Contacts of the helix formed by residues 160 - 166 (chain A) in PDB entry 2YXE
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 160 (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* 3.3 31.9 - - - +
158A LYS* 3.3 13.2 - - - +
159A ILE* 1.4 83.0 - - + +
161A GLU* 1.3 65.7 + - - +
162A PRO* 3.9 0.4 - - + -
163A LEU* 2.9 35.1 + - + +
164A ILE* 3.3 10.0 + - - +
175A MET* 3.8 16.8 - - + -
207A LEU* 4.6 8.7 - - + -
211A GLU* 3.5 30.1 - - + +
212A GLY* 5.5 0.2 - - - -
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Residues in contact with GLU 161 (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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158A LYS* 5.2 2.4 - - - +
159A ILE 3.3 4.2 + - - -
160A PRO* 1.3 71.4 - - - +
162A PRO* 1.4 65.9 - - + +
164A ILE* 3.2 27.1 + - - +
165A ARG* 2.8 52.2 + - + +
211A GLU* 4.9 6.6 + - - +
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Residues in contact with PRO 162 (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 3.5 18.2 - - - +
139A LEU* 3.6 31.4 - - + +
142A GLU* 5.7 0.2 - - - +
160A PRO 3.4 4.9 - - - -
161A GLU* 1.4 92.9 - - + +
163A LEU* 1.3 61.3 + - - +
165A ARG* 3.5 27.3 + - + +
166A GLN* 3.1 34.4 + - - +
211A GLU* 3.9 23.6 - - + -
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Residues in contact with LEU 163 (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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82A LEU* 4.0 8.1 - - + -
84A ILE* 3.4 32.1 - - + -
137A GLY 3.8 3.4 - - - +
138A THR* 4.5 0.9 - - - +
140A GLY* 3.4 35.9 - - - +
150A ILE* 3.2 30.8 - - + +
152A THR* 4.2 15.0 - - + -
160A PRO* 2.9 40.2 + - + +
162A PRO* 1.3 72.8 - - - +
164A ILE* 1.3 66.8 + - - +
166A GLN* 3.3 2.0 + - - -
167A LEU* 3.3 9.5 + - - +
173A LEU* 3.6 20.6 - - + -
175A MET* 4.8 0.7 - - - -
207A LEU* 5.6 0.2 - - + -
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Residues in contact with ILE 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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159A ILE* 3.7 41.7 - - + +
160A PRO 3.3 1.8 + - - +
161A GLU* 3.2 29.3 + - - +
163A LEU* 1.3 77.0 - - - +
165A ARG* 1.3 64.2 + - + +
167A LEU* 3.2 17.6 + - + +
173A LEU* 5.0 2.5 - - + -
189A LYS* 3.0 33.8 + - - -
194A ILE* 3.8 45.3 - - + -
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Residues in contact with ARG 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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142A GLU* 4.4 18.6 + - - -
146A PRO* 5.6 1.2 - - - +
161A GLU* 2.8 43.1 + - - +
162A PRO* 3.8 30.9 - - - +
164A ILE* 1.3 74.4 - - + +
166A GLN* 1.3 60.7 + - + +
167A LEU 3.2 8.5 + - - +
189A LYS* 3.9 7.6 + - - +
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Residues in contact with GLN 166 (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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82A LEU* 4.0 1.2 - - - +
139A LEU 3.0 26.7 + - - -
140A GLY* 3.4 5.2 - - - -
141A TYR 2.5 31.6 + - - +
142A GLU* 3.7 33.3 + - + +
145A ALA 4.0 14.6 - - - +
146A PRO* 3.0 8.1 - - - +
147A TYR* 2.8 38.6 + - + -
150A ILE* 4.2 3.8 - - + -
162A PRO* 3.1 22.1 + - - +
163A LEU* 3.7 5.6 - - - +
164A ILE 3.3 0.6 - - - -
165A ARG* 1.3 76.9 - - + +
167A LEU* 1.3 58.7 + - - +
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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