Contacts of the helix formed by residues 109 - 116 (chain H) in PDB entry 6V96
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 109 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67H GLN* 5.9 2.5 - - - -
107H TYR* 3.1 9.0 + - - +
108H GLU* 1.3 78.9 - - - +
110H THR* 1.3 59.6 + - - -
112H ASP* 3.1 2.9 + - - +
113H ALA* 2.8 28.0 + - - +
230H SER 4.5 1.3 - - - -
231H ARG 3.1 17.5 - - - -
232H ASP* 4.8 3.8 - - - -
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Residues in contact with THR 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H LEU* 3.7 33.4 - - + +
109H GLY* 1.3 70.5 - - - -
111H ALA* 1.3 63.3 + - - +
113H ALA* 3.5 18.1 + - - +
114H VAL* 3.6 4.5 + - - +
231H ARG 3.1 1.6 + - - -
232H ASP* 3.0 17.7 + - - +
233H PHE* 2.9 44.9 + - - +
234H GLY 4.7 0.2 + - - -
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Residues in contact with ALA 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110H THR* 1.3 80.2 + - - +
112H ASP* 1.3 57.8 + - - +
114H VAL* 3.1 4.2 + - - -
115H TYR* 2.9 25.3 + - - +
220H LEU* 3.6 12.3 - - + +
223H ASP* 3.7 16.6 - - - +
231H ARG* 3.0 20.5 + - - +
232H ASP 3.9 2.2 - - - +
233H PHE* 3.6 10.5 - - - -
237H ILE* 3.7 28.3 - - + -
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Residues in contact with ASP 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H THR* 6.0 1.6 - - - +
106H TRP 4.6 1.9 - - - +
107H TYR* 3.7 7.4 - - - -
108H GLU* 2.9 31.0 + - + +
109H GLY 3.1 13.6 + - - +
111H ALA* 1.3 78.4 - - - +
113H ALA* 1.3 57.8 + - - +
115H TYR* 3.7 1.9 - - - -
116H GLN* 2.9 63.7 + - - +
231H ARG* 2.8 46.8 + - + +
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Residues in contact with ALA 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H TYR* 2.8 19.0 + - - -
18H LEU* 4.2 7.6 - - + -
65H ALA* 3.9 15.8 - - + +
67H GLN* 6.1 0.2 - - - +
107H TYR* 3.7 32.1 - - + -
109H GLY 2.8 12.9 + - - +
110H THR* 3.6 12.8 - - - +
111H ALA 3.2 0.6 - - - -
112H ASP* 1.3 77.5 - - - +
114H VAL* 1.3 56.5 + - - +
117H ASN* 2.8 16.1 + - - -
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Residues in contact with VAL 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H TYR* 3.6 32.5 - - + -
18H LEU* 4.2 4.3 - - + -
110H THR 3.8 3.1 - - - +
111H ALA 3.1 6.1 + - - +
113H ALA* 1.3 75.8 - - - +
115H TYR* 1.3 67.3 + - - +
117H ASN* 2.9 15.4 + - - +
118H ILE* 3.4 9.0 + - - +
121H ILE* 3.7 23.3 - - + -
131H ILE* 4.3 12.3 - - + -
216H LEU* 4.7 2.0 - - + -
217H MET* 4.6 3.4 - - + -
220H LEU* 3.6 21.1 - - + -
233H PHE* 3.6 27.4 - - + -
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Residues in contact with TYR 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111H ALA 2.9 17.3 + - - +
112H ASP* 3.0 7.5 + - - +
114H VAL* 1.3 77.6 - - - +
116H GLN* 1.3 93.0 + - - +
117H ASN 3.0 1.6 + - - -
118H ILE* 3.2 44.3 + - + +
220H LEU* 3.8 25.4 - - + +
221H ARG* 4.0 19.2 + - + +
224H ALA* 3.4 25.2 - - + +
231H ARG* 3.6 15.9 - - - +
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Residues in contact with GLN 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H ARG* 3.7 11.1 + - - -
101H VAL* 3.7 27.5 - - + +
102H SER* 3.7 20.3 + - - -
104H THR* 5.6 6.4 - - + +
106H TRP 6.1 0.2 - - - +
107H TYR* 3.9 22.7 - - + -
112H ASP* 2.9 47.7 + - - +
115H TYR* 1.3 98.4 - - - +
117H ASN* 1.3 59.2 + - - +
118H ILE 3.5 0.2 - - - -
119H ASP* 3.8 5.0 + - - +
231H ARG* 4.8 1.0 - - - +
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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