Contacts of the helix formed by residues 139 - 143 (chain A) in PDB entry 1D2G
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 139 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ALA* 3.8 20.5 + - - +
117A TRP* 3.2 10.0 - - - -
135A CYS* 4.5 4.0 + - - -
136A LEU 3.5 17.9 + - - -
137A GLY* 4.2 4.2 + - - -
138A ASN* 1.3 73.6 - - - +
140A PHE* 1.3 66.8 + - - +
141A ALA 3.0 2.7 - - - -
142A HIS* 3.0 32.2 + - - +
173A ASP* 4.4 1.4 + - - -
15B GLU* 3.5 31.1 + - - +
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Residues in contact with PHE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A TRP* 3.5 24.8 - + - -
135A CYS* 4.2 7.4 + - - -
138A ASN* 3.5 0.8 - - - +
139A SER* 1.3 77.7 - - - +
141A ALA* 1.3 59.0 + - - +
142A HIS 3.0 5.0 + - - -
143A LEU* 3.1 22.6 + - + +
153A HIS* 3.5 33.9 - + + -
156A ALA* 3.9 19.1 - - + -
157A LEU* 3.5 27.8 - - + -
160A ILE* 4.2 9.9 - - + -
172A ILE* 4.0 28.3 - - + -
173A ASP 4.6 7.5 + - - +
174A HIS* 6.2 0.4 - - + -
245A HIS* 3.7 27.7 - + - -
250A PHE* 3.8 15.5 - + + -
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Residues in contact with ALA 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ASN* 3.4 34.2 - - - +
139A SER 3.0 0.4 - - - -
140A PHE* 1.3 78.6 - - - +
142A HIS* 1.3 59.9 + - - +
143A LEU 3.2 1.7 + - - -
173A ASP 5.5 0.8 + - - -
174A HIS* 5.5 2.8 - - + +
177A TYR* 3.9 14.8 - - + +
242A TYR* 3.2 9.8 - - + -
243A TYR* 2.8 39.6 + - - +
245A HIS* 4.2 14.8 + - - +
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Residues in contact with HIS 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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117A TRP* 5.1 0.7 - - + -
137A GLY 5.6 1.1 + - - -
138A ASN 4.0 6.0 + - - -
139A SER* 3.0 23.8 + - - +
140A PHE 3.0 0.8 - - - -
141A ALA* 1.3 79.7 - - - +
143A LEU* 1.3 56.7 + - - +
144A PRO* 3.2 14.2 - - - +
240A LEU* 5.0 7.4 - - + +
241A SER 4.4 12.9 - - - +
242A TYR* 3.7 33.5 + + - -
14B ALA* 4.1 16.7 - - + +
15B GLU* 2.6 63.5 + - + +
17B ILE* 3.9 19.5 - - + +
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Residues in contact with LEU 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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116A ASN* 5.9 0.4 - - - +
117A TRP* 3.9 19.9 - - + -
118A LEU* 4.2 22.7 - - + -
139A SER 4.4 0.2 + - - -
140A PHE* 3.1 18.1 + - + +
141A ALA 4.1 1.5 - - - +
142A HIS* 1.3 76.9 - - - +
144A PRO* 1.3 79.0 - - + +
152A GLU* 3.8 30.1 - - + +
153A HIS* 2.9 34.6 + - + +
156A ALA* 3.8 17.9 - - + -
243A TYR* 3.7 10.2 - - - +
16B GLY 5.3 1.3 - - - +
17B ILE* 4.4 14.1 - - + +
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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