Contacts of the helix formed by residues 195 - 205 (chain B) in PDB entry 5C16
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 195 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194B LEU* 1.3 84.6 - - - +
196B ILE* 1.3 63.4 + - - -
197B PHE 3.3 2.7 - - - -
198B GLU* 3.1 13.6 + - - -
199B ASN* 2.6 33.6 + - - -
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Residues in contact with ILE 196 (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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108B ALA* 6.5 0.4 - - - -
110B VAL* 4.0 24.7 - - + -
113B VAL* 3.6 30.5 - - + -
127B LEU* 3.7 24.2 - - + -
129B VAL* 5.4 2.9 - - + -
172B ILE* 4.2 11.4 - - + -
184B LEU* 4.9 6.3 - - + -
185B ALA 6.4 0.2 - - - -
186B TYR* 5.9 9.9 - - + -
194B LEU* 4.3 1.8 - - + +
195B GLY* 1.3 71.4 - - - -
197B PHE* 1.3 62.7 + - - +
199B ASN* 3.3 4.8 + - - +
200B LEU* 3.1 45.5 + - + +
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Residues in contact with PHE 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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157B VAL* 3.4 42.7 - - + +
158B GLU* 5.1 0.2 - - - -
159B LYS* 3.5 50.9 - - + -
172B ILE* 3.7 19.0 - - + +
195B GLY 3.3 0.8 - - - -
196B ILE* 1.3 80.4 - - - +
198B GLU* 1.3 82.1 + - + +
200B LEU* 4.1 2.8 - - - +
201B ASN* 3.3 38.0 + - - +
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Residues in contact with GLU 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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159B LYS* 4.3 9.0 + - - -
194B LEU 3.1 13.2 - - - +
195B GLY* 3.1 27.9 - - - -
196B ILE 3.3 0.4 - - - -
197B PHE* 1.3 99.0 + - + +
199B ASN* 1.3 60.6 + - - +
201B ASN* 3.6 4.5 + - - +
202B LYS* 2.8 32.9 + - + +
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Residues in contact with ASN 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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107B LYS 4.3 7.8 - - - +
108B ALA* 4.2 11.2 - - + +
129B VAL* 4.2 17.3 - - + +
194B LEU* 3.5 33.7 + - - +
195B GLY 2.6 26.4 + - - +
196B ILE* 3.3 3.8 + - - +
198B GLU* 1.3 77.1 - - - +
200B LEU* 1.3 65.5 + - - +
202B LYS* 4.3 5.2 - - - +
203B HIS* 3.0 50.7 + - - +
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Residues in contact with LEU 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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127B LEU* 5.4 0.2 - - + -
129B VAL* 3.8 12.1 - - + -
134B LEU* 3.4 39.5 - - + -
151B LEU* 4.3 7.4 - - + -
154B ILE* 4.9 4.0 - - + -
157B VAL* 4.3 15.3 - - + -
172B ILE* 4.4 12.8 - - + -
174B ILE* 3.9 29.4 - - + -
184B LEU* 4.8 2.2 - - + -
196B ILE* 3.1 36.2 + - + +
197B PHE 4.1 2.9 - - - +
199B ASN* 1.3 75.1 - - - +
201B ASN* 1.3 55.6 + - - +
203B HIS* 5.3 0.2 - - - -
204B ALA* 2.6 41.3 + - - +
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Residues in contact with ASN 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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157B VAL* 4.5 13.0 + - + +
197B PHE* 3.3 37.2 + - + +
198B GLU* 3.6 6.1 - - - +
200B LEU* 1.3 78.1 - - - +
202B LYS* 1.3 64.1 + - - +
205B PHE* 3.1 52.3 + - - +
209B ASN* 3.8 11.8 + - - +
490B ASP* 4.8 7.6 - - - +
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Residues in contact with LYS 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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198B GLU* 2.8 23.0 + - + +
199B ASN* 3.9 8.5 - - - +
201B ASN* 1.3 75.3 + - - +
203B HIS* 1.3 85.0 + - + +
205B PHE 3.8 14.7 - - - +
206B PRO* 3.8 7.3 - - - +
209B ASN* 3.9 29.7 + - + +
211B GLN* 5.6 12.3 - - + +
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Residues in contact with HIS 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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107B LYS* 3.5 50.5 + - + +
129B VAL* 4.6 1.8 - - + +
130B THR 4.0 4.3 - - - +
131B ASP* 4.3 18.5 - - + +
151B LEU* 3.5 28.2 - - + +
199B ASN* 3.0 39.9 + - - +
202B LYS* 1.3 100.7 - - + +
204B ALA* 1.3 65.4 + - - +
205B PHE 3.2 1.3 - - - -
206B PRO* 3.5 16.7 - - - +
211B GLN* 6.0 6.7 - - + +
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Residues in contact with ALA 204 (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* 3.8 32.3 - - + +
152B GLY* 4.9 3.8 - - - -
154B ILE* 4.0 25.4 - - + +
157B VAL* 5.4 0.2 - - + -
200B LEU 2.6 25.2 + - - +
203B HIS* 1.3 73.0 - - - +
205B PHE* 1.3 79.1 + - + +
206B PRO* 3.3 8.0 - - - +
488B GLY* 3.7 8.0 + - - -
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Residues in contact with PHE 205 (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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154B ILE* 3.6 22.9 - - + -
155B SER* 3.4 32.5 - - - -
156B ARG* 3.9 10.1 - - - -
157B VAL* 4.7 6.3 - - + -
201B ASN* 3.1 44.0 + - - +
202B LYS 3.8 4.0 - - - -
204B ALA* 1.3 97.1 - - + +
206B PRO* 1.3 62.8 - - - +
208B SER* 3.1 6.4 + - - -
209B ASN* 2.8 23.3 + - - +
488B GLY 3.2 12.1 - - - +
489B ASN 3.5 25.1 - - - -
490B ASP* 3.7 28.3 - - + +
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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