Contacts of the helix formed by residues 155 - 164 (chain D) 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 VAL 155 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154D PRO* 1.3 71.4 - - - +
156D HIS* 1.3 62.8 + - - +
158D PHE* 3.1 4.8 + - + +
159D ILE* 3.0 39.3 + - + +
181D LEU* 4.8 10.5 - - + -
185D LEU* 3.7 41.7 - - + -
192D VAL* 3.2 25.5 + - + +
194D LEU* 3.6 35.7 - - + -
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Residues in contact with HIS 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D PRO* 3.3 30.1 - - + +
155D VAL* 1.3 83.0 - - + +
157D LYS* 1.3 62.6 + - + +
159D ILE* 4.0 6.2 - - - +
160D THR* 3.0 35.8 + - - +
192D VAL* 5.6 7.2 - - + -
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Residues in contact with LYS 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D ILE* 3.9 22.2 - - + +
147D ALA 4.0 4.1 + - - +
148D GLU* 3.0 35.5 + - - +
150D GLN* 5.9 0.2 - - - +
153D ILE* 3.7 11.0 - - + -
154D PRO* 3.3 36.1 + - + +
155D VAL 3.2 0.8 - - - -
156D HIS* 1.3 85.1 - - + +
158D PHE* 1.3 64.2 + - - +
160D THR* 4.2 3.6 - - - -
161D ALA* 3.2 23.7 + - + +
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Residues in contact with PHE 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D LEU* 5.6 0.4 - - + -
146D ILE* 3.9 21.3 - - + -
153D ILE* 4.2 10.1 - - + -
154D PRO 3.2 10.9 + - - +
155D VAL* 3.1 10.4 + - - +
157D LYS* 1.3 77.0 - - - +
159D ILE* 1.3 81.0 + - + +
161D ALA* 3.4 5.9 + - - +
162D LEU* 3.0 39.5 + - + +
177D CYS* 4.7 2.0 - - - -
178D MET* 4.5 2.7 - - + -
181D LEU* 3.8 27.1 - - + -
194D LEU* 4.7 7.9 - - + -
199D PHE* 3.5 32.3 - + - -
203D VAL* 3.9 19.5 - - + -
210D LEU* 4.5 10.5 - - + -
214D PHE* 4.3 12.4 - + - -
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Residues in contact with ILE 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D VAL* 3.0 25.4 + - + +
156D HIS* 4.3 5.4 - - - +
158D PHE* 1.3 84.3 - - + +
160D THR* 1.3 67.6 + - - +
162D LEU* 2.9 9.6 + - + +
163D LYS* 2.9 50.6 + - + +
169D THR* 5.0 8.5 - - - +
178D MET* 4.3 14.1 - - + -
181D LEU* 3.5 30.5 - - + -
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Residues in contact with THR 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D HIS* 3.0 24.5 + - - +
157D LYS* 4.2 4.7 - - - +
159D ILE* 1.3 77.7 - - - +
161D ALA* 1.3 63.1 + - - +
163D LYS* 3.5 9.7 + - - +
164D SER* 3.2 22.7 + - - -
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Residues in contact with ALA 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D ILE* 4.3 11.7 - - + -
157D LYS* 3.2 18.6 + - + +
158D PHE 3.6 5.2 - - - +
159D ILE 3.2 0.4 - - - -
160D THR* 1.3 79.3 - - - +
162D LEU* 1.3 59.3 + - - +
164D SER* 2.7 24.8 + - - -
165D THR* 3.6 10.2 - - - +
214D PHE* 3.6 21.5 - - + -
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Residues in contact with LEU 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D PHE* 3.0 25.2 + - + +
159D ILE* 2.9 13.8 + - + +
161D ALA* 1.3 74.9 - - - +
163D LYS* 1.3 67.7 + - + +
165D THR* 2.9 28.4 + - - +
166D GLY 3.9 0.5 + - - -
167D LEU* 3.9 25.8 - - + +
169D THR* 5.5 6.5 - - - +
174D LEU* 3.8 13.0 - - + -
178D MET* 3.7 30.7 - - + -
210D LEU* 3.6 26.0 - - + -
213D ALA* 4.9 1.6 - - + -
214D PHE* 3.9 15.9 - - + -
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Residues in contact with LYS 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D ILE* 2.9 40.6 + - + +
160D THR* 3.7 8.5 - - - +
162D LEU* 1.3 76.0 - - + +
164D SER* 1.3 53.3 + - - +
166D GLY* 2.7 29.6 + - - -
167D LEU 3.7 13.6 - - - +
169D THR* 4.8 22.5 - - - +
224D MET* 3.7 7.5 - - - +
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Residues in contact with SER 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D THR* 3.2 11.6 + - - -
161D ALA* 2.7 24.8 + - - -
162D LEU 3.2 0.2 - - - -
163D LYS* 1.3 77.2 - - - +
165D THR* 1.3 62.2 + - - +
166D GLY 3.0 1.5 + - - -
223D PHE* 4.4 1.9 + - - +
224D MET* 3.3 47.1 + - - +
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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