Contacts of the helix formed by residues 137 - 148 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136B PRO* 1.3 77.1 - - - +
138B LEU* 1.3 64.2 + - - +
139B GLU* 3.6 15.7 + - - +
140B ASP* 3.5 26.9 + - - -
141B LEU* 3.1 25.0 + - - +
200B LYS* 5.6 3.4 - - - +
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Residues in contact with LEU 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 PRO 4.1 0.6 + - - -
137B SER* 1.3 71.4 - - - +
139B GLU* 1.3 62.6 + - + +
140B ASP 2.9 7.6 + - - -
141B LEU* 3.4 15.0 + - + +
142B LEU* 3.2 22.5 + - - +
207B ILE* 4.1 24.4 - - + +
208B VAL* 5.8 6.5 - - + -
211B THR* 3.8 32.2 - - + +
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Residues in contact with GLU 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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137B SER* 3.1 12.1 - - - +
138B LEU* 1.3 80.1 - - + +
140B ASP* 1.3 61.4 + - - +
142B LEU* 4.2 3.3 - - - +
143B PHE 4.0 0.7 + - - -
199B PHE* 3.4 26.5 - - - -
200B LYS* 2.6 48.5 + - + +
203B VAL* 4.0 6.0 - - + +
204B GLN* 3.5 19.8 - - - +
207B ILE* 3.6 36.8 - - + +
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Residues in contact with ASP 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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136B PRO* 5.0 7.1 - - - +
137B SER* 3.5 15.9 + - - +
138B LEU 3.1 0.2 - - - -
139B GLU* 1.3 80.5 - - + +
141B LEU* 1.3 68.4 + - - +
143B PHE* 3.3 24.1 - - + +
144B TYR* 3.0 31.0 + - - -
196B LYS* 3.0 50.5 - - + +
199B PHE* 5.0 0.4 - - + -
200B LYS* 5.2 7.1 - - + +
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Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PRO* 4.2 34.1 - - + +
137B SER 3.1 28.1 + - - +
138B LEU* 3.8 14.8 - - + +
140B ASP* 1.3 77.3 + - - +
142B LEU* 1.3 63.2 + - - +
143B PHE 3.1 0.7 + - - -
144B TYR* 3.2 16.3 + - + +
145B THR* 3.0 24.3 + - - -
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Residues in contact with LEU 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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138B LEU 3.2 13.9 + - - +
139B GLU 4.2 3.4 - - - +
141B LEU* 1.3 80.7 - - - +
143B PHE* 1.3 60.3 + - - +
145B THR* 3.1 24.9 - - + -
146B ILE* 3.2 27.1 + - + +
158B PHE* 5.6 0.2 - - + -
199B PHE* 4.1 18.4 - - + -
203B VAL* 4.8 1.6 - - + -
207B ILE* 3.6 25.8 - - + -
210B LEU* 4.2 24.9 - - + +
211B THR* 4.5 11.9 - - + +
214B PHE* 3.7 28.3 - - + -
215B ARG* 5.7 2.9 - - - -
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Residues in contact with PHE 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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139B GLU 4.0 0.8 + - - -
140B ASP* 3.3 30.6 - - + +
141B LEU 3.1 0.8 - - - -
142B LEU* 1.3 75.3 - - - +
144B TYR* 1.3 79.1 + + - +
146B ILE* 2.9 4.0 + - - +
147B ALA* 2.7 48.3 + - + +
150B GLN 5.2 1.1 - - - -
151B GLU* 3.2 32.5 - - - -
153B ILE* 3.3 31.2 - - + -
194B LEU 3.8 5.2 - - - -
195B ASP 3.8 15.9 - - - -
196B LYS* 4.0 24.2 - - + -
199B PHE* 3.7 26.9 - + + -
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Residues in contact with TYR 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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136B PRO* 5.8 6.5 - - + -
140B ASP* 3.0 28.5 + - - -
141B LEU* 3.2 16.4 + - + +
143B PHE* 1.3 95.1 - + - +
145B THR* 1.3 61.6 + - - +
147B ALA* 4.0 5.8 - - + -
148B GLU* 3.4 26.2 + - - +
150B GLN 6.1 0.7 - - - -
196B LYS* 2.4 36.1 + - + -
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Residues in contact with THR 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 LEU 3.0 14.7 + - - -
142B LEU* 3.1 22.9 - - + +
144B TYR* 1.3 78.0 - - - +
146B ILE* 1.3 65.8 + - + +
148B GLU* 4.2 5.2 + - - +
214B PHE* 4.9 5.4 - - + +
215B ARG* 3.2 42.9 + - - +
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Residues in contact with ILE 146 (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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142B LEU* 3.3 30.5 - - + +
143B PHE 2.9 3.7 + - - +
145B THR* 1.3 77.3 - - + +
147B ALA* 1.3 58.6 + - - +
148B GLU* 3.1 7.9 + - - +
153B ILE* 4.1 22.0 - - + -
157B LYS* 2.9 32.3 + - + +
158B PHE* 3.7 29.8 - - + -
161B ALA* 4.5 12.6 - - + -
199B PHE* 4.0 7.9 - - + -
214B PHE* 3.6 34.8 - - + -
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Residues in contact with ALA 147 (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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143B PHE* 2.7 45.0 + - + +
144B TYR* 3.4 6.9 + - + +
146B ILE* 1.3 72.4 - - - +
148B GLU* 1.3 70.1 + - - +
149B GLY 3.2 0.2 + - - -
150B GLN* 3.1 31.6 + - - +
152B LYS 5.9 0.6 - - - -
153B ILE* 3.8 22.9 - - + +
157B LYS* 4.0 4.0 + - - +
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Residues in contact with GLU 148 (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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144B TYR* 3.4 16.5 + - - +
145B THR 4.2 4.6 + - - +
146B ILE 3.1 5.0 - - - +
147B ALA* 1.3 79.3 - - - +
149B GLY* 1.3 61.8 + - - +
150B GLN* 3.3 16.1 + - - +
157B LYS* 2.7 28.6 + - - +
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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