Contacts of the helix formed by residues 112 - 133 (chain G) in PDB entry 2A27
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 SER 112 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111G LEU* 1.3 77.4 - - - +
113G GLU* 1.3 60.2 + - - +
114G GLU* 3.3 8.9 + - - +
115G GLU* 3.3 35.6 + - - +
116G ALA* 3.1 25.6 + - - +
287G ARG* 3.6 25.0 + - - +
289G SER 3.5 8.1 - - - -
290G VAL* 4.2 4.3 - - - +
291G VAL* 4.3 3.1 - - - -
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Residues in contact with GLU 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112G SER* 1.3 70.8 - - - +
114G GLU* 1.3 59.3 + - - +
116G ALA* 3.7 6.9 - - - +
117G THR* 2.9 33.8 + - - +
211G LEU* 4.1 19.2 - - + +
243G GLN 4.0 1.0 - - - +
244G THR* 3.4 17.8 + - - +
245G SER* 2.5 45.8 + - - -
248G ALA* 3.9 8.5 - - - -
274G TRP* 3.1 13.4 + - + +
286G ARG* 3.3 20.8 + - + +
289G SER* 2.9 28.2 + - - +
290G VAL 4.4 7.3 - - - +
291G VAL 4.6 0.2 - - - +
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Residues in contact with GLU 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112G SER* 3.3 8.7 - - - +
113G GLU* 1.3 76.9 - - - +
115G GLU* 1.3 64.7 + - + +
117G THR* 2.8 19.7 + - - -
118G SER* 3.3 11.8 + - - -
283G ALA* 3.9 8.1 - - - +
286G ARG* 3.2 36.9 + - - +
287G ARG* 3.0 51.1 + - + +
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Residues in contact with GLU 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108G LYS* 4.5 10.6 + - - +
109G GLU* 5.5 0.5 - - - +
110G SER* 4.2 8.0 + - - +
111G LEU* 3.4 31.2 + - + +
112G SER* 3.3 27.8 + - - +
114G GLU* 1.3 80.0 - - + +
116G ALA* 1.3 62.4 + - - +
118G SER* 3.3 15.8 - - - -
119G PHE* 3.2 23.5 - - + -
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Residues in contact with ALA 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111G LEU* 3.7 16.6 - - + +
112G SER 3.1 18.2 + - - +
113G GLU* 3.7 7.9 - - - +
114G GLU 3.2 0.2 - - - -
115G GLU* 1.3 77.1 - - - +
117G THR* 1.3 63.6 + - + +
119G PHE* 3.1 20.5 + - - +
120G ILE* 3.1 17.2 + - + +
210G LEU* 4.1 13.8 - - + +
211G LEU* 4.5 7.9 - - + -
274G TRP* 5.2 0.4 - - + -
291G VAL* 3.8 13.0 - - + -
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Residues in contact with THR 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113G GLU 2.9 18.7 + - - +
114G GLU* 2.8 21.3 + - - -
116G ALA* 1.3 70.8 - - - +
118G SER* 1.3 59.7 + - - +
120G ILE* 3.6 8.5 - - - +
121G LYS* 2.8 31.5 + - - +
274G TRP* 3.3 55.6 - - + +
275G ILE* 4.3 8.4 - - + +
286G ARG* 3.5 20.8 + - - -
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Residues in contact with SER 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114G GLU 3.3 10.8 + - - -
115G GLU* 3.3 18.5 - - - -
116G ALA 3.1 0.2 - - - -
117G THR* 1.3 76.5 - - - +
119G PHE* 1.3 63.6 + - - +
121G LYS* 3.6 5.3 - - - +
122G GLN* 3.2 28.3 + - - +
154G ILE* 5.0 16.6 - - - +
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Residues in contact with PHE 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G LEU* 4.0 26.7 - - + -
104G PHE* 3.9 22.7 - + - -
105G LEU* 3.9 22.0 - - + -
108G LYS* 5.0 4.0 - - - -
111G LEU* 4.7 8.1 - - + -
115G GLU* 3.2 29.2 - - + -
116G ALA* 3.1 10.1 + - - +
118G SER* 1.3 73.8 - - - +
120G ILE* 1.3 66.7 + - + +
122G GLN* 3.2 14.6 + - - +
123G ILE* 3.1 19.5 + - - +
147G LEU* 5.8 0.2 - - + -
154G ILE* 4.0 22.9 - - + -
155G PRO* 3.8 28.9 - - + -
157G ILE* 3.3 24.0 - - + +
210G LEU* 5.4 4.3 - - + -
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Residues in contact with ILE 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G ALA* 3.1 18.0 + - + +
117G THR* 3.3 14.6 + - - +
119G PHE* 1.3 76.5 - - - +
121G LYS* 1.3 58.4 + - - +
123G ILE* 3.1 17.1 + - + +
124G LEU* 2.8 37.0 + - + +
203G ILE* 5.2 3.6 - - + -
206G ILE* 5.6 1.8 - - + -
207G THR* 3.8 29.4 - - + +
210G LEU* 4.0 24.5 - - + -
211G LEU* 6.4 0.7 - - + -
251G PHE* 4.5 12.1 - - + -
274G TRP* 4.4 9.6 - - + -
275G ILE* 3.8 21.3 - - + -
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Residues in contact with LYS 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G THR 2.8 18.2 + - - +
118G SER* 3.6 7.2 - - - +
120G ILE* 1.3 74.9 - - - +
122G GLN* 1.3 54.8 + - + +
124G LEU* 3.1 8.2 + - - +
125G ASP* 2.8 69.3 + - - +
270G LEU* 3.9 17.1 - - + +
275G ILE* 3.8 26.7 - - + +
276G THR* 5.5 4.0 - - - -
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Residues in contact with GLN 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G ASN* 3.2 36.6 + - - +
118G SER* 3.2 13.4 + - - +
119G PHE* 3.4 24.5 - - - +
121G LYS* 1.3 78.8 - - - +
123G ILE* 1.3 61.8 + - - +
125G ASP* 3.2 5.0 + - - +
126G GLY* 3.1 17.5 + - - -
154G ILE* 4.1 12.1 - - - +
155G PRO 3.0 20.8 + - - -
156G HIS* 3.6 7.3 + - - -
157G ILE* 2.9 35.0 + - + +
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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
----------------------------------------------------------
101G LEU* 4.2 12.3 - - + -
119G PHE 3.1 13.9 + - - +
120G ILE* 3.1 24.5 + - + +
122G GLN* 1.3 76.2 - - - +
124G LEU* 1.3 59.9 + - + +
126G GLY* 3.3 1.9 + - - -
127G VAL* 2.9 40.2 + - + +
140G LEU* 5.8 3.4 - - + -
145G ILE* 4.0 34.1 - - + -
157G ILE* 3.9 20.4 - - + -
159G LEU* 4.2 13.9 - - + +
203G ILE* 4.8 16.4 - - + -
206G ILE* 5.1 8.3 - - + -
210G LEU* 5.8 0.2 - - + -
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Residues in contact with LEU 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120G ILE* 2.8 22.6 + - + +
121G LYS* 3.5 5.6 - - - +
123G ILE* 1.3 77.4 - - + +
125G ASP* 1.3 58.8 + - - +
127G VAL* 4.4 0.7 - - - -
128G ASN* 2.8 31.4 + - - +
203G ILE* 4.0 31.9 - - + -
251G PHE* 4.4 3.8 - - + -
266G ILE* 3.5 25.4 - - + +
269G ALA* 4.2 17.0 - - + +
270G LEU* 3.5 26.6 - - + +
275G ILE* 3.8 37.5 - - + -
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Residues in contact with ASP 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G HIS* 3.5 19.5 + - + +
74G HIS* 5.1 5.5 + - + +
75G ASN* 3.8 11.3 - - - +
121G LYS* 2.8 56.4 + - - +
122G GLN* 3.5 8.6 - - - +
123G ILE 3.2 0.2 - - - -
124G LEU* 1.3 75.2 - - - +
126G GLY* 1.3 63.5 + - - +
128G ASN* 3.6 6.7 + - - +
129G TYR* 3.2 16.6 + - - +
270G LEU* 3.7 9.0 - - - +
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Residues in contact with GLY 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G HIS* 3.9 16.3 - - - -
75G ASN* 3.9 10.8 - - - -
76G VAL* 4.0 9.4 - - - +
122G GLN 3.1 10.9 + - - -
123G ILE 3.7 3.1 - - - -
125G ASP* 1.3 76.3 - - - +
127G VAL* 1.3 62.0 + - - +
129G TYR* 3.2 13.5 + - - +
130G LEU* 3.2 16.8 + - - +
159G LEU* 4.1 11.2 - - - -
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Residues in contact with VAL 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G ILE* 2.9 26.1 + - + +
124G LEU 4.0 2.7 - - - +
126G GLY* 1.3 75.6 - - - +
128G ASN* 1.3 63.1 + - - +
130G LEU* 3.4 10.0 + - + +
131G HIS* 3.0 52.9 + - + +
140G LEU* 4.0 21.1 - - + -
159G LEU* 3.9 14.8 - - + +
199G ASP* 4.6 3.8 - - + +
200G MET* 4.7 0.4 - - - -
203G ILE* 4.1 17.3 - - + -
266G ILE* 4.0 16.4 - - + -
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Residues in contact with ASN 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G LEU 2.8 20.0 + - - +
125G ASP* 3.8 8.1 + - - +
127G VAL* 1.3 77.6 - - - +
129G TYR* 1.3 56.8 + - - +
131G HIS* 3.4 1.2 + - - +
132G THR* 2.6 42.1 + - - -
266G ILE* 3.3 27.6 - - + +
267G GLN* 3.1 26.9 + - - +
270G LEU* 3.8 16.4 - - + +
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Residues in contact with TYR 129 (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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70G GLN 3.4 9.9 + - - -
71G VAL* 4.0 11.9 - - + -
72G LEU* 3.2 48.4 + - - +
73G HIS* 3.5 32.3 - + + -
76G VAL* 4.8 2.0 - - + -
125G ASP 3.2 10.5 + - - +
126G GLY 3.2 9.9 + - - +
128G ASN* 1.3 80.7 - - - +
130G LEU* 1.3 70.7 + - + +
132G THR* 3.5 8.4 + - + -
133G LYS* 3.3 55.6 + - + +
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Residues in contact with LEU 130 (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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71G VAL* 3.6 34.8 - - + -
76G VAL* 4.6 7.0 - - + -
126G GLY 3.2 14.5 + - - +
127G VAL* 3.7 15.0 - - + +
128G ASN 3.3 0.2 - - - -
129G TYR* 1.3 80.1 - - + +
131G HIS* 1.3 59.6 + - + +
133G LYS* 3.0 17.0 + - - -
134G LYS 3.2 0.2 + - - -
135G ILE* 2.9 45.0 + - + +
137G HIS* 4.6 16.4 - - + +
159G LEU* 4.4 14.1 - - + -
162G PHE* 3.7 31.2 - - + -
199G ASP* 6.0 0.2 - - - +
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Residues in contact with HIS 131 (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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127G VAL* 3.0 44.5 + - + +
128G ASN 3.9 3.4 - - - +
130G LEU* 1.3 79.0 - - + +
132G THR* 1.3 59.7 + - - +
134G LYS* 3.4 9.5 + - - +
135G ILE 3.3 18.4 - - - +
196G LEU* 3.3 58.7 + - + +
199G ASP* 3.0 25.6 + - + -
200G MET* 4.1 10.5 - - + -
266G ILE* 4.0 25.2 + - + +
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Residues in contact with THR 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128G ASN* 2.6 32.7 + - - -
129G TYR* 3.6 11.1 - - + -
130G LEU 3.1 0.2 - - - -
131G HIS* 1.3 75.1 - - - +
133G LYS* 1.3 64.7 + - + +
134G LYS* 3.2 13.8 + - - +
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Residues in contact with LYS 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G GLN* 4.2 19.4 - - + +
71G VAL* 6.2 0.2 - - + -
129G TYR* 3.3 51.6 + - + +
130G LEU* 3.0 8.5 + - - +
132G THR* 1.3 83.9 - - - +
134G LYS* 1.3 70.5 + - - +
135G ILE* 3.3 23.2 - - + +
167G GLU* 5.4 1.9 - - - +
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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
------------------------------------------------------------
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