Contacts of the strand formed by residues 86 - 95 (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 86 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144D GLN* 5.1 7.7 - - - +
148D LEU* 3.5 48.2 - - + +
159D LEU* 3.5 42.8 - - + +
160D ILE* 6.1 0.7 - - + -
84G GLY 4.8 4.7 - - - +
85G GLU* 1.3 76.7 - - - +
87G VAL* 1.3 65.3 + - - +
144G ARG* 3.7 25.8 - - - +
145G LEU 3.8 3.1 - - - -
146G LYS* 5.1 5.4 - - + +
168G LEU* 4.3 7.6 - - + -
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Residues in contact with VAL 87 (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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108D TYR* 3.4 22.2 - - - +
148D LEU* 5.9 0.4 - - - -
79G TRP* 6.2 1.6 - - + -
85G GLU* 3.4 43.7 - - + +
86G VAL* 1.3 76.2 - - - +
88G ASP* 1.3 60.6 + - - +
103G VAL* 3.6 26.0 - - + -
144G ARG* 3.2 8.1 - - - +
145G LEU* 2.9 54.1 + - + +
147G VAL* 5.1 3.4 - - + +
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Residues in contact with ASP 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D TYR* 3.1 29.9 + - - -
112D PHE* 3.3 35.1 - - + -
148D LEU* 6.3 0.2 - - - +
87G VAL* 1.3 72.9 - - - +
89G ALA* 1.3 64.0 + - - +
142G LYS* 4.8 4.2 - - + +
143G VAL 3.7 1.3 - - - -
144G ARG* 3.2 43.0 + - - +
171G ILE* 3.4 29.7 - - - +
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Residues in contact with ALA 89 (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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108D TYR* 4.7 2.9 - - - -
112D PHE* 4.3 3.0 - - - -
87G VAL 4.9 1.6 - - - +
88G ASP* 1.3 79.2 - - - +
90G ILE* 1.3 62.1 + - - +
101G ALA* 4.2 8.5 - - + -
102G ASP 2.9 21.8 - - - +
103G VAL* 3.5 24.9 - - + -
142G LYS* 3.2 9.4 - - - +
143G VAL 2.9 36.3 + - - +
145G LEU* 5.1 1.8 - - + -
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Residues in contact with ILE 90 (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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107D ASP* 6.2 4.7 - - + -
111D THR* 4.6 13.9 - - + +
112D PHE* 5.7 1.8 - - + -
89G ALA* 1.3 78.6 - - - +
91G VAL* 1.3 73.9 + - + +
92G SER 3.4 0.5 + - - -
101G ALA* 4.1 1.3 - - - -
102G ASP* 2.8 42.4 + - + +
140G GLY* 5.3 12.8 - - - +
141G SER 6.4 0.4 - - - -
142G LYS* 3.6 37.9 - - + +
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Residues in contact with VAL 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G ALA 4.3 0.2 + - - -
90G ILE* 1.3 82.9 - - - +
92G SER* 1.3 60.5 + - - +
93G ASN 4.5 5.6 - - - +
94G VAL* 5.2 7.4 - - + -
99G PHE* 4.4 15.5 - - + -
100G PHE 3.4 10.3 - - - +
101G ALA* 3.6 18.6 - - + +
137G ILE* 5.2 2.9 - - + -
138G THR 3.3 25.8 - - - +
139G LYS* 3.5 28.1 - - + +
140G GLY 4.5 2.2 - - - +
141G SER 4.9 1.7 + - - +
143G VAL* 3.7 25.9 - - + +
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Residues in contact with SER 92 (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 ILE* 3.4 1.6 + - - -
91G VAL* 1.3 73.4 - - - +
93G ASN* 1.3 79.1 + - - +
100G PHE* 2.9 17.9 + - - +
102G ASP* 4.2 21.1 - - - -
107G ASN* 3.2 27.8 + - - -
139G LYS* 5.3 11.5 + - - +
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Residues in contact with ASN 93 (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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91G VAL* 4.5 2.3 - - - +
92G SER* 1.3 99.9 + - - +
94G VAL* 1.3 74.7 + - - +
99G PHE* 4.5 0.2 - - - -
100G PHE* 3.2 36.3 + - + +
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Residues in contact with VAL 94 (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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91G VAL* 5.2 13.0 - - + -
93G ASN* 1.3 84.7 - - - +
95G SER* 1.3 60.5 + - - +
96G PRO* 4.8 0.9 - - - +
98G GLY 4.4 3.8 - - - -
99G PHE* 4.9 10.3 - - + +
100G PHE* 5.5 0.4 - - - -
121G TYR* 3.5 20.4 + - + +
128G PRO* 3.5 50.3 - - + +
129G ALA* 5.9 0.7 - - - -
130G TYR* 5.5 3.6 - - + -
138G THR* 6.1 0.4 - - - -
139G LYS* 5.7 5.4 - - + +
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Residues in contact with SER 95 (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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94G VAL* 1.3 74.5 - - - +
96G PRO* 1.3 71.0 - - - +
97G ILE* 2.7 31.9 + - - +
98G GLY 2.6 36.4 + - - +
100G PHE* 4.0 13.2 - - - -
109G PHE* 3.8 8.3 - - - -
121G TYR* 3.1 17.2 - - - -
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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