Contacts of the helix formed by residues 132 - 137 (chain B) in PDB entry 3SAJ
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 ASP 132 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B TYR* 1.3 93.8 - - - +
133B ALA* 1.3 64.8 + - - +
134B ASP* 3.4 6.2 + - - +
135B ARG* 2.3 37.7 + - - +
158B ASN* 3.7 3.8 - - - -
159B ILE* 3.6 22.5 - - + +
160B LEU* 5.0 1.3 - - + +
185B ASP 3.5 2.4 + - - -
186B CYS* 3.4 17.9 - - + +
187B GLU* 3.5 17.6 + - - +
190B ARG* 4.4 14.6 - - - +
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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
----------------------------------------------------------
72B GLU* 4.8 5.4 - - - +
73B ARG* 3.3 40.2 - - - +
131B TYR* 5.1 1.1 - - - -
132B ASP* 1.3 75.5 - - - +
134B ASP* 1.3 64.6 + - - +
135B ARG 3.2 0.7 + - - -
136B GLY* 3.2 13.2 + - - +
137B LEU 4.0 2.3 + - - -
158B ASN* 3.9 10.1 + - - +
160B LEU* 4.5 20.6 - - + +
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Residues in contact with ASP 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B TYR* 6.6 0.2 - - - -
72B GLU* 3.8 12.0 - - - +
73B ARG* 3.3 39.7 + - - +
95B PHE* 3.3 47.8 - - + +
132B ASP* 3.4 3.4 + - - +
133B ALA* 1.3 77.2 - - - +
135B ARG* 1.3 69.8 + - + +
137B LEU* 3.1 30.0 - - - +
138B SER 4.3 0.5 + - - -
187B GLU* 5.0 5.4 - - - +
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Residues in contact with ARG 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B PHE* 3.4 37.7 - - + -
108B ARG* 4.0 3.6 - - - +
129B TYR* 4.1 7.6 - - - +
131B TYR* 4.4 5.6 - - + -
132B ASP* 2.3 44.9 + - - +
133B ALA 3.2 0.8 - - - -
134B ASP* 1.3 81.9 + - - +
136B GLY* 1.3 59.9 + - - +
137B LEU 3.0 2.5 - - - -
139B VAL* 2.9 27.7 + - + +
140B LEU* 2.8 26.2 + - - -
185B ASP* 2.5 45.2 + - - -
186B CYS* 3.7 18.3 + - - +
187B GLU* 3.0 28.3 + - - +
213B ALA 5.0 2.2 + - - -
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Residues in contact with GLY 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B TYR* 4.2 11.8 - - - -
132B ASP 4.0 3.0 + - - -
133B ALA 3.2 11.6 + - - -
135B ARG* 1.3 78.0 - - - +
137B LEU* 1.3 61.9 + - - +
138B SER* 3.4 1.4 + - - -
140B LEU* 3.7 24.4 + - - +
141B GLN* 4.4 6.9 + - - +
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Residues in contact with LEU 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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73B ARG* 4.7 15.9 - - + -
76B VAL* 4.5 21.8 - - + -
77B ASN* 5.8 1.1 - - - +
97B VAL* 4.7 16.6 - - + -
98B ASP* 5.9 4.7 - - + +
99B THR* 5.9 7.0 - - - +
133B ALA 4.0 3.5 + - - +
134B ASP* 3.1 17.6 + - - +
136B GLY* 1.3 77.7 - - - +
138B SER* 1.3 62.2 + - - +
141B GLN* 5.5 2.6 - - - +
73D ARG* 3.9 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