Contacts of the helix formed by residues 150 - 160 (chain K) in PDB entry 3EAB
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 150 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149K VAL* 1.3 76.5 - - - +
151K MET* 1.3 70.0 + - - +
152K LEU* 3.6 24.8 + - - +
153K LEU* 2.9 19.7 + - + +
154K GLN* 2.8 20.4 + - - +
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Residues in contact with MET 151 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149K VAL 3.1 6.0 + - - -
150K ASP* 1.3 75.0 + - - +
152K LEU* 1.3 73.2 + - + +
154K GLN* 3.0 10.2 - - - +
155K GLU* 3.0 53.3 + - - +
176K VAL* 3.8 26.2 - - + +
179K SER* 4.0 28.0 - - - +
180K VAL* 4.6 8.8 - - + +
183K ALA* 5.5 1.8 - - + -
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Residues in contact with LEU 152 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150K ASP* 3.3 13.5 + - - +
151K MET* 1.3 91.6 - - + +
153K LEU* 1.3 66.6 + - - +
155K GLU* 3.5 28.8 - - - +
156K MET* 3.4 18.9 + - - +
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Residues in contact with LEU 153 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149K VAL* 4.6 15.9 - - + -
150K ASP* 2.9 24.0 + - + +
152K LEU* 1.3 77.0 - - - +
154K GLN* 1.3 66.2 + - - +
156K MET* 2.9 23.8 + - + +
157K ALA* 3.0 15.1 + - + +
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Residues in contact with GLN 154 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E LYS* 5.4 4.8 - - - +
149K VAL* 4.4 22.8 - - + +
150K ASP 2.8 15.7 + - - +
151K MET* 3.0 18.2 - - - +
153K LEU* 1.3 71.8 - - - +
155K GLU* 1.3 54.9 + - - +
157K ALA* 3.4 10.1 + - - +
158K ASP* 2.9 65.2 + - - +
162K LEU 5.8 1.0 + - - -
180K VAL* 4.1 19.5 - - + -
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Residues in contact with GLU 155 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E PHE* 4.9 0.9 - - - -
151K MET* 3.0 40.9 + - - +
152K LEU* 3.5 20.4 - - - +
153K LEU 3.1 0.6 + - - -
154K GLN* 1.3 75.3 - - - +
156K MET* 1.3 57.9 + - - +
158K ASP* 3.2 1.4 + - - +
159K GLU* 2.8 32.6 + - - +
180K VAL* 4.1 16.2 - - + +
183K ALA* 3.8 24.8 - - - +
184K GLU* 3.4 26.2 - - + +
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Residues in contact with MET 156 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152K LEU 3.4 11.1 + - - +
153K LEU* 2.9 18.5 + - + +
155K GLU* 1.3 79.9 - - - +
157K ALA* 1.3 63.2 + - - +
159K GLU* 3.4 19.2 - - + +
160K ALA* 3.1 30.4 + - + +
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Residues in contact with ALA 157 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153K LEU* 3.0 12.2 + - + +
154K GLN* 3.6 16.4 - - - +
156K MET* 1.3 78.3 - - - +
158K ASP* 1.3 58.0 + - - +
160K ALA 3.4 0.9 + - - -
161K GLY 2.9 10.7 + - - -
162K LEU* 2.9 54.1 + - + +
163K ASP* 5.2 4.3 - - + -
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Residues in contact with ASP 158 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E LYS* 4.2 20.4 - - - -
124E PHE* 3.7 15.7 - - + -
125E GLU* 4.7 7.4 - - - +
128E SER* 5.2 0.7 + - - -
154K GLN* 2.9 43.7 + - - +
155K GLU 3.5 0.7 - - - +
157K ALA* 1.3 74.3 - - - +
159K GLU* 1.3 67.7 + - - +
161K GLY* 3.0 13.6 + - - -
162K LEU 5.0 3.0 - - - +
180K VAL* 3.9 4.2 - - - +
184K GLU* 2.6 39.6 - - - +
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Residues in contact with GLU 159 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E PHE* 3.7 18.1 - - + -
125E GLU* 5.4 1.2 - - - +
128E SER* 3.4 26.3 + - - -
129E ILE* 5.9 2.1 - - - +
132E ARG* 5.8 1.6 + - - -
155K GLU 2.8 20.9 + - - +
156K MET* 3.3 22.7 + - + +
158K ASP* 1.3 76.0 - - - +
160K ALA* 1.3 59.0 + - - +
161K GLY 3.4 1.7 + - - -
187K GLU* 3.8 15.8 - - + +
191K ARG* 3.1 30.8 + - - -
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Residues in contact with ALA 160 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E ARG* 5.8 5.8 - - - +
156K MET* 3.1 18.7 + - + +
157K ALA 3.5 0.2 - - - -
159K GLU* 1.3 80.2 - - + +
161K GLY* 1.3 69.7 + - - +
162K LEU* 3.6 21.2 - - + +
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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