Contacts of the helix formed by residues 1240 - 1244 (chain A) in PDB entry 5EPG
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 ALA1240 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A GLY* 5.1 9.4 - - - +
147A ASN 5.5 2.0 - - - +
148A LEU* 4.2 14.8 - - + -
154A TYR* 3.5 18.8 - - - -
433A ARG* 4.1 15.3 - - - +
435A GLU 5.3 0.7 - - - +
436A ASN* 5.7 1.3 - - + -
1209A ILE* 6.1 0.3 - - - +
1238A ILE 3.4 0.6 + - - -
1239A PRO* 1.3 76.3 - - - +
1241A ILE* 1.3 66.9 + - - +
1242A CYS* 3.2 20.4 - - - -
1243A ASP* 2.9 21.9 + - - +
1244A MET* 3.7 4.2 + - - +
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Residues in contact with ILE1241 (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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121A MET* 5.7 1.6 - - - -
141A THR* 4.7 13.2 - - - +
144A LEU* 3.5 52.9 - - + +
145A GLY* 5.6 3.3 - - - -
147A ASN 4.6 1.1 - - - +
154A TYR* 3.6 36.0 - - + +
157A ILE* 5.8 1.1 - - + -
158A ILE* 4.0 26.2 - - + -
561A HIS* 3.6 25.7 - - + +
1240A ALA* 1.3 75.6 - - - +
1242A CYS* 1.3 61.2 + - - +
1243A ASP 3.1 0.2 - - - -
1244A MET* 3.1 23.2 + - + +
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Residues in contact with CYS1242 (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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145A GLY* 6.5 0.2 - - - -
433A ARG* 4.4 1.6 - - - -
434A GLN* 3.9 21.2 - - + +
435A GLU* 3.6 50.7 - - + +
558A SER* 6.5 0.4 - - - -
561A HIS* 5.0 5.2 - - - -
1181A LYS* 3.6 22.7 + - - +
1240A ALA* 3.9 17.3 - - - -
1241A ILE* 1.3 78.3 - - - +
1243A ASP* 1.3 72.3 + - - +
1244A MET 3.5 0.4 - - - -
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Residues in contact with ASP1243 (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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433A ARG* 3.4 27.0 - - - +
434A GLN* 4.2 4.5 + - - +
1181A LYS* 5.8 0.9 - - - -
1182A ASN* 3.4 26.0 + - - +
1209A ILE* 5.4 0.7 - - - -
1212A MET* 3.5 25.0 - - + +
1217A ILE* 3.3 22.7 - - + +
1239A PRO* 4.4 0.7 - - + -
1240A ALA 2.9 29.0 + - - +
1241A ILE 3.1 1.0 - - - -
1242A CYS* 1.3 87.0 - - - +
1244A MET* 1.3 62.4 + - - +
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Residues in contact with MET1244 (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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153A GLY 3.4 21.1 - - - +
154A TYR* 4.1 15.0 - - + -
155A ARG* 4.2 13.7 - - - +
158A ILE* 3.9 26.9 - - + -
561A HIS* 3.9 38.9 + - + +
562A CYS 6.0 0.9 - - - +
1181A LYS* 4.4 6.8 + - - -
1182A ASN* 5.0 0.2 - - - -
1209A ILE* 4.1 13.2 - - + -
1240A ALA 3.7 4.8 + - - +
1241A ILE* 3.1 16.6 + - + +
1243A ASP* 1.3 77.8 - - - +
1245A PRO* 1.3 88.8 - - + +
1246A THR 3.3 1.9 + - - -
1248A LEU* 4.7 14.6 - - + -
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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