Contacts of the helix formed by residues 196 - 203 (chain B) in PDB entry 5I7L
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 GLY 196 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194B GLY 3.2 4.2 + - - -
195B LEU* 1.3 80.9 - - - +
197B PRO* 1.3 78.3 - - - +
198B LEU 3.2 3.1 - - - -
199B PRO* 3.1 11.2 - - - +
200B ILE* 3.2 23.8 - - - +
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Residues in contact with PRO 197 (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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196B GLY* 1.3 83.6 - - - +
198B LEU* 1.3 63.4 + - + +
200B ILE* 3.9 6.2 - - + -
201B GLN* 2.8 42.5 + - + +
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Residues in contact with LEU 198 (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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98A VAL* 5.1 7.2 - - + +
99A ILE* 3.3 38.9 - - + +
100A PRO 4.9 5.8 - - - +
196B GLY 3.2 0.2 - - - -
197B PRO* 1.3 82.1 - - + +
199B PRO* 1.4 75.4 - - + +
201B GLN* 3.2 5.4 + - + +
202B GLY 2.8 21.3 + - - -
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Residues in contact with PRO 199 (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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99A ILE* 3.5 30.2 - - + -
150B LEU* 3.6 23.3 - - + +
151B LEU* 3.9 10.8 - - + +
195B LEU* 3.5 31.6 - - + -
196B GLY* 3.1 19.1 - - - +
198B LEU* 1.4 93.8 - - + +
200B ILE* 1.3 61.6 + - + +
203B LEU* 2.9 29.4 + - + +
204B LEU 3.3 3.3 + - - -
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Residues in contact with ILE 200 (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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151B LEU* 4.2 15.5 - - + -
191B LEU* 3.8 34.5 - - + -
193B ASP 5.5 0.2 - - - -
194B GLY* 4.7 16.2 - - - +
196B GLY* 3.2 24.2 - - - +
197B PRO* 3.9 5.6 - - + +
198B LEU 3.1 0.8 - - - -
199B PRO* 1.3 80.0 - - + +
201B GLN* 1.3 76.6 + - - +
202B GLY 3.4 0.2 + - - -
204B LEU* 3.4 23.7 + - + +
205B ASP* 4.9 4.0 + - - +
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Residues in contact with GLN 201 (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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197B PRO* 2.8 32.8 + - + +
198B LEU* 4.1 6.1 - - + +
200B ILE* 1.3 86.9 - - + +
202B GLY* 1.3 58.4 + - - +
205B ASP* 4.8 8.9 - - - +
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Residues in contact with GLY 202 (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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95A VAL* 3.9 21.0 - - - +
98A VAL* 6.0 1.6 - - - -
99A ILE* 4.2 9.8 - - - +
198B LEU 2.8 13.5 + - - -
201B GLN* 1.3 80.5 - - - +
203B LEU* 1.3 60.3 + - - +
205B ASP* 6.5 0.2 - - - -
206B SER* 4.0 9.5 + - - -
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Residues in contact with LEU 203 (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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93A GLY 5.6 3.4 - - - +
94A LYS* 6.4 0.2 - - - -
95A VAL* 4.7 7.2 - - + +
96A THR* 4.2 26.7 - - - +
99A ILE* 4.3 17.0 - - + -
106B ILE* 5.9 6.1 - - + -
141B VAL* 5.4 4.0 - - + -
150B LEU* 4.1 28.0 - - + -
151B LEU* 4.2 18.4 - - + -
199B PRO* 2.9 14.3 + - + +
201B GLN 3.8 0.6 - - - -
202B GLY* 1.3 81.4 - - - +
204B LEU* 1.3 57.5 + - - +
205B ASP* 3.4 2.4 - - - +
206B SER* 3.0 14.8 + - - -
207B LEU* 2.8 45.7 + - + +
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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