
162A PHE* 3.7 30.1 - - + -
163A LEU* 4.5 0.2 - - + -
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Residues in contact with VAL 149 (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 ILE* 2.9 29.2 + - + +
146A ALA* 3.8 8.1 - - - +
147A GLU 3.4 0.2 - - - -
148A LEU* 1.3 75.9 - - - +
150A GLN* 1.3 73.7 + - - +
151A LEU 3.1 3.0 - - - +
154A ILE 3.1 19.5 - - - +
155A GLY* 3.6 5.6 - - - +
156A ARG* 3.5 37.2 - - + +
159A ALA* 4.4 0.9 - - + -
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Residues in contact with GLN 150 (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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146A ALA 3.4 14.2 + - - +
147A GLU* 3.7 19.1 - - - +
148A LEU 3.1 1.4 - - - -
149A VAL* 1.3 89.2 - - - +
151A LEU* 1.3 63.7 + - + +
152A PRO* 3.7 3.8 - - - +
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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