Contacts of the strand formed by residues 112 - 118 (chain H) in PDB entry 2B8K
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 ILE 112 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104H PHE* 5.2 8.1 - - + -
105H GLU 3.7 8.1 - - - +
106H GLU* 4.1 22.9 - - + +
110H ASP 4.1 1.4 + - - -
111H LEU* 1.3 77.8 - - - +
113H ALA* 1.3 67.8 + - - +
114H VAL* 4.6 10.8 - - + -
126H GLU* 5.0 0.9 - - - -
127H GLY 3.5 15.2 + - - +
128H ASN* 4.6 13.1 + - - +
130H ARG* 3.2 25.0 + - - +
131H ASN* 4.8 14.8 - - - +
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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
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104H PHE* 3.8 0.3 - - - -
105H GLU* 3.0 36.8 + - + +
107H VAL* 3.8 16.7 - - + +
111H LEU 4.2 0.6 + - - -
112H ILE* 1.3 74.2 - - - +
114H VAL* 1.3 66.3 + - - +
115H TYR* 5.0 2.0 - - + -
124H ARG* 4.5 10.1 - - + +
125H LEU 2.7 22.7 - - - +
126H GLU* 3.5 19.3 - - + +
130H ARG* 4.7 0.2 - - - +
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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
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103H LYS 3.5 6.7 - - - +
104H PHE* 3.3 45.5 - - + -
112H ILE* 4.6 8.5 - - + +
113H ALA* 1.3 79.6 - - - +
115H TYR* 1.3 64.1 + - - +
116H TYR* 3.9 25.7 - - + -
123H MET* 4.0 0.5 - - - +
124H ARG* 3.7 1.0 - - - -
125H LEU* 3.1 38.8 + - + +
130H ARG* 5.3 3.5 - - - +
134H ASN* 4.3 21.1 - - + +
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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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596A THR 4.5 5.5 + - - -
597A LEU* 3.5 28.7 - - + +
598A LEU* 3.9 27.1 - - + -
101H ALA* 3.3 18.4 - - - +
102H TYR* 3.4 27.6 + + + -
103H LYS* 3.1 27.0 + - + +
105H GLU* 2.8 45.9 + - + -
113H ALA* 4.8 3.4 - - + -
114H VAL* 1.3 76.0 - - - +
116H TYR* 1.3 71.5 + - - +
123H MET 3.1 12.3 - - - +
124H ARG* 3.5 28.7 + - + -
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Residues in contact with TYR 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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59H ILE* 4.6 16.3 - - + +
100H THR* 3.4 14.4 - - - -
101H ALA* 3.5 24.2 - - + +
102H TYR* 3.2 12.8 + - - -
104H PHE* 5.9 0.8 - + - -
114H VAL* 3.9 26.2 - - + -
115H TYR* 1.3 91.9 - - - +
117H SER* 1.3 56.4 + - - +
118H PHE* 3.8 24.2 - + + -
121H LEU 4.3 0.7 - - - -
122H LEU* 3.1 5.2 - - - -
123H MET* 2.7 62.4 + - + -
125H LEU* 6.2 0.7 - - + -
134H ASN* 3.3 20.4 + - - -
135H LEU 5.4 2.9 + - - -
137H GLN 5.1 1.6 + - - -
139H ASN 5.0 0.3 + - - -
140H ALA* 3.2 35.6 - - + +
142H LEU* 6.2 1.1 - - + -
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Residues in contact with SER 117 (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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613A ILE* 3.0 27.2 + - - -
99H GLY* 3.1 0.9 - - - -
100H THR* 2.6 41.7 + - - -
102H TYR* 3.5 17.9 - - - -
116H TYR* 1.3 77.4 - - - +
118H PHE* 1.3 62.4 + - - +
119H GLY* 3.5 4.7 + - - -
120H GLY 3.5 13.3 + - - -
121H LEU 3.3 6.7 + - - -
122H LEU* 3.6 11.4 - - - +
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Residues in contact with PHE 118 (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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540A PHE* 6.1 0.3 - - - -
564A ALA* 3.6 19.3 - - + +
40H LEU* 4.2 13.5 - - + -
97H MET* 3.7 33.4 - - + -
98H TYR* 3.0 19.5 - - - +
99H GLY* 2.7 39.0 - - - -
116H TYR* 3.8 36.6 - + + -
117H SER* 1.3 70.7 + - - +
119H GLY* 1.3 68.5 + - - +
120H GLY 3.2 1.3 + - - -
121H LEU* 3.0 35.5 + - + +
123H MET* 4.2 3.4 - - + -
140H ALA 3.8 15.3 - - - -
142H LEU* 4.1 22.4 - - + -
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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