Contacts of the helix formed by residues 136 - 145 (chain B) in PDB entry 3U44
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 136 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131B LYS* 5.3 3.4 - - - +
134B CYS 4.1 0.8 - - - -
135B LEU* 1.3 73.0 - - - +
137B PRO* 1.3 83.3 - - + +
138B GLU* 3.7 29.3 - - + +
139B ASP* 2.6 30.4 + - - +
140B ILE* 3.0 16.1 + - - +
169B TYR* 3.5 3.6 - - - -
173B GLU* 5.7 5.1 - - - +
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Residues in contact with PRO 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LYS* 4.3 3.4 - - - +
136B GLU* 1.3 95.7 - - + +
138B GLU* 1.3 53.7 + - + +
140B ILE* 3.0 3.7 + - + +
141B ARG* 2.8 37.3 + - - +
166B SER* 3.9 2.7 + - - +
169B TYR* 3.3 43.9 - - + +
170B GLN* 3.7 42.6 - - + +
173B GLU* 4.3 15.3 - - + -
174B LYS* 5.2 2.2 - - - +
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Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B GLU* 3.2 27.4 - - - +
137B PRO* 1.3 80.4 - - + +
139B ASP* 1.3 57.8 + - - +
141B ARG* 3.2 11.0 - - - +
142B ARG* 2.8 37.4 + - + +
170B GLN* 4.7 13.2 + - - +
174B LYS* 6.0 1.6 - - - +
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Residues in contact with ASP 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B CYS 4.4 3.1 - - - +
135B LEU* 3.6 18.9 - - + -
136B GLU* 2.6 43.6 + - - +
138B GLU* 1.3 77.7 - - - +
140B ILE* 1.3 63.3 + - - +
142B ARG* 2.7 54.3 + - - +
143B MET* 3.0 18.0 + - - +
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Residues in contact with ILE 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B PHE* 3.4 38.4 - - + -
135B LEU* 3.6 33.2 - - + +
136B GLU 3.0 15.1 + - - +
137B PRO 3.5 7.2 - - - +
139B ASP* 1.3 74.2 - - + +
141B ARG* 1.3 56.6 + - - +
143B MET* 3.3 12.4 + - - +
144B ALA* 2.8 27.9 + - - +
162B LEU* 3.2 35.5 - - + +
165B LEU 4.8 0.2 - - - -
166B SER* 3.4 17.5 - - - +
169B TYR* 3.8 10.3 - - + -
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Residues in contact with ARG 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B PRO 2.8 11.7 + - - +
138B GLU* 3.2 13.7 - - - +
140B ILE* 1.3 73.5 - - - +
142B ARG* 1.3 64.3 + - + +
144B ALA* 3.2 17.0 + - - +
145B GLU* 3.4 33.1 + - - +
163B HIS* 3.0 45.9 + - - +
166B SER* 2.8 24.8 + - - +
167B ILE* 3.7 23.4 - - - +
170B GLN* 3.8 20.2 + - - +
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Residues in contact with ARG 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B LEU* 4.7 7.9 - - - +
138B GLU* 2.8 26.2 + - + +
139B ASP* 2.7 51.8 + - - +
141B ARG* 1.3 77.6 - - + +
143B MET* 1.3 72.5 + - - +
145B GLU* 3.3 11.9 + - - +
146B SER* 3.5 10.4 + - - -
637B VAL* 6.3 1.2 - - - +
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Residues in contact with MET 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B PHE* 5.9 3.8 - - + -
135B LEU* 4.8 13.0 - - + -
139B ASP 3.0 17.4 + - - +
140B ILE* 3.8 22.0 - - - +
142B ARG* 1.3 85.2 - - + +
144B ALA* 1.3 58.7 + - - +
146B SER* 2.8 31.5 + - - -
147B GLY* 3.5 4.9 + - - -
158B LEU* 5.7 1.2 - - - +
159B SER* 5.0 0.7 - - - -
162B LEU* 4.0 18.4 - - + +
631B TRP* 6.1 0.7 - - - -
632B LEU* 4.0 24.9 - - + -
635B ILE* 6.3 1.8 - - + -
637B VAL* 3.6 43.5 - - + -
639B LEU* 5.7 1.6 - - + -
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Residues in contact with ALA 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B ILE 2.8 18.0 + - - +
141B ARG* 3.2 13.4 + - - +
143B MET* 1.3 76.9 - - - +
145B GLU* 1.3 62.1 + - + +
148B THR* 2.9 15.8 + - - -
159B SER* 3.0 25.1 - - - +
162B LEU* 3.8 11.0 - - + +
163B HIS* 3.7 34.8 - - + +
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Residues in contact with GLU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B ARG* 3.4 28.7 + - - +
142B ARG* 3.3 9.1 + - - +
143B MET 3.0 0.4 - - - -
144B ALA* 1.3 81.8 - - + +
146B SER* 1.3 62.1 + - - +
147B GLY 3.4 0.9 - - - -
148B THR* 3.5 29.2 + - + +
163B HIS* 5.9 3.3 - - + -
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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