Contacts of the strand formed by residues 106 - 111 (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 LEU 106 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44G TYR* 4.3 19.5 - - + +
79G TRP* 4.7 6.1 - - + -
81G PRO* 4.5 16.8 - - + -
102G ASP* 3.6 5.3 - - - +
103G VAL* 2.7 37.2 + - + +
104G GLY 3.1 5.9 - - - +
105G PRO* 1.3 80.6 - - - +
107G ASN* 1.3 84.9 + - - +
108G VAL* 3.8 16.6 - - + -
147G VAL* 6.2 0.4 - - + -
157G ILE* 4.4 31.4 - - + +
158G TYR* 5.9 0.9 - - + -
159G ALA* 4.6 17.3 - - + +
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Residues in contact with ASN 107 (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 SER* 3.2 21.0 + - - -
100G PHE* 4.0 14.8 - - - +
101G ALA 2.7 39.4 + - - +
102G ASP* 3.7 17.6 + - - +
106G LEU* 1.3 87.6 - - - +
108G VAL* 1.3 68.3 + - - +
109G PHE 4.5 0.2 + - - -
159G ALA 4.6 2.1 - - - +
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Residues in contact with VAL 108 (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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99G PHE* 3.7 1.4 - - - +
100G PHE* 3.4 3.4 - - - -
101G ALA* 2.9 30.2 + - - +
103G VAL* 3.7 34.1 - - + -
106G LEU* 3.8 13.2 - - + -
107G ASN* 1.3 83.5 + - - +
109G PHE* 1.3 65.0 + - - +
110G VAL* 4.3 0.3 + - - +
145G LEU* 3.7 22.9 - - + +
147G VAL* 4.6 10.1 - - + -
159G ALA 4.0 9.2 - - - +
160G ILE* 4.2 2.2 - - - -
161G GLY* 3.3 31.9 - - - +
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Residues in contact with PHE 109 (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 SER* 3.8 2.7 - - - -
97G ILE* 3.6 15.7 - - + -
98G GLY* 3.3 22.9 - - - -
99G PHE 3.1 34.3 - - - -
100G PHE* 3.3 52.0 - + + -
107G ASN 4.5 0.2 + - - -
108G VAL* 1.3 74.8 - - - +
110G VAL* 1.3 67.2 + - - +
111G SER* 3.5 24.0 - - - -
159G ALA 5.2 1.2 + - - -
160G ILE* 4.6 11.2 - - + +
161G GLY 3.7 10.4 + - - +
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Residues in contact with VAL 110 (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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99G PHE* 2.9 71.2 + - + -
108G VAL* 4.3 0.7 - - + +
109G PHE* 1.3 76.6 - - - +
111G SER* 1.3 63.3 + - - +
114G LEU* 4.0 22.7 - - + +
145G LEU* 4.0 19.1 - - + -
161G GLY 3.1 29.2 - - - +
162G SER* 3.8 21.3 - - - +
163G ILE* 4.5 2.9 - - + +
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Residues in contact with SER 111 (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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97G ILE 3.7 10.1 - - - -
109G PHE* 3.5 23.8 - - - -
110G VAL* 1.3 74.3 - - - +
112G THR* 1.3 66.6 + - - +
113G ARG* 3.5 24.8 + - - +
114G LEU* 3.4 17.1 + - - +
115G ILE* 3.1 21.9 - - - +
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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