Contacts of the helix formed by residues 137 - 148 (chain A) in PDB entry 5I94
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 SER 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A PRO* 1.3 76.6 - - - +
138A LEU* 1.3 55.0 + - - +
139A GLU* 2.7 29.3 + - - +
140A ASP* 2.7 37.8 + - - +
141A LEU* 3.0 17.7 + - - +
200A LYS* 4.5 7.4 + - - +
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Residues in contact with LEU 138 (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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137A SER* 1.3 71.8 - - - +
139A GLU* 1.3 62.3 - - + +
141A LEU* 4.0 10.8 - - + +
142A LEU* 3.5 20.1 + - - +
207A ILE* 3.7 32.4 - - + +
208A VAL* 5.2 9.4 - - + -
211A THR* 3.9 12.9 + - + +
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Residues in contact with GLU 139 (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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137A SER* 2.7 21.0 + - - +
138A LEU* 1.3 80.9 - - + +
140A ASP* 1.3 63.7 + - - +
141A LEU 3.1 0.9 - - - -
142A LEU* 3.2 4.2 + - - +
143A PHE 3.1 14.9 + - - -
199A PHE* 3.4 15.1 - - - -
200A LYS* 3.1 43.6 + - + +
203A VAL* 4.6 3.4 - - + -
204A GLN* 3.3 32.9 + - - +
207A ILE* 3.7 28.5 - - + +
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Residues in contact with ASP 140 (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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136A PRO* 4.7 8.8 - - - +
137A SER* 2.7 39.7 + - - +
139A GLU* 1.3 74.4 - - - +
141A LEU* 1.3 63.0 + - - +
143A PHE* 2.9 28.6 + - - +
144A TYR* 3.2 23.3 + - - +
196A LYS* 3.0 52.4 + - + +
199A PHE* 5.2 0.2 - - - -
200A LYS* 5.1 3.1 - - + +
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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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136A PRO* 3.7 31.6 - - + -
137A SER* 3.0 26.9 + - - +
138A LEU* 4.0 11.2 - - + +
140A ASP* 1.3 86.0 + - - +
142A LEU* 1.3 61.4 + - - +
143A PHE 3.3 0.2 + - - -
144A TYR* 3.4 25.5 + - + +
145A THR* 3.5 12.9 + - - -
215A ARG* 5.1 6.0 + - - +
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Residues in contact with LEU 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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138A LEU 3.5 11.1 + - - +
139A GLU 3.2 8.6 + - - +
141A LEU* 1.3 77.0 - - - +
143A PHE* 1.3 65.2 + - - +
145A THR* 3.3 20.6 + - + +
146A ILE* 3.4 18.2 + - + +
158A PHE* 5.8 0.2 - - + -
199A PHE* 3.9 19.7 - - + -
203A VAL* 5.0 1.3 - - + -
207A ILE* 3.6 23.8 - - + -
210A LEU* 4.0 26.0 - - + +
211A THR* 4.3 10.1 - - + +
214A PHE* 3.7 36.1 - - + -
215A ARG* 5.7 5.8 - - - +
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Residues in contact with PHE 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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139A GLU 3.1 4.4 + - - -
140A ASP* 2.9 19.8 + - - +
142A LEU* 1.3 79.0 - - - +
144A TYR* 1.3 81.9 + + - +
147A ALA* 3.0 34.0 + - + +
150A GLN 5.7 1.1 - - - -
151A GLU 3.9 21.8 - - - -
153A ILE* 3.3 39.7 - - + +
194A LEU 3.6 14.6 - - - -
195A ASP 3.8 5.8 - - - -
196A LYS* 3.7 32.3 - - + -
199A PHE* 3.6 36.1 - + + -
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Residues in contact with TYR 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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136A PRO* 6.2 1.8 - - + -
140A ASP* 3.2 26.8 + - + -
141A LEU* 3.4 20.8 + - + +
142A LEU 3.3 0.2 - - - -
143A PHE* 1.3 98.7 - + - +
145A THR* 1.3 64.9 + - - +
147A ALA* 3.3 14.5 + - + +
148A GLU* 3.3 12.3 + - - -
149A GLY 5.1 0.3 + - - -
196A LYS* 4.3 20.6 - - + +
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Residues in contact with THR 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 LEU 3.5 11.9 + - - -
142A LEU* 3.3 22.5 + - + -
143A PHE 3.3 0.4 - - - -
144A TYR* 1.3 80.1 - - - +
146A ILE* 1.3 62.0 + - + +
148A GLU* 3.7 15.2 - - - +
214A PHE* 5.3 11.9 - - + +
215A ARG* 3.6 39.0 + - - +
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Residues in contact with ILE 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 LEU* 3.4 21.6 + - + +
144A TYR 3.4 0.2 - - - -
145A THR* 1.3 76.3 - - + +
147A ALA* 1.3 66.4 + - - +
148A GLU* 3.6 4.7 - - - +
153A ILE* 3.6 27.4 - - + +
157A LYS* 3.2 35.7 - - + +
158A PHE* 3.8 20.6 - - + -
161A ALA* 4.6 11.2 - - + -
199A PHE* 3.6 35.4 - - + -
214A PHE* 4.2 20.4 - - + -
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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 PHE* 3.0 29.3 + - + +
144A TYR* 3.3 15.4 + - + +
146A ILE* 1.3 80.9 - - - +
148A GLU* 1.3 67.6 + - - +
149A GLY 3.8 2.5 - - - +
150A GLN* 3.5 34.3 - - - +
153A ILE* 3.5 17.5 - - + +
157A LYS* 4.0 8.0 + - - -
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Residues in contact with GLU 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 TYR 3.3 8.8 + - - -
145A THR 3.7 17.0 - - - +
146A ILE* 3.9 3.1 - - - +
147A ALA* 1.3 78.6 - - - +
149A GLY* 1.3 56.2 + - - +
150A GLN* 3.0 15.4 + - - +
157A LYS* 2.9 31.9 + - - +
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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