Contacts of the helix formed by residues 113 - 127 (chain F) in PDB entry 1I43
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 ASN 113 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F VAL* 2.9 26.7 + - - +
84F THR 4.6 6.7 + - - -
87F TYR* 3.2 10.8 + - - -
106F PHE* 3.8 11.2 - - - -
109F GLY* 5.2 1.1 - - - +
112F GLY* 1.3 75.5 - - - +
114F PRO* 1.3 69.9 - - - +
115F THR* 2.6 44.8 + - - +
116F THR* 2.9 33.2 + - - +
117F VAL* 3.0 16.6 + - - +
295F LEU 5.7 1.1 - - - +
297F PRO* 3.0 17.8 - - + +
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Residues in contact with PRO 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E THR* 5.5 2.9 - - + -
75E ASP* 5.8 1.8 - - - +
70F ARG 5.0 2.8 - - - +
72F ILE* 4.2 26.5 - - + +
82F VAL* 3.3 37.7 - - + -
87F TYR* 3.3 20.6 - - + +
106F PHE* 3.5 18.8 - - + -
113F ASN* 1.3 86.9 - - - +
115F THR* 1.3 56.0 + - - +
117F VAL* 2.9 27.2 - - + +
118F VAL* 3.6 11.3 - - - +
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Residues in contact with THR 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F ILE* 6.1 0.2 - - - -
79F THR* 4.0 15.9 - - - +
80F PRO 3.3 20.7 + - - -
81F VAL* 4.0 4.7 - - - -
82F VAL* 3.3 15.9 - - + +
113F ASN* 2.6 29.2 + - - +
114F PRO* 1.3 75.5 - - - +
116F THR* 1.3 60.7 + - - +
118F VAL* 4.1 2.5 - - - +
119F LEU 4.4 0.2 + - - -
297F PRO* 3.3 41.1 + - + -
300F ALA* 3.8 6.0 - - - +
301F TYR* 4.5 8.1 + - - +
304F ILE* 3.5 22.3 - - - +
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Residues in contact with THR 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F GLY* 5.6 2.2 - - - -
113F ASN* 2.9 31.1 + - - +
115F THR* 1.3 78.1 - - - +
117F VAL* 1.3 68.5 + - + +
118F VAL 3.1 1.8 - - - -
119F LEU* 3.1 16.1 + - - +
120F GLU* 3.2 25.3 + - + +
134F LEU* 4.7 14.4 - - + +
295F LEU* 4.1 22.5 + - + +
297F PRO* 4.5 2.8 - - - +
300F ALA* 3.9 16.6 - - - +
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Residues in contact with VAL 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F ARG 5.0 8.7 - - - +
106F PHE* 3.9 25.4 - - + -
112F GLY* 5.8 0.9 - - - -
113F ASN 3.0 15.2 + - - +
114F PRO* 2.9 27.1 - - + +
116F THR* 1.3 76.7 - - + +
118F VAL* 1.3 65.6 + - + +
120F GLU* 2.8 32.5 + - + +
121F GLU* 2.8 26.0 + - + +
285F ARG* 6.0 0.9 - - - +
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Residues in contact with VAL 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F GLY* 3.4 23.0 - - - +
66F GLU* 3.7 11.0 - - + +
70F ARG* 3.7 30.3 - - + +
72F ILE* 5.7 0.7 - - + -
79F THR* 3.6 26.5 - - + +
114F PRO 3.6 15.3 - - - +
115F THR 4.1 1.3 - - - +
116F THR 3.1 0.2 - - - -
117F VAL* 1.3 80.2 - - + +
119F LEU* 1.3 57.0 + - - +
121F GLU* 3.4 5.5 + - - +
122F LYS* 2.9 30.2 + - - +
304F ILE* 3.7 20.0 - - + -
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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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115F THR 4.8 0.4 - - - +
116F THR* 3.1 10.8 + - - +
118F VAL* 1.3 80.0 - - - +
120F GLU* 1.3 64.2 + - - +
122F LYS* 4.0 7.0 - - + -
123F ILE* 3.0 28.8 + - + +
134F LEU* 3.4 34.3 - - + -
300F ALA* 3.8 14.8 - - + +
303F ILE* 3.4 45.5 - - + -
304F ILE* 3.8 25.7 - - + +
307F MET* 3.7 19.7 - - - -
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Residues in contact with GLU 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F THR* 3.2 19.4 + - - +
117F VAL* 2.8 26.6 + - + +
119F LEU* 1.3 78.9 - - - +
121F GLU* 1.3 58.5 + - + +
124F SER* 2.9 32.5 + - - -
132F THR* 2.9 33.9 - - - +
133F LEU* 3.8 1.6 - - - +
134F LEU* 3.6 35.1 + - + +
285F ARG* 3.1 30.0 + - - -
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Residues in contact with GLU 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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50F TYR* 5.8 2.1 - - - -
64F ALA* 4.8 0.8 - - - +
65F GLY* 4.3 19.4 + - - +
117F VAL* 2.8 24.7 + - + +
118F VAL* 4.0 5.0 - - - +
120F GLU* 1.3 75.5 - - + +
122F LYS* 1.3 60.0 + - - +
124F SER* 3.4 8.7 - - - -
125F ALA* 3.0 29.6 + - - +
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Residues in contact with LYS 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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60F VAL 4.4 1.1 - - - +
61F ALA* 3.2 18.2 + - - +
62F ILE 2.9 19.2 + - - -
64F ALA* 2.9 41.1 + - + +
66F GLU* 2.8 29.4 + - - -
118F VAL* 2.9 20.5 + - - +
119F LEU* 3.6 12.1 - - + +
121F GLU* 1.3 78.1 - - - +
123F ILE* 1.3 62.4 + - - +
125F ALA* 3.2 12.6 + - - +
126F LEU* 3.3 14.4 + - - +
304F ILE* 4.1 12.9 + - + +
307F MET* 4.0 26.7 - - + -
308F LYS* 3.1 14.5 - - - +
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Residues in contact with ILE 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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119F LEU* 3.0 40.3 + - + +
120F GLU 4.1 1.8 - - - +
122F LYS* 1.3 76.5 - - - +
124F SER* 1.3 66.6 + - - +
125F ALA 3.2 0.2 + - - -
126F LEU* 3.2 7.6 + - + +
127F GLU* 3.0 29.7 + - + +
132F THR* 3.5 19.7 - - + +
134F LEU* 4.3 6.7 - - + -
242F PRO* 6.1 2.7 - - + -
257F HIS* 6.1 1.6 - - + -
259F ALA* 5.9 0.4 - - + -
263F LEU* 4.1 17.0 - - + -
273F CYS* 3.5 27.8 - - - -
275F SER* 3.6 13.0 - - - +
303F ILE* 5.2 1.1 - - + -
307F MET* 3.9 20.2 - - + -
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Residues in contact with SER 124 (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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120F GLU 2.9 17.8 + - - -
121F GLU* 3.4 11.1 - - - -
123F ILE* 1.3 78.2 - - - +
125F ALA* 1.3 57.0 + - - +
128F GLY* 3.0 4.2 + - - -
129F ALA* 2.7 46.0 + - - +
130F GLU 5.1 1.1 - - - -
131F SER* 3.2 8.5 - - - -
132F THR* 2.9 36.6 + - - -
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Residues in contact with ALA 125 (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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50F TYR* 4.4 18.4 - - + +
60F VAL* 3.7 20.5 - - + +
64F ALA* 3.7 9.4 - - + -
121F GLU 3.0 12.2 + - - +
122F LYS 3.4 10.3 - - - +
123F ILE 3.1 0.2 - - - -
124F SER* 1.3 74.9 - - - +
126F LEU* 1.3 65.4 + - - +
128F GLY* 3.0 14.1 + - - -
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Residues in contact with LEU 126 (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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57F ASP* 3.6 43.2 - - + +
60F VAL* 3.9 15.3 - - + -
61F ALA* 4.0 9.6 - - + +
122F LYS 3.3 7.5 + - - +
123F ILE* 3.2 8.0 + - + +
125F ALA* 1.3 80.0 - - - +
127F GLU* 1.3 62.4 + - - +
128F GLY* 3.3 1.0 + - - -
242F PRO* 4.2 21.3 - - + -
243F LEU* 4.2 7.0 - - + -
246F LYS* 2.9 28.5 + - - +
307F MET* 3.6 29.8 - - + -
310F LEU* 4.0 19.5 - - + -
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Residues in contact with GLU 127 (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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123F ILE* 3.0 21.1 + - + +
126F LEU* 1.3 73.6 - - - +
128F GLY* 1.3 64.6 + - - +
129F ALA* 3.2 9.8 + - + +
242F PRO* 3.5 24.1 - - + +
245F GLN 4.3 8.1 - - - +
246F LYS* 4.5 16.4 - - - +
247F ALA 4.7 2.1 + - - -
248F LEU* 3.6 29.2 + - + +
249F ALA 5.5 0.2 + - - -
255F VAL* 3.3 20.1 - - - +
257F HIS* 2.5 36.4 + - - -
275F SER* 4.1 13.9 - - - +
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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