Contacts of the strand formed by residues 109 - 115 (chain C) in PDB entry 2I6A
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 109 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C ASN* 2.8 31.9 + - - +
82C LYS* 3.6 43.2 - - + +
84C ALA 3.0 13.4 + - - +
85C THR* 3.5 2.6 - - - -
86C PHE 3.2 19.5 + - - -
107C HIS 3.8 2.8 + - - -
108C VAL* 1.3 68.9 - - - +
110C ALA* 1.3 55.1 + - - +
111C HIS* 2.9 39.9 + - - -
158C LEU* 3.9 5.9 - - - +
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Residues in contact with ALA 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C PHE* 3.4 16.2 - - + +
103C ALA* 3.7 21.1 - - + -
108C VAL* 2.8 11.7 + - + +
109C ASP* 1.3 71.9 + - - +
111C HIS* 1.3 66.8 + - - +
112C TYR* 3.4 33.3 - - + +
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Residues in contact with HIS 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C THR* 4.3 0.2 - - + -
86C PHE 2.8 18.4 + - - +
87C PHE* 3.1 34.5 - + + +
88C GLY 3.4 1.2 + - - -
109C ASP* 2.9 46.2 + - - -
110C ALA* 1.3 74.5 + - - +
112C TYR* 1.3 61.9 + - - +
149C HIS* 3.8 4.9 + - - +
154C LYS* 6.1 1.6 - - + +
155C ASN* 4.1 16.4 + - - +
158C LEU* 3.0 36.3 - - + +
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Residues in contact with TYR 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PRO* 3.9 17.7 - - + -
67C GLN* 2.6 29.4 + - - -
86C PHE* 3.9 13.0 - + - -
88C GLY 3.1 23.1 - - - -
90C ILE* 3.6 29.2 - - + -
99C LEU* 3.7 9.3 + - + -
100C LYS* 3.7 34.1 - - + -
103C ALA* 3.3 15.9 - - - +
110C ALA* 3.4 26.9 - - + +
111C HIS* 1.3 77.7 - - - +
113C TYR* 1.3 61.2 + - - +
114C GLU* 3.8 10.4 + - + +
149C HIS* 3.8 10.1 + - - -
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Residues in contact with TYR 113 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A ASN* 3.8 30.2 + - + +
117A GLU* 4.7 7.1 + - - -
88C GLY 2.6 14.4 + - - +
89C CYS* 3.2 27.0 - - + -
90C ILE* 2.8 28.8 + - - +
112C TYR* 1.3 72.5 - - - +
114C GLU* 1.3 63.4 + - - +
115C GLN* 3.8 21.6 - - + +
143C CYS* 4.6 7.6 - - + -
144C TYR* 4.5 5.2 - + + -
145C LYS 6.0 0.7 - - - -
148C LYS* 3.2 65.1 + - + +
149C HIS* 3.9 22.9 - + + -
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Residues in contact with GLU 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ILE* 4.1 24.9 - - + +
116A ASN* 3.4 25.7 + - - +
90C ILE* 3.4 29.0 - - + +
91C GLY 4.3 6.1 - - - +
92C ILE* 3.9 26.6 - - + +
96C GLY 5.7 0.3 - - - -
100C LYS* 2.9 36.2 + - - +
112C TYR* 3.8 12.7 + - + +
113C TYR* 1.3 80.5 - - - +
115C GLN* 1.3 62.7 + - - +
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Residues in contact with GLN 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A GLU 6.0 0.2 - - - -
116A ASN* 5.5 0.7 - - - +
89C CYS* 3.8 16.8 - - - -
90C ILE 2.8 24.9 + - - +
91C GLY* 3.3 2.3 - - - -
92C ILE* 2.9 27.7 + - - +
113C TYR* 3.8 15.3 - - + +
114C GLU* 1.3 77.1 - - - +
116C ASN* 1.3 58.7 + - - +
117C GLU* 3.3 19.7 + - - +
118C GLN* 2.5 52.1 - - - +
140C ALA* 3.3 5.9 - - - +
143C CYS* 3.8 16.0 - - + -
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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