Contacts of the strand formed by residues 128 - 132 (chain G) in PDB entry 6D6Q
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 ILE 128 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124G LYS* 4.7 0.7 - - - -
125G SER* 2.7 49.0 + - - +
126G GLY 5.0 0.2 - - - -
127G ASP* 1.3 86.0 - - + +
129G PHE* 1.3 59.7 + - - +
130G LYS* 4.5 13.5 - - - +
140G SER* 3.4 20.0 - - - +
141G LEU 2.9 22.7 - - - +
142G SER* 4.2 12.3 - - - -
175G GLU* 5.8 2.0 - - - +
81I ARG* 4.6 17.7 - - - +
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Residues in contact with PHE 129 (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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121G VAL* 3.7 19.1 - - + -
123G ALA 3.1 15.3 - - - +
124G LYS* 3.5 19.3 - - + +
127G ASP 4.9 6.3 - - - -
128G ILE* 1.3 75.6 - - - +
130G LYS* 1.3 61.9 + - - +
131G VAL 3.9 1.3 + - - -
140G SER* 4.7 0.2 - - - -
141G LEU* 3.0 56.1 + - + +
143G TYR* 4.7 14.1 - - + -
146G PHE* 3.3 37.9 - + - -
155G PRO* 5.2 2.7 - - + -
157G VAL* 3.7 27.6 - - + -
163G ILE* 3.8 7.4 - - + -
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Residues in contact with LYS 130 (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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121G VAL* 3.5 2.1 - - - -
122G THR* 2.6 34.7 + - - -
123G ALA* 2.8 26.3 + - + +
125G SER* 4.5 20.2 - - - +
128G ILE* 4.5 10.7 - - + +
129G PHE* 1.3 74.1 - - - +
131G VAL* 1.3 52.7 + - - +
138G PRO* 4.7 22.4 + - + +
139G ALA 3.3 12.3 - - - +
140G SER* 4.4 15.1 - - - +
175G GLU* 4.0 24.2 + - - -
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Residues in contact with VAL 131 (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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119G GLY* 3.4 10.3 - - - -
120G ILE 3.0 40.6 - - - +
121G VAL* 3.6 8.5 - - + +
122G THR* 4.0 2.0 - - - -
129G PHE 4.9 0.2 - - - +
130G LYS* 1.3 74.3 - - - +
132G ASP* 1.3 63.3 + - - +
133G VAL* 4.8 0.2 - - + -
138G PRO* 3.6 4.1 - - - +
139G ALA* 2.9 42.9 + - + +
141G LEU* 4.5 15.7 - - + -
163G ILE* 4.5 10.5 - - + -
178G MET* 3.3 33.9 - - + -
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Residues in contact with ASP 132 (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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4A THR* 3.3 25.5 + - - -
5A PRO* 3.5 15.8 - - + +
63D GLU* 5.7 1.7 - - - +
119G GLY* 3.2 9.7 - - - -
120G ILE* 2.9 35.0 + - + +
122G THR* 3.5 15.8 + - - +
131G VAL* 1.3 75.4 - - - +
133G VAL* 1.3 78.1 + - - +
134G GLY* 2.9 16.2 + - - -
135G GLY 4.4 2.4 + - - +
137G GLU 5.3 1.7 - - - +
138G PRO* 4.6 10.2 - - + +
236G ARG* 4.1 5.8 + - - +
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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