Contacts of the helix formed by residues 1044 - 1052 (chain B) in PDB entry 3CQC
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 ASN1044 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1042B ARG 2.8 9.0 + - - +
1043B ALA* 1.3 72.4 - - - +
1045B GLU* 1.3 78.8 + - - +
1046B TYR* 3.0 35.1 + - - +
1047B ASP* 3.2 26.9 + - - +
1048B PHE* 3.0 22.6 - - - -
1096B SER* 5.5 5.2 - - - -
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Residues in contact with GLU1045 (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 ASN* 1.3 94.4 + - - +
1046B TYR* 1.3 65.9 + - + +
1048B PHE* 3.0 9.2 + - - +
1049B LYS* 2.7 35.0 + - + +
1096B SER* 5.0 7.1 - - - -
1099B SER* 3.0 36.7 + - - +
1100B ILE* 4.3 17.1 - - + +
1103B LYS* 6.0 3.4 - - + -
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Residues in contact with TYR1046 (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 ASN* 3.0 30.3 - - - +
1045B GLU* 1.3 86.0 - - + +
1047B ASP* 1.3 62.1 + - - +
1049B LYS* 4.0 12.3 - - + -
1050B LYS* 2.7 49.4 + - + +
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Residues in contact with ASP1047 (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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1009B PRO* 3.7 14.0 - - - +
1035B TYR* 4.1 38.1 - - + +
1040B ASN* 3.0 27.9 + - - +
1042B ARG 4.8 0.5 - - - -
1043B ALA* 3.4 15.2 + - + -
1044B ASN* 3.2 32.0 + - - +
1045B GLU 3.3 0.4 - - - -
1046B TYR* 1.3 77.3 - - - +
1048B PHE* 1.3 60.6 + - + +
1050B LYS* 4.1 6.1 + - - +
1051B ALA* 3.3 22.9 + - - +
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Residues in contact with PHE1048 (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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1035B TYR 5.0 1.1 - - - -
1036B ILE* 3.2 44.9 - - + -
1043B ALA* 3.7 35.0 - - + -
1044B ASN 3.0 22.0 - - - -
1045B GLU* 3.0 7.8 + - - +
1047B ASP* 1.3 78.3 - - - +
1049B LYS* 1.3 65.8 + - - +
1050B LYS 3.2 0.9 - - - -
1051B ALA* 2.9 6.2 + - + +
1052B LEU* 2.9 36.9 + - + +
1073B ILE* 4.4 8.3 - - + -
1076B LYS 4.0 15.0 - - - -
1077B ALA* 4.2 26.7 - - + -
1080B ARG* 5.5 6.3 - - + -
1096B SER* 5.9 6.3 - - - -
1100B ILE* 4.5 15.7 - - + -
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Residues in contact with LYS1049 (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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1045B GLU* 2.7 20.7 + - + +
1046B TYR* 3.8 15.5 - - + +
1048B PHE* 1.3 70.9 - - - +
1050B LYS* 1.3 55.9 + - + +
1052B LEU* 3.3 16.6 + - + +
1053B ASP* 2.7 56.6 + - - +
1100B ILE* 5.2 9.0 - - + +
1103B LYS* 3.5 42.2 - - + +
1104B ILE* 5.0 8.7 - - + +
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Residues in contact with LYS1050 (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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1004B HIS* 3.8 26.6 - - + +
1007B THR* 3.1 24.2 + - + -
1035B TYR* 2.6 46.8 + - + -
1046B TYR* 2.7 33.3 + - + +
1047B ASP* 4.1 8.6 + - - +
1049B LYS* 1.3 72.2 - - + +
1051B ALA* 1.3 60.8 + - - +
1053B ASP* 2.9 28.2 + - - +
1054B LEU* 3.1 18.4 + - - +
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Residues in contact with ALA1051 (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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1032B ILE* 2.7 48.0 - - + +
1035B TYR* 4.7 11.2 - - + -
1036B ILE* 5.7 1.3 - - + -
1047B ASP 3.3 16.0 + - - +
1048B PHE* 2.9 21.9 + - + +
1050B LYS* 1.3 80.0 - - - +
1052B LEU* 1.3 59.3 + - + +
1053B ASP 3.2 0.6 + - - -
1054B LEU* 3.6 1.1 + - - -
1055B LEU* 3.0 13.9 - - - +
1073B ILE* 5.1 4.9 - - + -
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Residues in contact with LEU1052 (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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1048B PHE* 2.9 34.7 + - + +
1049B LYS* 3.8 11.2 - - + +
1050B LYS 3.1 0.4 - - - -
1051B ALA* 1.3 78.1 - - + +
1053B ASP* 1.3 64.0 + - - +
1055B LEU* 3.4 29.5 - - + +
1070B LYS* 4.2 26.4 - - + -
1073B ILE* 3.3 45.8 - - + -
1074B LEU* 4.8 7.0 - - + -
1100B ILE* 5.4 6.3 - - + -
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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