Contacts of the helix formed by residues 139 - 151 (chain G) in PDB entry 6CP3
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 139 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137G ALA 4.2 7.9 - - - +
138G PRO* 1.3 77.8 - - - +
140G PHE* 1.3 65.1 + - - +
141G GLN* 3.3 7.1 + - - +
142G GLU* 3.5 19.7 + - - +
143G SER* 3.6 5.0 + - - -
219G LEU* 3.4 14.9 - - - +
17H PRO* 6.1 0.2 - - - -
33I SER 5.6 0.4 - - - +
36I ASN* 4.0 10.9 + - + +
37I ARG* 3.3 52.2 + - + +
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Residues in contact with PHE 140 (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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44G MET* 5.2 0.2 - - + -
139G THR* 1.3 74.3 - - - +
141G GLN* 1.3 60.7 + - - +
144G ALA* 2.8 57.2 + - + +
212G TYR* 4.5 13.9 - + - -
215G ALA* 4.0 24.7 - - + -
216G ASN* 3.3 21.8 - - - -
219G LEU* 3.6 26.9 - - + +
17H PRO* 3.8 29.7 - - + +
88H ILE* 3.6 38.1 - - + -
11I ALA* 4.5 10.5 - - + -
14I LEU* 5.2 0.4 - - + -
15I ASN* 5.0 6.7 - - + -
18I ALA* 5.6 1.6 - - + -
37I ARG* 5.0 5.2 - - + +
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Residues in contact with GLN 141 (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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139G THR* 3.2 2.5 + - - +
140G PHE* 1.3 78.6 - - - +
142G GLU* 1.3 64.8 + - - +
145G LEU* 2.9 55.5 + - - +
15I ASN* 3.1 36.7 + - - +
19I GLN* 3.3 31.1 - - + +
37I ARG* 3.3 28.4 - - + +
38I SER* 4.8 3.8 - - - -
39I GLN 4.6 0.5 - - - -
40I THR* 3.3 31.1 + - - -
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Residues in contact with GLU 142 (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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132G GLY 5.3 1.6 - - - -
133G ILE* 4.4 17.6 - - + +
135G LYS* 3.9 17.7 + - - -
138G PRO* 3.7 25.1 - - - +
139G THR* 3.5 14.4 + - - +
140G PHE 3.4 0.2 - - - -
141G GLN* 1.3 89.7 - - - +
143G SER* 1.3 58.6 + - - +
145G LEU* 3.2 7.0 + - - +
146G ILE* 3.0 38.6 + - + +
222G MET* 4.2 12.5 - - + +
39I GLN 3.3 21.1 - - - +
40I THR* 4.8 4.7 - - - -
41I ASP 4.5 2.4 + - - -
42I ALA* 5.3 8.7 - - + -
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Residues in contact with SER 143 (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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139G THR 3.6 2.2 + - - -
140G PHE* 3.6 3.2 + - - -
141G GLN 3.4 0.2 - - - -
142G GLU* 1.3 78.2 - - - +
144G ALA* 1.3 58.0 + - - +
146G ILE* 3.4 5.9 + - - +
147G ALA* 2.9 27.3 + - - +
215G ALA 3.2 8.7 + - - -
218G MET* 3.2 11.9 - - - +
219G LEU* 2.9 54.3 + - - -
222G MET* 4.0 17.4 - - - -
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Residues in contact with ALA 144 (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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140G PHE* 2.8 47.6 + - + +
143G SER* 1.3 77.4 - - - +
145G LEU* 1.3 57.0 + - - +
147G ALA* 3.2 9.9 + - - +
148G ASP* 2.9 26.9 + - - +
215G ALA* 4.7 3.8 - - - -
11I ALA* 4.1 18.4 - - + +
12I ALA* 4.6 3.3 + - - -
15I ASN* 3.8 14.6 - - - +
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Residues in contact with LEU 145 (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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141G GLN* 2.9 42.6 + - - +
142G GLU* 3.2 7.1 + - + +
144G ALA* 1.3 74.9 - - - +
146G ILE* 1.3 60.2 + - + +
148G ASP* 3.2 12.7 + - + +
149G LYS* 2.9 46.9 + - - +
12I ALA* 5.9 3.4 - - + -
15I ASN* 4.0 6.7 - - - +
40I THR* 4.5 6.1 - - - -
42I ALA* 6.3 2.0 - - + -
59I ILE* 3.5 42.4 - - + +
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Residues in contact with ILE 146 (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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108G VAL* 6.0 1.1 - - + -
110G ILE* 3.9 20.2 - - + -
128G LEU* 6.0 1.1 - - + -
130G ILE* 3.7 43.7 - - + -
133G ILE* 4.3 13.2 - - + -
142G GLU* 3.0 20.8 + - + +
143G SER 3.8 4.3 - - - +
145G LEU* 1.3 74.7 - - + +
147G ALA* 1.3 60.5 + - - +
149G LYS* 3.1 8.3 + - + +
150G LEU* 2.9 36.6 + - + +
218G MET* 3.6 19.7 - - + -
222G MET* 4.4 11.4 - - - -
42I ALA* 5.1 6.1 - - + -
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Residues in contact with ALA 147 (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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143G SER 2.9 18.3 + - - +
144G ALA* 3.2 11.2 + - - +
146G ILE* 1.3 78.6 - - - +
148G ASP* 1.3 60.5 + - - +
150G LEU* 3.6 10.0 + - - +
151G LEU* 3.6 14.2 + - - +
211G GLU* 4.9 1.3 - - + +
214G LEU* 4.0 26.8 - - + +
215G ALA* 4.0 23.3 - - + +
218G MET* 4.8 2.6 - - - -
9I SER* 4.7 1.6 + - - -
11I ALA* 4.5 7.6 - - + -
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Residues in contact with ASP 148 (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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144G ALA 2.9 8.8 + - - +
145G LEU* 3.5 14.6 - - + +
146G ILE 3.2 0.4 - - - -
147G ALA* 1.3 78.1 - - - +
149G LYS* 1.3 67.5 + - - +
151G LEU 3.1 3.6 + - - -
152G SER* 2.9 49.9 + - - -
118H ARG* 4.0 13.6 + - - -
8I ILE* 4.3 1.9 - - - -
9I SER* 2.6 45.8 + - - +
11I ALA* 5.5 0.4 - - - +
12I ALA* 3.5 20.2 - - + +
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Residues in contact with LYS 149 (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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128G LEU* 4.6 12.0 - - + +
130G ILE* 5.5 4.7 - - + -
145G LEU* 2.9 33.4 + - - +
146G ILE* 3.1 12.5 + - + +
148G ASP* 1.3 85.3 + - - +
150G LEU* 1.3 62.5 + - - +
152G SER* 4.4 8.1 - - - +
153G VAL* 3.3 34.0 + - + +
154G MET* 3.8 1.4 + - - +
44I TYR* 3.6 48.9 - - + -
59I ILE* 3.9 22.0 + - + +
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Residues in contact with LEU 150 (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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73G LEU* 4.5 13.7 - - + -
75G VAL* 5.0 6.3 - - + -
108G VAL* 4.3 25.4 - - + -
128G LEU* 4.5 5.2 - - + -
146G ILE* 2.9 24.3 + - + +
147G ALA* 3.9 6.5 - - - +
148G ASP 3.2 0.4 - - - -
149G LYS* 1.3 78.2 - - - +
151G LEU* 1.3 60.0 + - + +
152G SER 3.4 0.2 - - - -
154G MET* 3.3 26.9 - - + +
155G LYS 3.1 22.5 + - - -
156G ALA* 3.5 12.1 + - + -
214G LEU* 3.8 26.7 - - + -
218G MET* 3.7 31.0 - - + -
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Residues in contact with LEU 151 (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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147G ALA 3.6 13.6 + - - +
148G ASP* 3.1 7.3 + - - +
150G LEU* 1.3 78.6 - - + +
152G SER* 1.3 59.0 + - - +
155G LYS* 4.4 11.8 - - - +
156G ALA* 3.4 33.7 - - + +
157G GLY* 3.4 17.5 - - - +
210G PHE* 4.1 16.6 - - + -
211G GLU* 3.6 39.3 - - + +
214G LEU* 4.5 9.2 - - + -
9I SER* 5.1 8.9 - - - -
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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