Contacts of the strand formed by residues 137 - 144 (chain G) in PDB entry 5T0J
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 CYS 137 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G ILE* 3.7 23.8 - - + -
80G MET* 3.2 32.2 - - - +
81G THR* 3.1 31.8 + - - +
135G GLY 3.6 0.8 + - - -
136G CYS* 1.3 74.7 - - - +
138G MET* 1.3 63.2 - - - +
139G ILE* 4.0 12.3 - - - -
153G LYS* 4.8 2.0 - - - -
154G CYS 3.7 3.4 - - - -
155G ASP* 3.1 32.1 - - - -
156G PRO* 4.1 1.3 - - - -
168G ALA 5.1 6.3 - - - -
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Residues in contact with MET 138 (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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72G ILE* 4.9 0.7 - - + -
78G CYS* 3.7 29.2 - - - -
80G MET* 3.5 33.2 - - + +
90G GLN* 4.1 33.0 - - + +
91G VAL* 4.8 1.8 - - - -
94G ALA* 4.5 13.0 - - + -
118G ILE* 5.5 8.5 - - + -
136G CYS* 4.3 0.9 + - - +
137G CYS* 1.3 75.1 - - - +
139G ILE* 1.3 68.2 + - - +
140G LEU* 3.5 27.4 - - + -
153G LYS* 3.4 2.1 - - - +
154G CYS* 2.5 56.7 + - + +
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Residues in contact with ILE 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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39G SER* 3.5 22.9 - - - +
41G ALA* 4.1 25.6 - - + -
50G ILE* 5.2 4.0 - - + -
78G CYS* 3.2 7.8 - - - +
79G VAL* 2.8 60.7 + - + +
80G MET 4.4 0.9 - - - -
81G THR* 3.9 19.3 - - + +
137G CYS* 4.0 8.1 - - - -
138G MET* 1.3 81.2 - - - +
140G LEU* 1.3 64.5 + - - +
141G ILE* 5.7 0.2 - - + -
151G VAL* 5.4 0.2 - - + -
152G TYR 3.3 14.6 - - - +
153G LYS* 3.5 26.9 - - + +
168G ALA 5.1 2.0 - - - +
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Residues in contact with LEU 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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72G ILE* 6.2 2.2 - - + -
76G ILE* 5.9 1.6 - - + -
77G GLY 4.2 6.3 - - - +
78G CYS* 4.4 2.9 - - + -
94G ALA* 5.8 0.7 - - + -
111G VAL* 4.4 9.0 - - + -
114G LEU* 3.8 27.4 - - + -
115G CYS* 3.6 32.1 - - + +
118G ILE* 5.8 1.8 - - + -
138G MET* 3.5 33.2 - - + -
139G ILE* 1.3 72.5 - - - +
141G ILE* 1.3 72.6 + - - +
151G VAL* 4.4 0.2 - - - +
152G TYR* 2.4 68.5 + - + +
153G LYS 4.1 3.1 - - - +
154G CYS* 4.1 12.6 - - + +
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Residues in contact with ILE 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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50G ILE* 3.8 33.4 - - + -
75G ASN 4.4 1.1 - - - +
76G ILE* 3.2 21.6 - - - +
77G GLY* 3.4 39.0 + - - +
78G CYS* 4.5 1.6 - - - +
111G VAL* 3.6 16.2 - - - +
139G ILE* 5.7 0.7 - - + -
140G LEU* 1.3 79.4 - - - +
142G GLY* 1.3 72.1 + - - +
150G GLN 3.7 19.7 - - - +
151G VAL* 4.4 5.8 - - + +
152G TYR* 4.6 1.8 - - - +
220G VAL* 3.8 24.7 - - + -
227G PHE* 3.7 26.5 - - + -
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Residues in contact with GLY 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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75G ASN 4.2 1.8 - - - -
76G ILE* 3.8 17.0 - - - -
111G VAL* 4.6 6.5 - - - -
141G ILE* 1.3 88.9 - - - +
143G ILE* 1.3 73.2 + - - +
150G GLN* 2.9 27.6 + - - +
220G VAL* 4.0 5.0 - - - +
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Residues in contact with ILE 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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75G ASN* 4.5 10.4 + - + +
76G ILE* 4.6 5.4 - - - +
108G GLU* 5.6 4.0 - - - +
109G ILE 4.9 8.5 - - - +
110G PRO* 4.9 5.3 + - - +
142G GLY* 1.3 82.8 - - - +
144G ASP* 1.3 70.0 + - - +
148G GLY 4.0 1.8 - - - +
149G PRO* 3.8 17.0 - - + -
150G GLN* 3.2 3.1 + - - -
220G VAL* 3.7 24.2 - - + -
221G THR 4.8 2.2 - - - +
222G VAL* 3.8 32.3 - - + -
225G PRO* 4.2 31.9 - - + +
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Residues in contact with ASP 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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110G PRO* 4.1 33.6 - - - +
143G ILE* 1.3 83.1 - - - +
145G GLU* 1.3 87.6 + - - +
146G GLU 3.2 3.5 + - - -
147G GLN* 3.3 28.5 + - + +
148G GLY 3.9 6.8 + - - +
150G GLN* 3.1 25.6 + - + +
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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