Contacts of the helix formed by residues 5 - 17 (chain 6) in PDB entry 6CP3
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 ASP 5 (chain 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46 GLN* 1.3 69.4 + - - +
66 LEU* 1.3 61.0 + - - +
86 LEU* 3.6 26.5 - - + +
96 ARG* 2.9 46.4 + - + +
188Z LYS* 4.8 1.1 + - - -
191Z GLU* 4.7 9.7 - - - +
195Z GLN* 2.8 39.2 + - + +
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Residues in contact with LEU 6 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46 GLN* 3.4 25.7 - - + +
56 ASP* 1.3 76.5 - - - +
76 TYR* 1.3 64.4 + - - +
106 GLU* 3.0 63.6 + - - +
178Y LEU 4.0 0.7 - - - +
179Y SER 3.8 21.3 - - - +
180Y ILE* 5.0 2.0 - - - -
183Y LYS* 3.3 31.4 - - + +
188Z LYS* 4.2 8.8 + - - +
192Z LYS* 3.7 34.5 - - + -
195Z GLN* 4.5 8.7 - - + +
196Z GLN* 3.8 9.6 - - - +
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Residues in contact with TYR 7 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46 GLN* 3.0 20.9 + - + +
66 LEU* 1.3 81.9 - - + +
86 LEU* 1.3 79.2 + - + +
106 GLU* 3.4 9.7 + - - +
116 LEU* 2.9 57.9 + - + +
12B SER* 3.9 6.6 + - - -
15B GLU* 3.5 35.7 - - + -
16B GLU* 3.3 29.8 + - + +
19B LYS* 3.5 34.3 - - + -
183Y LYS* 5.2 3.6 - - - +
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Residues in contact with LEU 8 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46 GLN 2.7 41.2 + - - +
56 ASP* 3.6 23.3 - - - +
66 LEU 3.2 0.2 - - - -
76 TYR* 1.3 94.0 - - + +
96 ARG* 1.3 75.8 + - - +
116 LEU* 3.3 3.2 + - - +
126 LYS* 2.8 37.1 + - + +
19B LYS* 5.9 0.4 - - - -
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Residues in contact with ARG 9 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56 ASP* 2.9 38.7 + - + +
86 LEU* 1.3 89.6 + - - +
106 GLU* 1.3 61.9 + - - +
126 LYS* 3.6 30.7 - - - +
136 ASP* 3.0 33.6 + - - +
183Z GLU* 4.0 2.2 - - - -
188Z LYS* 3.4 29.6 - - + +
191Z GLU* 5.7 4.0 - - - +
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Residues in contact with GLU 10 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66 LEU* 3.0 55.0 + - - +
76 TYR* 3.4 8.5 - - - +
96 ARG* 1.3 76.9 - - - +
116 LEU* 1.3 55.3 + - + +
136 ASP* 3.5 1.9 + - - +
146 THR* 2.3 38.5 + - - +
15B GLU* 5.5 0.2 - - - +
180Y ILE* 6.1 0.7 - - - -
183Y LYS* 4.3 3.5 + - - +
184Y ILE* 5.5 4.7 - - - +
187Y LEU* 3.9 35.7 - - + +
179Z ARG* 5.5 0.3 - - - +
183Z GLU* 3.7 18.7 - - + +
188Z LYS* 4.0 12.5 + - - +
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Residues in contact with LEU 11 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76 TYR* 2.9 55.5 + - + +
86 LEU* 4.0 3.6 - - - +
106 GLU* 1.3 76.8 - - + +
126 LYS* 1.3 62.8 + - + +
146 THR* 3.5 20.2 - - + +
156 LYS* 2.8 32.8 + - + +
8B THR 5.4 1.1 - - - +
12B SER* 3.7 23.3 - - - -
15B GLU* 3.9 19.3 - - + -
187Y LEU* 4.6 9.2 - - + -
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Residues in contact with LYS 12 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86 LEU* 2.8 23.4 + - + +
96 ARG* 3.6 31.0 - - - +
106 GLU 3.3 0.2 - - - -
116 LEU* 1.3 76.8 - - + +
136 ASP* 1.3 63.1 + - - +
156 LYS* 3.4 12.3 + - + +
166 LEU* 2.9 44.3 + - + +
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Residues in contact with ASP 13 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96 ARG* 3.0 21.1 + - - +
106 GLU 4.0 1.1 - - - +
126 LYS* 1.3 77.4 - - - +
146 THR* 1.3 57.5 + - - +
166 LEU* 4.5 5.5 - - - +
176 ALA* 3.0 39.7 + - + +
179Z ARG* 3.9 12.0 - - + +
182Z SER* 5.8 8.3 - - - -
183Z GLU* 2.9 27.1 - - - +
186Z ASN* 5.5 1.7 - - - +
188Z LYS* 5.0 1.4 + - - +
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Residues in contact with THR 14 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106 GLU* 2.3 29.6 + - - +
116 LEU* 3.5 24.9 - - + +
136 ASP* 1.3 78.1 - - - +
156 LYS* 1.3 60.3 + - - +
186 PRO* 3.2 6.9 - - - +
8B THR* 5.6 11.0 - - + -
187Y LEU* 5.2 6.0 - - + +
176Z VAL* 5.8 4.3 - - + -
179Z ARG* 2.8 41.0 + - - +
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Residues in contact with LYS 15 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116 LEU* 2.8 19.2 + - + +
126 LYS* 3.9 15.5 - - + +
146 THR* 1.3 80.2 - - - +
166 LEU* 1.3 57.7 + - + +
186 PRO* 3.8 2.1 - - - +
196 SER* 2.3 37.8 + - - +
226 GLN* 5.9 1.0 + - - -
5B ALA* 5.2 13.3 - - + +
8B THR* 6.1 0.4 - - - +
9B GLU* 5.6 6.5 + - - +
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Residues in contact with LEU 16 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126 LYS* 2.9 29.3 + - + +
136 ASP* 4.7 4.7 - - - +
156 LYS* 1.3 79.6 - - + +
176 ALA* 1.3 62.8 + - - +
196 SER* 3.0 30.0 + - - +
206 THR* 4.0 5.7 + - - +
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Residues in contact with ALA 17 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136 ASP* 3.0 24.4 + - + +
166 LEU* 1.3 78.6 - - - +
186 PRO* 1.3 64.2 - - + +
206 THR* 4.1 13.7 - - - +
216 LEU* 4.2 4.9 - - - +
306 PRO* 6.1 1.0 - - - +
175Z SER* 5.4 0.4 - - - +
179Z ARG* 3.7 16.8 - - + -
182Z SER* 5.9 2.5 - - - +
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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