Contacts of the helix formed by residues 130 - 140 (chain B) in PDB entry 3A4S
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 GLN 130 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B LEU 3.5 9.9 + - - +
82B PHE* 3.8 13.0 - - - -
83B HIS 2.7 43.8 + - - +
84B PRO* 2.9 6.1 + - + +
86B VAL 3.0 21.3 + - - +
87B TYR* 4.9 2.4 + - - -
88B PRO* 5.1 14.6 - - + +
128B PRO* 5.3 0.7 - - - -
129B ALA* 1.3 76.8 - - - +
131B ALA* 1.3 65.3 + - - +
132B GLU* 3.3 26.8 - - + +
133B ALA* 3.8 14.9 + - - +
134B TYR* 3.1 24.8 + - - +
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Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B PRO* 6.1 0.6 - - - +
129B ALA 3.9 3.2 + - - -
130B GLN* 1.3 71.4 - - - +
132B GLU* 1.3 60.9 + - - +
134B TYR* 3.7 6.2 - - - +
135B THR* 2.8 40.6 + - - +
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PHE* 3.6 19.1 - - + -
130B GLN* 3.3 20.5 - - + +
131B ALA* 1.3 81.5 - - - +
133B ALA* 1.3 67.0 + - - +
135B THR* 3.6 3.5 - - - -
136B ILE* 2.9 30.0 + - + +
147B ARG* 2.6 32.7 + - - +
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Residues in contact with ALA 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PHE* 3.4 29.6 - - + -
83B HIS* 3.5 14.1 - - - +
84B PRO* 3.4 32.3 - - + -
130B GLN* 3.8 9.5 - - - +
131B ALA 3.6 0.2 - - - -
132B GLU* 1.3 79.0 - - - +
134B TYR* 1.3 57.1 + - - +
136B ILE* 3.9 0.2 - - - +
137B TYR* 2.9 31.4 + - - +
144B TYR* 3.7 4.6 - - + -
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Residues in contact with TYR 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B PRO* 4.3 7.8 - - + +
125B ILE* 3.4 32.0 + - + +
128B PRO* 3.3 40.5 - - + +
130B GLN 3.1 20.8 + - - +
131B ALA* 3.7 5.6 - - - +
132B GLU 3.1 0.6 - - - -
133B ALA* 1.3 76.2 - - - +
135B THR* 1.3 72.3 + - - +
137B TYR* 3.1 7.3 + - - +
138B CYS* 2.9 50.2 + - + +
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Residues in contact with THR 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ALA* 2.8 30.2 + - - +
132B GLU* 3.6 3.6 - - - -
134B TYR* 1.3 79.1 - - - +
136B ILE* 1.3 66.4 + - + +
138B CYS* 2.9 6.6 + - - +
139B GLN* 2.8 60.9 + - - +
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Residues in contact with ILE 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B PHE* 4.0 9.2 - - + -
132B GLU* 2.9 23.1 + - + +
133B ALA 3.9 3.1 - - - +
135B THR* 1.3 77.9 - - + +
137B TYR* 1.3 57.2 + - - +
139B GLN* 4.4 6.3 - - - +
140B ASN* 2.8 43.1 + - + +
143B GLU* 3.9 21.8 - - + +
144B TYR* 3.6 33.0 - - + +
147B ARG* 3.6 30.7 - - - +
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Residues in contact with TYR 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B PRO* 4.6 2.0 - - + -
123B PRO* 4.1 19.5 + - + +
125B ILE* 3.4 38.2 - - + +
133B ALA 2.9 21.2 + - - +
134B TYR* 3.1 7.6 + - - +
136B ILE* 1.3 76.2 - - - +
138B CYS* 1.3 66.5 + - - +
139B GLN 3.8 0.2 + - - -
140B ASN 4.8 0.2 - - - -
141B ARG* 3.4 58.3 + - - +
144B TYR* 3.2 46.2 - + + -
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Residues in contact with CYS 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ILE* 4.2 11.0 - - - -
134B TYR* 2.9 56.9 + - + +
135B THR* 2.9 6.0 + - - +
137B TYR* 1.3 82.8 - - - +
139B GLN* 1.3 58.8 + - + +
140B ASN 3.8 0.2 - - - -
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Residues in contact with GLN 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B THR* 2.8 48.7 + - + +
136B ILE* 4.4 3.9 - - - +
138B CYS* 1.3 79.5 - - + +
140B ASN* 1.3 66.0 + - + +
141B ARG 4.2 0.2 - - - -
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Residues in contact with ASN 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ILE* 2.8 19.8 + - + +
138B CYS 3.8 0.2 - - - -
139B GLN* 1.3 83.4 - - + +
141B ARG* 1.3 64.2 + - - +
142B VAL* 3.1 13.6 + - - +
143B GLU* 3.1 44.3 + - + +
144B TYR 3.1 6.9 + - - -
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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