Contacts of the strand formed by residues 144 - 152 (chain G) in PDB entry 6RI7
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 GLY 144 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140G ASN* 4.5 2.2 - - - -
141G THR* 2.8 36.3 + - - +
142G PRO 3.8 0.2 - - - -
143G ALA* 1.3 76.7 - - - +
145G GLU* 1.3 61.3 + - - -
146G ALA* 4.6 0.4 - - - +
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Residues in contact with GLU 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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139G VAL 3.4 13.0 - - - +
140G ASN* 4.0 8.9 - - + +
144G GLY* 1.3 70.5 - - - -
146G ALA* 1.3 59.4 + - - +
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Residues in contact with ALA 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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138G VAL* 3.4 2.1 - - - +
139G VAL* 2.9 32.4 + - + +
141G THR* 4.1 19.7 - - - +
144G GLY 3.5 2.0 + - - +
145G GLU* 1.3 75.4 - - - +
147G SER* 1.3 65.1 + - - +
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Residues in contact with SER 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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95G ASN* 4.2 12.8 - - - +
99G VAL* 5.2 3.8 - - - +
136G LEU* 5.6 2.5 - - - -
137G ALA 3.4 7.9 - - - -
138G VAL* 3.6 18.6 - - - -
146G ALA* 1.3 79.2 - - - +
148G TRP* 1.3 63.2 + - - +
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Residues in contact with TRP 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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93G ILE* 3.8 18.7 - - + +
94G GLU 3.4 13.9 - - - +
95G ASN* 4.7 1.1 - - - +
99G VAL* 4.5 10.3 - - + +
101G HIS* 6.5 0.4 - - + -
135G ASP 3.4 0.9 - - - +
136G LEU* 4.5 2.2 - - - -
137G ALA* 2.9 38.7 + - + +
147G SER* 1.3 77.7 - - - +
149G TYR* 1.3 62.6 + - - +
150G VAL 3.5 0.9 + - - -
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Residues in contact with TYR 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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93G ILE* 4.1 0.7 - - - -
94G GLU* 2.9 37.4 + - + +
95G ASN* 4.8 2.3 - - - +
134G GLY* 5.4 3.6 - - - +
135G ASP 3.4 5.4 - - - +
136G LEU* 4.3 9.2 - - + +
148G TRP* 1.3 70.7 - - - +
150G VAL* 1.3 66.8 + - - +
151G ASN* 3.1 2.1 + - - +
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Residues in contact with VAL 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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92G GLU 4.4 3.6 - - - +
93G ILE* 3.9 13.0 - - + +
131G LYS* 5.4 4.3 - - + -
132G GLU 3.3 26.0 - - - +
133G VAL 2.8 20.7 - - - +
134G GLY* 3.5 5.0 - - - -
135G ASP* 2.5 33.0 + - + +
137G ALA* 6.2 1.3 - - + -
148G TRP 3.5 1.6 + - - -
149G TYR* 1.3 70.1 - - - +
151G ASN* 1.3 60.3 + - - +
152G ALA 5.2 0.7 - - - +
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Residues in contact with ASN 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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92G GLU* 2.9 8.3 + - + +
93G ILE 4.4 0.4 - - - -
94G GLU* 3.6 32.8 - - + +
133G VAL* 4.3 7.4 - - - +
149G TYR 3.1 1.9 + - - +
150G VAL* 1.3 75.2 - - - +
152G ALA* 1.3 64.3 + - + +
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Residues in contact with ALA 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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90G TRP 5.1 0.7 - - - -
91G VAL* 3.3 2.0 - - - +
92G GLU* 2.4 52.9 + - + +
132G GLU 5.5 2.6 - - - +
133G VAL* 5.0 5.0 + - - +
150G VAL* 3.8 0.8 - - - +
151G ASN* 1.3 82.4 - - + +
153G ILE* 1.3 58.9 + - - +
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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