Contacts of the strand formed by residues 126 - 135 (chain E) in PDB entry 6S7T
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 LYS 126 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34E GLU* 4.2 17.3 - - + -
54E VAL* 3.7 23.5 - - + +
55E LEU 3.3 3.4 - - - -
56E ALA* 3.8 18.4 - - + -
124E GLY 5.7 0.9 - - - -
125E ALA* 1.3 78.8 - - - +
127E ILE* 1.3 65.0 + - - +
128E SER* 5.5 0.4 + - - -
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Residues in contact with ILE 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E VAL* 3.2 6.0 - - - -
55E LEU* 2.9 61.7 + - + +
88E VAL* 6.1 2.5 - - + -
117E LEU* 3.5 44.0 - - + -
119E VAL 5.4 4.5 - - - +
121E LEU* 4.2 25.4 - - + -
125E ALA* 5.8 1.1 - - + -
126E LYS* 1.3 78.3 - - - +
128E SER* 1.3 62.6 + - - +
129E VAL* 3.7 6.3 + - + +
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Residues in contact with SER 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E VAL 3.9 3.6 - - - -
54E VAL* 3.8 20.1 - - - +
88E VAL* 3.4 27.9 - - - +
89E LYS* 4.1 8.1 + - - +
126E LYS 4.4 0.5 + - - -
127E ILE* 1.3 72.7 - - - +
129E VAL* 1.3 60.9 + - - +
130E ILE* 5.3 2.4 - - - +
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Residues in contact with VAL 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E ALA 3.9 0.2 - - - +
52E GLU* 3.6 3.1 - - - +
53E VAL* 2.9 58.5 + - + +
55E LEU* 4.8 5.2 - - + -
69E PHE* 4.1 30.3 - - + -
86E VAL* 3.4 28.7 - - + -
87E GLN 4.2 2.9 - - - +
88E VAL* 4.8 3.8 - - + +
94E GLU* 4.2 11.0 - - - +
117E LEU* 5.4 2.2 - - + -
127E ILE* 3.7 9.4 + - + +
128E SER* 1.3 74.0 - - - +
130E ILE* 1.3 65.9 + - - +
131E VAL* 4.5 9.2 - - + -
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Residues in contact with ILE 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E THR* 3.8 13.9 - - + -
51E ALA 3.5 5.4 - - - +
52E GLU* 4.4 24.0 - - + +
85E GLY 3.9 0.3 - - - +
86E VAL* 3.3 7.1 - - - +
87E GLN* 2.9 51.0 + - + +
89E LYS* 5.1 10.3 - - - +
90E GLY 5.3 4.5 - - - +
128E SER* 5.3 2.5 - - - +
129E VAL* 1.3 80.0 - - - +
131E VAL* 1.3 64.5 + - - +
132E GLU* 3.8 31.8 + - + +
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Residues in contact with VAL 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E VAL* 3.8 2.4 - - - +
50E THR* 3.4 1.7 - - - -
51E ALA* 2.8 48.7 + - + +
53E VAL* 5.3 1.6 - - + -
69E PHE* 5.3 1.8 - - + -
71E LEU* 4.0 40.8 - - + -
84E LEU* 4.5 1.6 - - + -
85E GLY 3.7 6.5 - - - +
86E VAL* 4.3 10.8 - - + -
129E VAL* 4.5 16.2 - - + -
130E ILE* 1.3 76.7 - - - +
132E GLU* 1.3 62.0 + - - +
133E THR* 4.2 19.1 - - + -
162E PHE* 5.1 11.9 - - + -
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Residues in contact with GLU 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E VAL 3.5 3.8 - - - -
50E THR* 3.4 32.9 + - + +
83E HIS* 4.0 4.0 + - - +
84E LEU* 3.9 0.7 - - - -
85E GLY* 3.0 35.6 + - - +
87E GLN* 4.5 25.5 + - + +
130E ILE* 3.8 20.2 - - + +
131E VAL* 1.3 72.5 - - - +
133E THR* 1.3 65.1 + - - +
134E VAL* 5.7 0.4 - - - -
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Residues in contact with THR 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E ALA 4.0 0.2 - - - +
48E LYS* 3.4 4.5 - - - +
49E VAL* 2.9 58.3 + - + +
73E LEU* 5.2 2.9 - - + -
81E LEU* 4.2 11.4 - - + -
83E HIS 3.8 4.3 - - - -
84E LEU* 3.7 31.4 - - + -
131E VAL* 4.2 13.0 - - + -
132E GLU* 1.3 78.1 - - - +
134E VAL* 1.3 64.2 + - - +
135E TYR* 3.4 19.6 + - - +
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Residues in contact with VAL 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E LEU* 3.6 35.4 - - + -
47E ALA 3.6 2.9 - - - +
48E LYS* 3.7 19.1 - - + -
81E LEU* 4.0 3.6 - - - +
82E ALA* 3.1 30.7 + - + +
83E HIS 3.5 12.1 + - - +
132E GLU* 5.7 1.1 - - + -
133E THR* 1.3 77.8 - - - +
135E TYR* 1.3 66.0 + - - +
417E VAL* 3.8 15.3 - - + -
419E GLN* 3.4 35.9 - - - +
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Residues in contact with TYR 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E LEU* 3.2 7.2 - - - +
47E ALA* 2.8 45.6 + - + +
49E VAL* 4.1 19.8 - - + +
73E LEU* 3.8 21.8 - - + +
74E GLU* 4.0 13.8 + - - -
77E LEU* 3.8 46.4 - - + -
80E ARG* 3.5 15.9 - - + +
81E LEU* 3.6 20.4 - - + -
133E THR* 3.4 26.3 + - - +
134E VAL* 1.3 73.4 - - - +
136E THR* 1.3 62.1 + - - +
138E VAL* 4.2 21.6 - - + +
156E PHE* 6.3 2.5 - + - -
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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