Contacts of the helix formed by residues 113 - 127 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82G VAL* 3.0 25.5 + - - +
84G THR 4.5 6.7 + - - -
87G TYR* 3.2 10.3 + - - -
106G PHE* 3.6 10.7 - - - -
109G GLY* 5.2 2.6 - - - +
112G GLY* 1.3 75.9 + - - +
114G PRO* 1.3 77.9 - - - +
115G THR* 2.7 43.0 + - - +
116G THR* 3.0 27.4 + - - +
117G VAL* 3.1 16.4 + - - +
295G LEU 5.8 1.1 - - - +
297G PRO* 3.0 17.5 - - + +
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Residues in contact with PRO 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G ARG 5.0 2.6 - - - +
71G GLY 6.2 0.2 - - - -
72G ILE* 4.3 27.5 - - + +
82G VAL* 3.4 35.2 - - + -
87G TYR* 3.4 17.5 - - + +
106G PHE* 3.4 21.1 - - + -
113G ASN* 1.3 90.6 - - - +
115G THR* 1.3 56.4 + - - +
116G THR 3.1 0.2 - - - -
117G VAL* 3.0 23.8 - - + +
118G VAL* 3.5 12.3 - - - +
74H THR* 5.4 3.6 - - + -
75H ASP* 5.8 2.2 - - - +
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Residues in contact with THR 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G THR* 4.1 15.8 - - - +
80G PRO 3.4 21.7 + - - -
81G VAL* 4.2 4.0 - - - -
82G VAL 3.4 15.3 - - - +
113G ASN* 2.7 31.3 + - - +
114G PRO* 1.3 73.2 - - - +
116G THR* 1.3 59.1 + - - +
118G VAL* 4.2 1.9 - - - +
297G PRO* 3.3 40.8 + - + -
300G ALA* 3.8 5.1 - - - +
301G TYR* 4.5 8.5 + - - +
304G ILE* 3.5 21.7 - - - +
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Residues in contact with THR 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112G GLY* 5.9 2.0 - - - -
113G ASN* 3.0 28.3 + - - +
115G THR* 1.3 78.9 - - - +
117G VAL* 1.3 66.6 + - + +
118G VAL 3.1 1.8 - - - -
119G LEU* 3.1 8.0 + - + +
120G GLU* 3.1 31.6 + - - +
134G LEU* 4.6 12.1 - - + +
295G LEU* 4.2 29.5 + - + +
297G PRO* 4.4 3.1 - - - +
300G ALA* 3.7 17.0 - - - +
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Residues in contact with VAL 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G ARG 4.9 8.7 - - - +
106G PHE* 3.8 25.8 - - + -
112G GLY* 5.9 0.7 - - - -
113G ASN 3.1 16.4 + - - +
114G PRO* 3.0 25.8 - - + +
116G THR* 1.3 75.9 - - + +
118G VAL* 1.3 54.9 + - + +
120G GLU* 2.7 25.2 + - + +
121G GLU* 2.6 48.8 + - + +
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Residues in contact with VAL 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G GLY* 3.4 21.1 - - - +
66G GLU* 3.7 12.1 - - + +
70G ARG* 3.7 29.8 - - + +
72G ILE* 5.7 0.9 - - + -
79G THR* 3.6 24.9 - - + +
114G PRO 3.5 16.4 - - - +
115G THR 4.2 2.5 - - - +
116G THR 3.1 0.2 - - - -
117G VAL* 1.3 81.0 - - + +
119G LEU* 1.3 53.1 + - - +
121G GLU* 3.3 7.4 + - - +
122G LYS* 2.8 37.2 + - - +
304G ILE* 3.8 19.3 - - + -
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Residues in contact with LEU 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115G THR 4.8 0.9 - - - +
116G THR* 3.1 11.4 + - - +
118G VAL* 1.3 77.2 - - - +
120G GLU* 1.3 60.8 + - - +
122G LYS* 3.9 6.7 - - + -
123G ILE* 3.0 34.6 + - + +
134G LEU* 3.5 35.2 - - + -
295G LEU* 4.6 0.2 - - + -
300G ALA* 3.8 17.5 - - + +
303G ILE* 3.5 42.6 - - + -
304G ILE* 3.8 25.3 - - + +
307G MET* 3.7 20.0 - - - -
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Residues in contact with GLU 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G THR* 3.1 19.1 + - - +
117G VAL* 2.7 31.4 + - + +
119G LEU* 1.3 78.0 - - - +
121G GLU* 1.3 56.8 + - + +
124G SER* 3.0 32.2 + - - -
132G THR* 3.1 35.2 - - - +
133G LEU* 4.3 1.0 - - - +
134G LEU* 3.6 36.7 + - + +
285G ARG* 3.0 29.1 + - - -
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Residues in contact with GLU 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G TYR* 5.1 8.2 - - + -
64G ALA* 4.7 0.7 - - - +
65G GLY* 4.2 21.6 + - - +
69G GLY 5.4 2.3 - - - +
117G VAL* 2.6 31.9 + - + +
118G VAL* 3.8 5.4 - - - +
120G GLU* 1.3 73.2 - - + +
122G LYS* 1.3 64.1 + - - +
124G SER* 3.6 8.9 - - - -
125G ALA* 3.1 23.4 + - - +
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Residues in contact with LYS 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G VAL 4.5 1.1 - - - +
61G ALA* 3.0 21.9 + - - +
62G ILE 2.8 20.0 + - - -
64G ALA* 3.0 36.9 + - + +
66G GLU* 2.7 31.2 + - - -
118G VAL* 2.8 20.0 + - - +
119G LEU* 3.6 11.9 - - + +
120G GLU 3.3 0.2 - - - -
121G GLU* 1.3 77.9 - - - +
123G ILE* 1.3 59.3 + - - +
125G ALA* 3.5 5.4 + - - +
126G LEU* 3.4 21.8 + - - +
304G ILE* 4.2 14.3 + - + +
307G MET* 4.0 24.9 - - + -
308G LYS* 3.1 11.3 - - - +
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Residues in contact with ILE 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119G LEU* 3.0 39.9 + - + +
120G GLU 4.1 1.8 - - - +
122G LYS* 1.3 73.5 - - - +
124G SER* 1.3 65.6 + - - +
125G ALA 3.1 0.7 - - - -
126G LEU* 3.4 6.6 + - + +
127G GLU* 3.1 29.9 + - + +
132G THR* 3.7 14.8 - - + +
134G LEU* 4.4 6.7 - - + -
242G PRO* 5.9 3.6 - - + -
257G HIS* 6.1 1.6 - - + -
259G ALA* 5.8 0.4 - - + -
263G LEU* 4.1 17.7 - - + -
273G CYS* 3.3 32.5 - - - -
275G SER* 3.7 12.6 - - - +
303G ILE* 5.2 1.8 - - + -
307G MET* 3.9 20.6 - - + -
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Residues in contact with SER 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120G GLU 3.0 16.4 + - - -
121G GLU* 3.6 10.9 - - - -
123G ILE* 1.3 78.2 - - - +
125G ALA* 1.3 55.2 + - - +
127G GLU 3.7 0.2 + - - -
128G GLY* 2.9 5.5 + - - -
129G ALA* 2.7 45.2 + - - +
130G GLU 5.2 0.7 - - - -
131G SER* 3.1 10.0 - - - -
132G THR* 3.0 37.0 + - - -
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Residues in contact with ALA 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G TYR* 4.6 17.5 - - + +
60G VAL* 3.7 20.4 - - + +
64G ALA* 3.7 9.4 - - + -
121G GLU 3.1 12.6 + - - +
122G LYS 3.6 9.6 - - - +
123G ILE 3.1 0.2 - - - -
124G SER* 1.3 74.5 - - - +
126G LEU* 1.3 62.3 + - - +
128G GLY* 2.8 19.9 + - - -
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Residues in contact with LEU 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G ASP* 3.8 31.9 - - + +
60G VAL* 3.8 13.7 - - + -
61G ALA* 4.0 8.3 - - + +
122G LYS 3.4 9.7 + - - +
123G ILE* 3.4 8.7 + - - +
125G ALA* 1.3 79.4 - - - +
127G GLU* 1.3 60.7 + - - +
128G GLY 3.4 0.2 + - - -
242G PRO* 4.2 20.4 - - + -
243G LEU* 4.1 17.7 - - + -
246G LYS* 2.8 30.0 + - - +
263G LEU* 5.2 0.2 - - + -
307G MET* 3.5 31.0 - - + -
310G LEU* 3.9 20.0 - - + -
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Residues in contact with GLU 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G ILE* 3.1 20.8 + - + +
124G SER 4.3 2.0 - - - +
126G LEU* 1.3 75.7 - - - +
128G GLY* 1.3 63.1 + - - +
129G ALA 3.3 3.5 + - - +
242G PRO* 3.2 27.5 - - + +
245G GLN 4.4 6.6 - - - +
246G LYS* 4.5 19.0 - - - +
247G ALA 4.6 2.1 + - - -
248G LEU* 3.8 24.0 + - + +
249G ALA* 5.4 0.5 + - - +
255G VAL* 3.8 18.8 - - - +
257G HIS* 2.5 35.4 + - + -
275G SER* 4.1 22.9 - - - +
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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
------------------------------------------------------------
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