Contacts of the helix formed by residues 136 - 141 (chain A) in PDB entry 6DWZ
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 ASN 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A VAL* 1.3 70.9 - - - +
137A VAL* 1.3 59.4 + - - +
138A GLU* 3.3 28.6 - - - +
139A GLU* 3.3 38.4 + - - +
140A LEU* 3.9 9.9 + - - +
83E LEU* 3.3 29.1 - - + +
84E LYS 3.1 14.4 + - - +
85E THR* 4.6 11.9 + - - +
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Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A VAL* 4.1 5.8 - - + +
136A ASN* 1.3 74.1 - - - +
138A GLU* 1.3 58.4 + - - +
139A GLU 3.4 0.2 - - - -
140A LEU* 3.5 29.4 - - + -
141A LEU* 2.6 60.5 + - + +
118E ILE* 4.3 6.1 - - + -
121E ILE* 3.9 15.9 - - + -
122E LYS* 3.1 48.0 - - + +
125E ILE* 4.1 10.8 - - + -
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Residues in contact with GLU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ASN* 3.3 17.9 - - - +
137A VAL* 1.3 85.5 + - - +
139A GLU* 1.3 62.5 + - + +
141A LEU* 3.1 21.7 - - - +
83E LEU* 5.4 1.0 - - - +
118E ILE* 5.6 9.5 - - + +
122E LYS* 3.4 26.3 + - - -
7G G 4.7 1.4 + - - +
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Residues in contact with GLU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ASN* 3.3 27.6 + - - +
138A GLU* 1.3 76.3 - - + +
140A LEU* 1.3 66.4 + - - +
141A LEU 3.4 5.5 - - - +
85E THR* 4.6 16.0 + - + +
91E LYS* 3.4 27.5 + - - +
7G G 3.6 7.1 + - - -
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Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A PHE* 5.1 0.2 - - + -
124A PHE* 4.0 21.3 - - + -
127A VAL* 4.7 11.0 - - + -
135A VAL* 5.8 2.7 - - + -
136A ASN* 3.9 7.5 + - - +
137A VAL* 3.2 35.9 + - + +
139A GLU* 1.3 80.2 - - - +
141A LEU* 1.3 65.2 + - + +
142A PRO* 3.5 5.9 - - - +
86E VAL* 3.9 32.8 - - + +
90E CYS* 4.6 5.6 - - - +
91E LYS* 4.4 21.7 - - - +
94E ALA* 3.8 25.0 - - + +
95E ILE* 4.8 0.5 - - - +
125E ILE* 4.4 10.3 - - + -
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A PHE* 4.0 27.4 - - + -
137A VAL* 2.6 40.3 + - + +
138A GLU* 3.1 16.7 - - - +
139A GLU 3.5 0.2 - - - +
140A LEU* 1.3 73.6 - - + +
142A PRO* 1.3 80.1 - - + +
94E ALA* 5.3 0.7 - - + -
98E CYS* 4.2 8.5 - - - -
112E VAL* 4.8 8.5 - - + +
117E PHE* 4.6 17.9 - - + -
118E ILE* 3.8 28.5 - - + -
121E ILE* 4.6 7.4 - - + -
7G G 3.1 15.8 + - - -
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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