Contacts of the strand formed by residues 138 - 148 (chain G) in PDB entry 3AOI
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 LEU 138 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58G ILE* 5.8 3.6 - - + -
60G ASP* 5.8 0.2 - - - -
68G ILE* 4.9 14.4 - - + -
71G VAL* 3.4 30.1 - - + -
78G ILE* 5.0 4.9 - - + -
101G LEU* 4.4 15.0 - - + -
102G LYS* 3.5 1.9 - - - -
103G ALA 3.0 32.4 + - - +
109G VAL* 5.0 8.5 - - + -
129G ILE* 6.3 1.3 - - + -
130G ALA* 3.7 17.0 - - + -
132G LEU* 3.6 27.8 - - + -
137G ARG* 1.3 76.1 - - - +
139G ASN* 1.3 59.9 + - - +
140G MET* 3.8 29.8 - - + -
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Residues in contact with ASN 139 (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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58G ILE* 3.6 5.5 - - - +
59G GLU* 2.8 57.2 + - - +
60G ASP* 5.6 0.2 + - - -
101G LEU 3.2 6.6 + - - +
102G LYS* 3.0 46.2 - - + +
137G ARG* 4.1 0.6 - - - +
138G LEU* 1.3 73.6 - - - +
140G MET* 1.3 74.4 + - - +
141G GLU* 5.6 3.3 + - - +
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Residues in contact with MET 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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56G VAL* 3.7 9.6 - - + -
57G TYR* 3.0 21.8 - - - +
58G ILE* 3.9 15.9 - - + -
59G GLU 4.8 0.2 - - - +
78G ILE* 4.5 12.6 - - + -
82G LEU* 3.6 28.0 - - + -
100G LEU* 3.9 0.5 - - - +
101G LEU* 3.0 43.4 + - + +
114G PHE* 5.0 5.7 - - + -
129G ILE* 5.0 6.1 - - + -
138G LEU* 3.8 23.6 - - + -
139G ASN* 1.3 80.0 + - - +
141G GLU* 1.3 68.5 + - - +
142G VAL* 3.3 30.7 + - + -
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Residues in contact with GLU 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G SER 3.9 0.5 - - - +
56G VAL* 3.7 2.8 - - - -
57G TYR* 3.0 58.1 + - + +
98G THR* 4.0 9.7 - - + +
99G LEU 3.4 4.7 - - - -
100G LEU* 3.2 32.5 - - + +
139G ASN* 5.6 4.3 + - - +
140G MET* 1.3 78.9 - - - +
142G VAL* 1.3 63.5 + - - +
143G ARG* 3.9 1.2 + - - +
161G ARG* 3.6 33.3 + - - +
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Residues in contact with VAL 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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53G VAL* 4.1 12.8 - - + -
55G SER 3.5 3.8 - - - -
56G VAL* 3.8 13.5 - - + -
82G LEU* 3.6 15.5 - - + -
85G LEU* 5.4 3.1 - - + -
97G VAL 4.1 0.2 - - - +
98G THR* 4.6 1.6 - - - -
99G LEU* 2.9 44.3 + - + +
114G PHE* 3.3 30.5 - - + -
140G MET* 3.3 34.7 - - + -
141G GLU* 1.3 72.3 - - - +
143G ARG* 1.3 62.1 + - - +
144G VAL* 4.1 4.2 - - + +
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Residues in contact with ARG 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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53G VAL* 3.0 11.4 - - - +
54G THR* 2.9 26.0 + - - -
55G SER* 2.6 22.5 + - - +
96G THR* 2.9 22.9 + - - +
97G VAL 3.8 4.5 - - - +
98G THR* 4.3 9.4 - - - +
141G GLU 3.9 2.0 + - - +
142G VAL* 1.3 69.4 - - - +
144G VAL* 1.3 67.1 + - - +
145G ASP* 2.8 34.0 + - - +
158G ILE* 2.9 52.3 - - - +
159G LYS* 6.0 0.2 - - - +
160G ASP* 3.5 30.1 + - - +
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Residues in contact with VAL 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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51G THR* 3.5 10.8 - - + -
52G ALA 3.2 19.5 - - - +
53G VAL* 4.2 12.3 - - + +
54G THR 4.3 0.7 - - - +
85G LEU* 5.8 0.7 - - + -
87G VAL* 3.4 33.0 - - + -
89G PHE* 4.1 10.5 - - + -
96G THR* 3.4 0.2 - - - -
97G VAL 2.9 38.3 + - - +
99G LEU* 4.2 21.1 - - + -
142G VAL* 4.1 8.5 - - + +
143G ARG* 1.3 81.2 - - - +
145G ASP* 1.3 74.7 + - - +
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Residues in contact with ASP 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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51G THR* 2.6 30.2 - - - +
52G ALA 3.3 5.8 + - - -
54G THR* 3.4 17.0 + - + +
89G PHE* 4.1 1.8 - - - -
95G GLN 3.6 9.5 - - - +
96G THR* 3.2 10.6 + - - -
143G ARG* 2.8 43.6 + - - +
144G VAL* 1.3 93.1 - - - +
146G ARG* 1.3 59.4 + - - +
171G PHE* 3.2 25.3 - - + -
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Residues in contact with ARG 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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49G PRO* 6.4 1.1 - - + -
50G GLY 3.4 12.1 - - - +
51G THR* 4.4 0.2 - - - -
89G PHE* 3.3 37.6 - - + +
90G LEU 5.2 0.2 - - - -
91G ASN* 3.6 17.5 + - - +
92G PRO* 3.7 22.1 - - - +
94G LEU 2.9 20.9 + - - +
95G GLN* 3.3 27.8 - - + +
145G ASP* 1.3 75.3 - - - +
147G GLY* 1.3 59.1 + - - +
171G PHE* 3.7 2.6 - - - -
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Residues in contact with GLY 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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49G PRO* 3.5 1.7 - - - +
50G GLY 3.2 21.4 + - - -
146G ARG* 1.3 76.2 - - - +
148G VAL* 1.3 71.0 + - - +
171G PHE* 3.0 35.6 - - - +
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Residues in contact with VAL 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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29F GLU* 5.7 4.9 - - - +
46G SER* 3.5 17.6 + - - +
47G SER* 3.1 22.2 - - - +
48G ILE 4.0 2.5 - - - -
49G PRO* 3.6 16.6 - - + -
147G GLY* 1.3 81.3 - - - +
149G GLY* 1.3 63.3 + - - +
150G TYR 4.0 0.7 + - - -
151G VAL* 4.7 6.9 - - - +
171G PHE* 3.4 8.5 - - - -
855I HIS* 5.2 1.0 - - - -
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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