Contacts of the helix formed by residues 1044 - 1048 (chain B) in PDB entry 4E4N
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 PRO1044 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002B ARG 4.2 2.0 - - - +
1003B ASP* 3.4 23.3 - - - +
1007B ARG* 3.6 21.1 - - - +
1024B LEU* 4.6 6.5 - - + -
1042B ASP 3.8 5.1 - - - +
1043B SER* 1.4 78.2 - - - +
1045B VAL* 1.3 58.8 + - - +
1046B PHE 3.2 2.7 - - - -
1047B TRP* 2.9 41.8 + - + +
1048B TYR* 3.5 36.7 + - + +
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Residues in contact with VAL1045 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1098A GLN* 3.4 33.2 - - - +
1099A MET* 4.1 6.7 - - - -
1043B SER* 3.0 25.2 + - - +
1044B PRO* 1.3 71.4 - - - +
1046B PHE* 1.3 82.9 + - + +
1047B TRP 3.2 0.4 - - - -
1048B TYR* 3.2 25.4 + - - +
1053B LEU* 3.7 21.7 - - + +
1100B THR* 5.3 1.8 - - + -
1101B VAL* 3.9 22.9 - - + -
1104B LEU* 3.6 18.0 - - + +
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Residues in contact with PHE1046 (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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1044B PRO 3.0 1.6 + - - -
1045B VAL* 1.3 89.1 - - + +
1047B TRP* 1.3 75.9 + + + +
1048B TYR 3.5 0.7 - - - -
1065B TRP* 5.2 0.9 + - - -
1069B VAL* 3.8 14.2 - - - +
1084B PRO* 4.2 1.0 - - - +
1085B MET* 3.7 41.7 - - + +
1088B PHE* 3.5 57.1 - + + -
1089B LEU* 3.7 25.8 - - + -
1092B ILE* 4.2 8.1 - - + -
1100B THR* 3.9 15.0 - - + -
1104B LEU* 3.8 23.8 - - + -
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Residues in contact with TRP1047 (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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1003B ASP 6.3 0.7 - - - -
1004B LEU 3.3 26.7 - - - +
1005B ALA* 3.4 16.6 - - + +
1007B ARG* 5.5 5.6 - - - -
1044B PRO* 2.9 31.1 + - + +
1046B PHE* 1.3 98.5 - + + +
1048B TYR* 1.3 60.0 + - + +
1065B TRP* 3.4 15.7 - - - -
1066B SER* 2.7 30.9 + - - +
1069B VAL* 3.6 29.3 - - + +
1070B THR* 4.1 3.1 + - - -
1073B GLU* 2.8 41.9 + - - -
1083B SER* 5.5 2.5 - - - -
1084B PRO* 3.6 20.9 - - + -
1085B MET* 4.5 11.2 - - + -
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Residues in contact with TYR1048 (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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1002B ARG* 2.8 44.5 + - - -
1003B ASP* 5.2 0.4 - - - -
1024B LEU* 4.0 4.3 - - - +
1043B SER* 3.7 28.7 + - - -
1044B PRO* 3.5 33.0 - - + +
1045B VAL* 3.2 14.7 + - - +
1046B PHE 3.5 1.3 - - - -
1047B TRP* 1.3 85.5 - - + +
1049B ALA* 1.3 65.4 + - - +
1050B PRO* 3.9 0.3 - - - +
1052B CYS* 3.9 18.4 - - + -
1053B LEU* 3.8 30.4 - - + +
1058B PHE* 3.4 32.1 - + - -
1065B TRP* 3.4 13.3 + - - -
1066B SER* 4.5 6.5 - - - -
1108B LEU* 4.5 2.1 - - - +
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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