Contacts of the helix formed by residues 138 - 144 (chain A) in PDB entry 2I6A
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 LEU 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ASN* 4.0 17.7 - - - +
16A LEU* 3.7 32.3 - - + -
40A LEU* 4.3 22.9 - - + -
121A GLY* 3.1 11.8 - - - -
136A ALA* 3.6 4.5 + - + +
137A ASN* 1.3 71.2 - - - +
139A ALA* 1.3 56.9 + - - +
140A ALA 2.9 1.7 + - - -
141A ALA* 2.7 25.8 + - - +
142A ASN* 4.0 20.2 - - + +
173A THR* 3.7 23.1 - - - +
174A VAL* 3.8 19.3 - - + -
500A 5I5 4.0 11.7 - - - +
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Residues in contact with ALA 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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118A GLN* 3.4 25.2 + - - +
119A PRO* 3.3 28.0 - - + +
120A THR 4.0 5.2 - - - +
137A ASN* 3.2 26.4 - - - +
138A LEU* 1.3 74.4 - - - +
140A ALA* 1.3 65.0 + - - +
142A ASN* 3.2 20.4 + - - +
143A CYS* 3.9 2.1 - - - -
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Residues in contact with ALA 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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89A CYS* 3.0 12.2 - - - -
90A ILE* 3.7 4.3 - - - -
91A GLY 3.6 11.7 - - - +
115A GLN* 3.6 22.7 - - - +
118A GLN* 3.6 5.7 - - - +
119A PRO 2.9 26.0 + - - +
120A THR* 3.8 4.0 - - - +
138A LEU 2.9 2.6 + - - -
139A ALA* 1.3 74.6 - - - +
141A ALA* 1.3 59.1 + - - +
142A ASN 2.9 6.5 - - - -
143A CYS* 2.6 28.7 + - - -
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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
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14A ASN* 3.6 43.2 - - + +
15A PRO* 3.9 8.7 - - + +
16A LEU* 3.8 12.8 - - + -
89A CYS* 3.4 14.7 + - - +
121A GLY 4.6 2.0 - - - +
138A LEU* 2.7 19.5 + - + +
140A ALA* 1.3 72.9 - - - +
142A ASN* 1.3 59.3 + - - +
143A CYS 3.4 1.0 + - - -
144A TYR* 3.8 9.2 + - - +
171A PHE* 4.4 2.3 - - - -
174A VAL* 3.5 13.6 - - - +
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Residues in contact with ASN 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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118A GLN* 5.5 3.3 + - - +
138A LEU* 4.0 20.0 + - + +
139A ALA 3.2 14.8 + - - +
140A ALA 2.9 0.4 - - - -
141A ALA* 1.3 78.9 - - - +
143A CYS* 1.3 59.9 + - - +
144A TYR 3.3 3.0 + - - +
145A LYS* 5.5 2.9 - - - -
173A THR* 3.9 13.5 + - - -
174A VAL* 3.6 33.3 + - - +
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Residues in contact with CYS 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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89A CYS* 3.4 19.3 - - - -
113A TYR* 5.0 7.0 - - + -
115A GLN* 3.9 12.1 - - + +
118A GLN* 3.8 19.1 - - - -
139A ALA 3.9 2.0 - - - -
140A ALA* 2.6 49.3 + - - -
142A ASN* 1.3 76.2 - - - +
144A TYR* 1.3 63.3 + - - +
145A LYS* 3.2 20.1 + - - +
148A LYS* 5.0 2.3 - - - +
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Residues in contact with TYR 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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12A MET* 3.2 27.2 - - + +
87A PHE* 3.8 2.1 - - - -
88A GLY* 3.9 36.3 - - - -
89A CYS* 3.9 9.7 - - + +
113A TYR* 4.5 6.7 - - + -
141A ALA 3.8 9.6 + - - +
142A ASN 3.3 3.9 - - - +
143A CYS* 1.3 76.7 - - - +
145A LYS* 1.3 72.8 + - - +
149A HIS* 2.8 44.2 + + + -
150A LEU* 3.1 20.9 - - + +
171A PHE* 3.7 26.2 - + + -
174A VAL* 4.2 7.2 - - + +
175A SER* 3.6 17.7 + - - -
178A SER* 3.5 20.4 - - - -
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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