Contacts of the helix formed by residues 140 - 149 (chain A) in PDB entry 2YNU
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 GLU 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A THR 3.8 0.2 + - - -
139A SER* 1.3 73.1 - - - +
141A LEU* 1.3 59.7 + - - +
143A LYS* 3.2 3.2 + - + +
144A LYS* 2.9 57.5 + - + +
171A TYR* 3.5 27.1 + - + -
172A PHE 2.9 21.4 + - - +
173A LYS* 2.8 48.7 + - - +
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Residues in contact with LEU 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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139A SER* 3.2 7.9 + - - +
140A GLU* 1.3 79.8 - - - +
142A THR* 1.3 65.3 + - - +
144A LYS* 3.3 8.5 + - + -
145A LEU* 2.9 46.2 + - + +
191A TYR* 4.8 8.7 - - + +
198A GLU* 4.0 18.6 - - + +
199A ASP* 3.7 24.9 - - + -
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Residues in contact with THR 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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114A SER 4.7 2.8 + - - +
115A THR 4.8 1.4 + - - -
116A HIS* 3.7 11.6 - - - +
117A SER* 3.6 25.8 - - - +
122A THR* 5.1 0.2 - - + -
138A THR* 3.5 32.3 - - + -
139A SER* 3.0 20.1 + - - -
141A LEU* 1.3 75.5 - - - +
143A LYS* 1.3 56.7 + - - +
145A LEU* 3.2 4.5 + - - +
146A LEU* 2.9 33.0 + - + +
199A ASP* 2.6 29.8 + - - +
201A ILE* 5.6 0.5 - - - +
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Residues in contact with LYS 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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138A THR* 3.2 16.4 + - - +
139A SER 3.1 9.1 + - - +
140A GLU* 3.4 9.4 - - + +
141A LEU 3.2 0.2 - - - -
142A THR* 1.3 75.0 - - - +
144A LYS* 1.3 69.2 + - + +
146A LEU* 3.3 5.0 + - - +
147A ALA* 3.0 21.4 + - + +
167A VAL* 3.6 17.7 - - + +
168A PRO* 3.9 35.9 + - + +
169A THR 6.1 0.6 - - - -
171A TYR* 3.1 49.4 + - + -
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Residues in contact with LYS 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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140A GLU* 2.9 49.8 + - + +
141A LEU* 3.7 11.2 - - + +
143A LYS* 1.3 81.8 - - + +
145A LEU* 1.3 62.9 + - + +
147A ALA* 3.3 9.3 + - + +
148A ARG* 3.0 25.4 + - - +
171A TYR* 5.7 2.2 + - - -
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Residues in contact with LEU 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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117A SER* 3.9 15.3 - - - +
141A LEU* 2.9 37.9 + - + +
142A THR 3.6 3.1 - - - +
144A LYS* 1.3 76.8 - - + +
146A LEU* 1.3 65.5 + - - +
148A ARG* 3.4 12.3 + - + +
149A GLU* 3.2 27.6 + - + +
198A GLU* 3.6 33.7 - - + +
199A ASP* 3.6 35.4 - - + +
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Residues in contact with LEU 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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117A SER* 3.0 31.4 - - - +
119A GLU* 6.1 0.4 - - - +
122A THR* 4.1 11.4 - - + +
125A ILE* 4.1 15.3 - - + -
142A THR* 2.9 33.4 + - + +
143A LYS 3.6 6.1 - - - +
145A LEU* 1.3 75.9 - - - +
147A ALA* 1.3 63.6 + - - +
149A GLU* 3.1 9.5 + - - -
165A LYS* 3.0 49.4 + - + +
166A PRO 3.9 16.6 - - - +
167A VAL* 3.9 8.3 - - + -
168A PRO* 4.0 19.5 - - + -
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Residues in contact with ALA 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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143A LYS* 3.0 14.9 + - + +
144A LYS* 3.3 14.3 + - + +
146A LEU* 1.3 76.5 - - - +
148A ARG* 1.3 62.1 + - - +
150A GLY* 3.1 14.6 + - - -
165A LYS 4.5 3.4 - - - -
167A VAL* 3.7 15.3 - - + +
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Residues in contact with ARG 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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144A LYS 3.0 16.8 + - - +
145A LEU* 3.8 15.4 - - + +
146A LEU 3.3 0.2 - - - -
147A ALA* 1.3 77.2 - - - +
149A GLU* 1.3 66.6 + - + +
150A GLY 3.2 2.6 + - - -
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Residues in contact with GLU 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 LEU* 3.2 16.5 + - + +
146A LEU* 3.1 6.1 + - - +
148A ARG* 1.3 84.3 - - + +
150A GLY* 1.3 61.4 + - - +
165A LYS* 3.5 21.7 + - + +
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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
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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