Contacts of the helix formed by residues 135 - 144 (chain A) in PDB entry 6B3I
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 SER 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A TYR* 4.2 0.7 - - - -
129A GLN* 3.5 14.7 + - - +
134A ARG* 1.3 74.1 - - - +
136A LEU* 1.3 66.2 + - - +
137A GLU* 3.6 10.7 + - - +
138A SER* 3.0 26.9 + - - -
139A ASP* 3.0 24.3 + - - +
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Residues in contact with LEU 136 (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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95A LEU* 3.9 19.1 - - + -
99A MET* 4.4 7.6 - - + -
109A LEU* 5.4 0.7 - - + -
113A LEU* 5.0 1.1 - - + -
121A ILE 5.5 0.2 - - - +
124A ILE* 3.8 30.5 - - + +
125A LYS* 4.1 21.6 + - + +
128A TYR* 3.6 49.5 - - + +
134A ARG 3.7 0.6 + - - -
135A SER* 1.3 71.7 + - - +
137A GLU* 1.3 62.2 + - - +
139A ASP 3.4 1.1 + - - +
140A VAL* 3.0 41.0 + - + +
156A LEU* 3.8 26.5 - - + -
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Residues in contact with GLU 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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125A LYS* 5.5 9.5 - - - +
135A SER* 3.2 9.7 + - - +
136A LEU* 1.3 78.7 - - - +
138A SER* 1.3 63.3 + - - +
140A VAL* 3.4 2.6 + - - +
141A LYS* 3.2 60.4 + - - +
153A VAL* 3.7 21.0 - - + +
156A LEU* 3.7 27.0 - - + +
157A GLN* 4.2 14.1 + - - +
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Residues in contact with SER 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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134A ARG* 6.1 1.5 - - - +
135A SER* 3.0 26.7 + - - -
137A GLU* 1.3 80.1 - - - +
139A ASP* 1.3 64.2 + - - +
141A LYS* 3.4 18.4 + - - +
142A GLY* 3.4 9.7 + - - -
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Residues in contact with ASP 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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99A MET* 3.6 22.2 - - + +
128A TYR* 2.7 24.8 + - + +
134A ARG* 3.0 43.8 + - - +
135A SER 3.0 13.7 + - - +
136A LEU 3.4 3.8 + - - +
138A SER* 1.3 77.0 + - - +
140A VAL* 1.3 65.3 + - - +
142A GLY* 3.4 2.2 + - - +
143A ASP* 3.2 23.9 + - - +
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Residues in contact with VAL 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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99A MET* 4.4 5.8 - - - -
109A LEU* 4.1 25.8 - - + -
113A LEU* 4.8 1.3 - - + -
136A LEU* 3.0 30.5 + - + +
137A GLU 3.7 5.2 - - - +
138A SER 3.2 0.2 - - - -
139A ASP* 1.3 78.6 - - - +
141A LYS* 1.3 52.9 + - - +
143A ASP* 4.6 0.4 - - - +
144A THR* 2.4 60.7 + - + +
152A LEU* 4.2 15.9 - - + -
153A VAL* 4.2 17.9 - - + -
156A LEU* 3.8 17.3 - - + -
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Residues in contact with LYS 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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137A GLU* 3.2 49.0 + - - +
138A SER* 3.8 9.0 - - - +
139A ASP 3.3 0.4 - - - -
140A VAL* 1.3 76.1 - - - +
142A GLY* 1.3 59.7 + - - +
144A THR* 3.8 14.5 - - - +
149A LYS* 3.7 37.6 + - - +
153A VAL* 3.8 20.4 - - + +
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Residues in contact with GLY 142 (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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101A GLY 5.3 0.2 - - - -
102A LEU* 4.7 14.4 + - - +
138A SER 3.4 10.0 + - - -
139A ASP* 3.4 4.0 + - - -
140A VAL 3.1 0.6 - - - -
141A LYS* 1.3 78.5 - - - +
143A ASP* 1.3 60.6 - - - +
144A THR 4.5 2.4 - - - +
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Residues in contact with ASP 143 (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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98A ALA 5.4 0.2 - - - +
99A MET* 3.3 29.2 - - + +
100A LYS 3.1 24.8 + - - -
101A GLY 2.8 26.8 + - - +
102A LEU* 3.0 25.6 - - - +
104A THR* 4.3 2.6 + - - -
106A GLU* 2.9 35.3 - - - +
109A LEU* 5.5 0.2 - - + -
139A ASP 3.2 9.8 + - - +
140A VAL* 3.2 3.6 + - - +
142A GLY* 1.3 77.7 - - - +
144A THR* 1.3 62.7 + - + +
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Residues in contact with THR 144 (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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102A LEU* 4.4 8.0 - - - +
106A GLU* 3.3 19.5 - - - +
109A LEU* 3.7 11.7 - - + -
140A VAL* 2.4 34.6 + - + +
141A LYS* 3.8 9.9 - - - +
142A GLY 4.5 1.2 - - - +
143A ASP* 1.3 79.8 - - - +
145A SER* 1.3 65.2 + - - +
148A LEU* 4.7 4.3 - - + -
149A LYS* 3.2 33.3 - - - +
152A LEU* 3.7 28.5 - - + -
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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