Contacts of the helix formed by residues 106 - 115 (chain B) in PDB entry 6P59
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 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A PHE 4.2 0.2 - - - +
18A PHE* 3.5 21.2 - - + -
19A ARG* 3.0 49.0 + - + +
104A ASN* 2.6 34.7 + - - -
12B TRP* 4.3 1.8 - - + -
105B ILE* 1.3 75.9 - - - +
107B PRO* 1.3 75.9 - - + +
108B ILE 3.2 1.6 + - - -
109B VAL* 3.0 34.5 + - - +
110B ALA* 3.1 10.0 + - - +
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Residues in contact with PRO 107 (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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19A ARG* 5.7 1.8 - - + -
12B TRP* 3.5 21.8 - - + +
90B LEU* 3.6 16.4 - - + -
106B ASP* 1.3 89.1 - - + +
108B ILE* 1.3 60.6 + - + +
110B ALA* 3.0 1.9 + - - +
111B ASP* 2.9 32.9 + - - +
212B LEU* 3.5 23.3 - - + +
213B ALA* 3.7 12.1 + - + +
216B CYS* 3.6 32.1 - - + -
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Residues in contact with ILE 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ARG* 3.5 33.9 - - - +
106B ASP* 3.2 1.6 + - - -
107B PRO* 1.3 79.2 - - + +
109B VAL* 1.3 61.6 + - - +
111B ASP* 4.3 5.1 - - - +
112B SER* 3.4 15.1 + - - -
143B ARG 5.2 1.4 - - - +
146B ARG* 3.3 52.9 - - + +
147B ASP* 3.4 13.5 + - - +
213B ALA* 4.3 17.9 - - + -
89E GLU* 5.6 9.6 - - + +
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Residues in contact with VAL 109 (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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19A ARG* 4.7 0.4 - - - +
104A ASN* 3.9 8.5 - - - +
143A PHE* 4.6 2.5 - - + -
147A ARG* 3.2 48.2 - - - +
105B ILE* 4.1 15.9 - - + -
106B ASP* 3.0 33.6 + - - +
108B ILE* 1.3 76.1 - - - +
110B ALA* 1.3 60.8 + - - +
112B SER* 3.2 3.3 + - - -
113B LEU* 2.8 48.1 + - + +
147B ASP* 3.6 10.3 - - - +
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Residues in contact with ALA 110 (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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68B ILE* 4.0 7.9 - - + -
90B LEU* 3.9 11.2 - - + -
105B ILE* 3.7 26.9 - - + -
106B ASP 3.1 5.1 + - - +
107B PRO 3.0 7.0 + - - +
109B VAL* 1.3 77.2 - - - +
111B ASP* 1.3 57.5 + - - +
113B LEU* 3.3 1.8 + - - +
114B ILE* 2.9 36.6 + - - +
212B LEU* 3.5 27.1 - - + -
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Residues in contact with ASP 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PRO 2.9 12.8 + - - +
108B ILE* 4.3 4.5 - - - +
110B ALA* 1.3 76.0 - - - +
112B SER* 1.3 57.6 + - - +
114B ILE* 3.1 9.3 + - - +
115B HIS* 2.9 31.2 + - - +
141B PHE* 3.8 17.2 - - + -
143B ARG* 3.8 19.3 - - - +
144B GLY* 4.1 2.7 - - - -
210B PRO 4.4 1.6 - - - +
211B SER* 2.7 29.4 + - - -
212B LEU* 3.0 26.0 + - - +
213B ALA* 2.9 22.0 + - - +
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Residues in contact with SER 112 (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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147A ARG* 4.9 4.9 + - - +
108B ILE 3.4 5.8 + - - -
109B VAL 3.2 3.9 + - - -
111B ASP* 1.3 80.4 - - - +
113B LEU* 1.3 63.2 + - - +
115B HIS 3.7 0.3 + - - -
116B LYS* 2.9 42.5 + - - +
143B ARG 4.8 0.2 + - - -
144B GLY* 3.1 25.4 + - - -
146B ARG 5.1 0.2 + - - -
147B ASP* 3.4 36.7 + - - +
148B GLN* 4.7 5.0 + - - +
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Residues in contact with LEU 113 (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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143A PHE* 4.0 17.7 - - + +
146A ALA* 3.6 33.2 - - + +
147A ARG* 3.8 18.6 - - + +
149A ARG* 6.0 0.2 - - - +
62B LEU* 4.1 24.0 - - + +
68B ILE* 4.2 11.4 - - + -
92B TYR* 4.0 27.8 - - + -
105B ILE* 4.6 2.5 - - + -
109B VAL* 2.8 30.8 + - + +
110B ALA 3.8 3.8 - - - +
112B SER* 1.3 78.0 - - - +
114B ILE* 1.3 62.7 + - - +
116B LYS* 3.2 21.8 + - + +
117B ILE* 4.2 1.0 + - - +
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Residues in contact with ILE 114 (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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40B TRP* 4.0 17.9 - - + -
60B ILE* 3.5 35.4 - - + -
62B LEU* 4.3 7.4 - - + -
68B ILE* 4.1 14.1 - - + -
110B ALA 2.9 22.4 + - - +
111B ASP* 3.6 10.1 - - - +
113B LEU* 1.3 76.4 - - - +
115B HIS* 1.3 56.8 + - - +
116B LYS 3.1 0.2 - - - -
117B ILE* 3.0 6.8 + - - +
118B TYR* 2.9 47.0 + - + -
119B PHE* 4.3 12.8 - - + -
141B PHE* 5.4 3.1 - - + -
210B PRO 5.9 2.0 - - - +
212B LEU* 4.1 20.2 - - + -
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Residues in contact with HIS 115 (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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151A ARG* 2.6 43.4 + - + +
111B ASP 2.9 16.1 + - - +
112B SER 4.1 3.8 - - - +
113B LEU 3.3 0.4 - - - -
114B ILE* 1.3 74.1 - - - +
116B LYS* 1.3 59.8 + - - +
117B ILE 3.1 0.4 - - - -
118B TYR 4.1 2.0 - - - +
119B PHE* 3.2 33.3 + - - +
120B PRO 3.5 11.2 - - - -
121B CYS* 3.3 5.5 - - + +
141B PHE* 3.7 33.7 - + + -
144B GLY* 3.8 9.4 - - - -
145B HIS* 3.0 21.5 + + - -
301B ZN 2.0 37.0 - - - -
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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