Contacts of the helix formed by residues 195 - 205 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A VAL* 5.9 4.0 - - - -
194A LEU* 1.3 79.9 + - - +
196A ILE* 1.3 58.9 + - - +
198A GLU* 2.8 7.4 + - - +
199A ASN* 2.8 43.7 + - - -
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Residues in contact with ILE 196 (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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108A ALA* 6.2 0.4 - - + -
110A VAL* 3.6 36.1 - - + +
113A VAL* 4.7 5.6 - - + -
127A LEU* 3.6 29.4 - - + -
129A VAL* 5.4 4.9 - - + -
172A ILE* 3.6 21.3 - - + -
184A LEU* 4.5 7.4 - - + -
186A TYR* 4.9 18.4 - - + -
195A GLY* 1.3 72.0 - - - +
197A PHE* 1.3 65.0 + - - +
198A GLU* 4.0 0.2 + - - -
199A ASN* 3.8 3.0 - - - +
200A LEU* 2.9 41.8 + - + +
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Residues in contact with PHE 197 (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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157A VAL* 3.8 35.9 - - + +
158A GLU* 4.3 0.4 - - - -
159A LYS* 3.6 57.0 - - + -
172A ILE* 3.7 18.8 - - + -
196A ILE* 1.3 78.9 - - - +
198A GLU* 1.3 84.4 + - + +
200A LEU* 4.1 3.5 - - - +
201A ASN* 3.1 45.9 + - + +
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Residues in contact with GLU 198 (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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159A LYS* 4.4 7.8 + - - -
194A LEU* 3.6 38.8 - - + +
195A GLY 2.8 28.9 + - - -
196A ILE 4.0 0.2 + - - -
197A PHE* 1.3 98.9 + - + +
199A ASN* 1.3 57.3 + - - +
201A ASN* 3.7 4.8 - - - +
202A LYS* 2.9 30.9 + - - +
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Residues in contact with ASN 199 (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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107A LYS 4.5 6.4 + - - +
108A ALA* 3.7 26.5 - - + +
129A VAL* 4.5 14.3 - - + +
194A LEU* 3.7 22.6 - - - +
195A GLY* 2.8 36.8 + - - +
196A ILE* 3.8 3.8 - - - +
198A GLU* 1.3 74.8 - - - +
200A LEU* 1.3 65.8 + - - +
202A LYS* 3.3 3.1 + - - +
203A HIS* 3.0 48.8 + - - +
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Residues in contact with LEU 200 (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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127A LEU* 5.3 1.6 - - + -
129A VAL* 4.4 17.5 - - + -
134A LEU* 3.6 31.0 - - + -
151A LEU* 4.2 15.3 - - + -
154A ILE* 4.5 4.5 - - + -
157A VAL* 4.4 19.7 - - + -
172A ILE* 4.5 3.4 - - + -
174A ILE* 3.8 26.5 - - + -
184A LEU* 4.5 6.5 - - + -
196A ILE* 2.9 39.2 + - + +
197A PHE 4.1 2.5 - - - +
199A ASN* 1.3 73.8 - - - +
201A ASN* 1.3 55.5 + - - +
203A HIS* 5.3 0.4 - - - -
204A ALA* 2.6 42.4 + - + +
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Residues in contact with ASN 201 (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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157A VAL* 4.2 18.9 + - - +
197A PHE* 3.1 39.1 + - + +
198A GLU* 3.7 6.3 - - - +
200A LEU* 1.3 79.3 - - - +
202A LYS* 1.3 62.7 + - - +
205A PHE* 3.3 47.2 + - - +
209A ASN* 3.8 9.3 + - - +
490A ASP* 4.8 9.9 + - - +
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Residues in contact with LYS 202 (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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194A LEU* 5.2 13.4 - - + +
198A GLU 2.9 22.2 + - - +
199A ASN* 3.3 5.1 + - - +
201A ASN* 1.3 75.0 - - - +
203A HIS* 1.3 84.2 + - + +
205A PHE 3.8 1.0 - - - -
206A PRO* 3.8 19.9 - - - +
209A ASN* 3.9 30.0 + - + +
211A GLN* 5.3 14.3 - - + +
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Residues in contact with HIS 203 (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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107A LYS* 3.5 54.8 - - + +
129A VAL* 4.7 3.1 - - + +
130A THR 4.1 3.8 - - - +
131A ASP* 4.4 15.2 - - + +
151A LEU* 3.6 28.6 - - + +
199A ASN* 3.0 37.4 + - - +
202A LYS* 1.3 101.3 - - + +
204A ALA* 1.3 64.5 + - - +
205A PHE 3.2 1.9 + - - -
206A PRO* 3.5 15.4 - - + +
211A GLN* 5.8 8.0 - - + +
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Residues in contact with ALA 204 (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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151A LEU* 3.9 26.7 - - + +
152A GLY* 5.3 1.7 - - - -
154A ILE* 4.0 33.1 - - + +
157A VAL* 5.1 0.2 - - + -
200A LEU 2.6 26.9 + - - +
203A HIS* 1.3 73.0 - - - +
205A PHE* 1.3 79.2 + - + +
206A PRO* 3.4 6.2 - - - +
488A GLY* 4.2 6.2 + - - -
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Residues in contact with PHE 205 (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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154A ILE* 3.4 26.5 - - + -
155A SER* 3.3 31.6 - - - -
156A ARG* 3.9 6.7 - - - -
157A VAL* 4.4 15.5 - - + -
177A LYS* 6.1 0.7 - - - -
201A ASN* 3.3 37.3 + - - +
202A LYS 3.8 0.9 - - - -
203A HIS 3.2 0.4 - - - -
204A ALA* 1.3 95.4 - - + +
206A PRO* 1.3 58.1 - - - +
208A SER* 2.9 12.2 + - - -
209A ASN* 2.9 23.5 + - - +
488A GLY* 3.2 10.8 - - - +
489A ASN 3.6 13.5 - - - -
490A ASP* 3.5 41.3 - - + +
497A ARG* 6.0 0.2 - - - -
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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