Contacts of the strand formed by residues 143 - 153 (chain G) in PDB entry 6A5T
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 VAL 143 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88G ASP* 4.1 3.4 - - - -
89G ALA* 2.9 37.5 + - - +
91G VAL* 3.7 23.3 - - + -
99G PHE* 4.2 20.6 - - + -
101G ALA* 5.3 3.8 - - + -
137G ILE* 3.5 41.1 - - + -
138G THR 4.2 3.8 - - - +
141G SER 3.7 8.7 - - - +
142G LYS* 1.3 80.4 - - - +
144G ARG* 1.3 73.2 + - - +
145G LEU* 5.4 1.7 - - + +
163G ILE* 5.2 2.5 - - + -
169G GLY 5.1 5.4 - - - +
170G ALA* 6.3 1.1 - - - +
171G ILE* 5.2 0.9 - - - +
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Residues in contact with ARG 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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148D LEU* 4.7 11.9 - - - +
149D GLY 5.7 3.0 + - - -
150D CYS* 5.3 6.3 - - - -
155D GLU* 4.3 15.6 + - - -
159D LEU* 5.1 2.0 - - - +
86G VAL* 3.7 20.7 - - + +
87G VAL 3.2 15.8 + - - +
88G ASP* 3.2 29.7 + - - +
143G VAL* 1.3 81.2 - - - +
145G LEU* 1.3 67.0 + - - +
163G ILE* 3.1 20.3 - - - +
167G PHE 4.7 9.1 + - - -
168G LEU* 3.7 32.2 - - + +
169G GLY* 4.0 22.4 + - - +
171G ILE* 4.7 21.0 - - + +
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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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85G GLU 3.2 1.6 - - - +
86G VAL* 3.8 2.6 - - - -
87G VAL* 2.9 41.0 + - + +
89G ALA* 5.1 2.2 - - + -
99G PHE* 4.8 5.6 - - + -
101G ALA* 4.6 14.4 - - + -
103G VAL* 3.5 36.3 - - + -
108G VAL* 3.7 30.1 - - + +
110G VAL* 4.0 13.2 - - + -
143G VAL* 4.1 2.0 + - + +
144G ARG* 1.3 81.0 - - - +
146G LYS* 1.3 83.0 + - - +
147G VAL* 4.1 3.4 - - + +
161G GLY* 4.1 2.0 - - - -
162G SER 3.9 5.6 - - - +
163G ILE* 3.8 17.5 - - + +
168G LEU* 4.8 4.4 - - - +
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Residues in contact with LYS 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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26D THR* 5.2 11.9 - - - +
84G GLY* 3.4 38.4 - - - +
85G GLU 3.1 8.3 - - - +
86G VAL* 5.3 4.0 - - + -
145G LEU* 1.3 78.7 - - - +
147G VAL* 1.3 61.2 + - - +
148G VAL* 3.3 23.1 + - + +
161G GLY* 2.9 21.4 - - - -
162G SER 3.0 17.5 + - - +
165G GLU* 3.2 38.5 + - + +
168G LEU* 3.8 20.2 - - + -
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Residues in contact with VAL 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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81G PRO* 5.2 11.9 - - + -
82G PHE 3.6 22.9 - - - +
83G LYS* 3.1 10.4 - - + -
84G GLY* 2.2 39.2 + - - -
85G GLU* 3.5 10.6 + - + +
87G VAL* 5.2 3.4 - - + -
103G VAL* 4.7 9.4 - - + -
106G LEU* 6.2 0.2 - - + -
108G VAL* 4.6 10.1 - - + -
145G LEU* 4.1 13.2 - - + +
146G LYS* 1.3 68.8 - - - +
148G VAL* 1.3 57.1 + - - +
149G GLY 4.5 4.0 - - - +
150G THR* 4.8 2.7 - - + -
159G ALA* 3.5 33.0 - - + -
160G ILE 3.8 5.2 - - - +
161G GLY* 4.0 1.1 - - - -
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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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83G LYS* 3.2 24.0 + - - +
84G GLY* 4.5 0.7 - - - +
114G LEU* 6.0 1.8 - - + -
146G LYS* 3.4 40.8 - - + +
147G VAL* 1.3 74.6 - - - +
149G GLY* 1.3 59.2 + - - +
160G ILE* 2.8 25.5 + - + +
161G GLY* 4.2 6.7 - - - -
162G SER* 4.6 11.7 - - - +
165G GLU* 5.9 1.3 - - - +
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Residues in contact with GLY 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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83G LYS* 4.0 2.8 - - - +
147G VAL* 3.9 0.6 - - - +
148G VAL* 1.3 82.0 - - - +
150G THR* 1.3 62.7 + - - +
151G ARG 4.3 0.2 - - - -
158G TYR 3.6 1.0 - - - +
159G ALA* 3.1 7.3 - - - +
160G ILE* 2.9 50.4 + - - +
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Residues in contact with THR 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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83G LYS* 3.6 42.8 + - + +
147G VAL* 4.8 7.2 - - + -
149G GLY* 1.3 77.1 - - - +
151G ARG* 1.3 59.8 + - - +
152G THR* 4.2 8.4 + - - -
157G ILE* 5.7 7.2 - - + -
158G TYR 3.4 5.8 - - - +
159G ALA* 4.9 3.1 - - + -
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Residues in contact with ARG 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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149G GLY 4.3 0.2 + - - -
150G THR* 1.3 73.6 - - - +
152G THR* 1.3 62.6 + - - +
153G ASP* 3.2 19.0 + - - +
157G ILE* 5.1 0.7 - - - -
158G TYR* 2.9 79.5 + - + +
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Residues in contact with THR 152 (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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1188B LYS* 5.7 4.0 - - - +
40G GLY* 5.7 2.2 - - - -
150G THR* 5.1 6.9 + - - -
151G ARG* 1.3 74.3 + - - +
153G ASP* 1.3 57.1 + - - +
154G VAL* 3.6 28.9 + - + +
157G ILE* 3.8 27.0 - - + +
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Residues in contact with ASP 153 (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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151G ARG* 3.2 17.5 + - - +
152G THR* 1.3 70.8 - - - +
154G VAL* 1.3 49.8 + - - +
155G ASN* 2.5 33.1 + - - +
156G GLU 2.6 24.7 + - - +
157G ILE* 4.1 0.2 - - - +
158G TYR* 3.5 34.0 + - + -
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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