Contacts of the helix formed by residues 115 - 123 (chain F) in PDB entry 5ITZ
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 THR 115 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F HIS* 3.9 2.5 - - - -
106F VAL 4.8 2.7 - - - -
107F ASN* 3.9 17.0 - - + +
108F ALA 3.4 1.1 - - - -
109F VAL* 3.8 25.4 - - + -
113F GLY 3.9 3.4 + - - +
114F ASP* 1.3 74.9 - - - +
116F PRO* 1.3 74.4 - - - +
117F LEU* 3.8 10.8 + - - +
118F HIS* 3.0 31.3 + - - +
119F LEU* 3.2 12.8 + - - +
138F ASP* 4.7 10.2 + - + +
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Residues in contact with PRO 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F THR* 4.7 0.2 - - - +
84F LEU* 3.8 37.0 - - + +
85F HIS* 3.7 25.3 - - + +
88F ALA* 3.4 27.2 - - + +
105F ASP 4.5 3.6 - - - +
106F VAL 3.6 15.7 - - - +
108F ALA 3.2 15.5 - - - +
115F THR* 1.3 86.5 - - - +
117F LEU* 1.3 61.7 + - - +
119F LEU* 3.2 3.5 + - + +
120F ALA* 3.0 19.4 + - - +
132F LEU* 3.8 6.7 - - + -
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Residues in contact with LEU 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F VAL 5.1 1.9 + - - +
115F THR* 3.2 9.2 - - - +
116F PRO* 1.3 79.8 - - - +
118F HIS* 1.3 63.1 + - + +
120F ALA* 3.1 4.5 + - - +
121F ALA* 2.8 35.1 + - + +
129F VAL* 3.5 42.8 - - + +
132F LEU* 3.5 22.6 - - + +
133F LEU* 4.3 12.8 - - + -
137F ALA* 4.2 11.4 - - + -
138F ASP 3.9 20.9 - - - +
139F VAL* 5.0 13.2 - - + -
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Residues in contact with HIS 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B GLU* 4.1 10.2 + - - -
113F GLY 5.4 0.6 + - - -
114F ASP* 2.9 27.6 + - - +
115F THR* 3.0 25.3 + - - +
117F LEU* 1.3 84.8 - - + +
119F LEU* 1.3 57.3 + - - +
121F ALA* 3.3 8.4 + - + +
122F ILE* 2.9 60.6 + - + +
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Residues in contact with LEU 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397B ALA* 4.5 7.9 - - + -
401B ARG* 3.4 46.9 - - + +
85F HIS* 3.7 45.8 - - + +
88F ALA 4.3 2.2 - - - +
89F LEU* 3.9 28.7 - - + +
114F ASP* 3.8 13.0 - - + +
115F THR 3.2 10.4 + - - +
116F PRO* 3.2 5.6 + - + +
118F HIS* 1.3 73.0 - - - +
120F ALA* 1.3 65.9 + - - +
122F ILE* 3.4 6.8 + - + +
123F MET* 3.1 30.4 + - - +
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Residues in contact with ALA 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F ALA* 3.7 12.2 + - + +
116F PRO 3.0 14.4 + - - +
117F LEU 3.4 8.3 - - - +
119F LEU* 1.3 76.6 - - - +
121F ALA* 1.3 56.1 + - - +
123F MET 3.4 0.3 + - - -
124F GLY 3.0 7.8 + - - -
125F HIS* 2.8 32.8 + - + +
128F ILE* 3.7 29.6 - - + -
129F VAL* 3.7 15.3 - - + +
132F LEU* 4.4 2.5 - - + -
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Residues in contact with ALA 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F LEU* 2.8 26.1 + - + +
118F HIS* 3.7 13.2 - - + +
119F LEU 3.3 0.2 - - - -
120F ALA* 1.3 71.7 - - - +
122F ILE* 1.3 67.9 + - + +
124F GLY* 3.0 13.9 + - - -
126F LEU* 5.2 3.9 - - - +
129F VAL* 3.6 14.8 - - + +
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Residues in contact with ILE 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393B GLU* 3.7 49.6 - - + +
394B GLN* 3.1 38.5 + - + +
397B ALA* 3.9 18.4 - - + -
114F ASP* 5.0 2.7 - - - +
118F HIS* 2.9 56.9 + - + +
119F LEU* 3.8 11.7 - - + +
121F ALA* 1.3 76.7 - - + +
123F MET* 1.3 60.4 + - - +
124F GLY 3.4 0.3 + - - -
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Residues in contact with MET 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B PRO* 3.2 19.8 - - - +
179B ASP* 3.5 8.0 - - - +
181B VAL* 3.8 29.4 - - + +
184B PRO* 4.1 12.8 - - + -
394B GLN* 3.8 30.5 - - + +
397B ALA* 4.2 7.9 - - - -
398B MET* 3.5 27.8 - - + -
89F LEU* 3.5 22.7 - - + +
119F LEU 3.1 18.7 + - - +
122F ILE* 1.3 76.0 - - + +
124F GLY* 1.3 62.4 + - - +
125F HIS* 3.4 20.5 + - + +
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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