Contacts of the helix formed by residues 1038 - 1051 (chain B) in PDB entry 4DAJ
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 SER1038 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1025B TYR* 3.9 3.1 - - - -
1036B SER* 3.1 18.9 + - - +
1037B PRO* 1.3 82.0 - - - +
1039B LEU* 1.3 64.4 + - - +
1040B ASN* 3.4 15.5 + - - +
1041B ALA* 3.8 14.8 + - - +
1042B ALA* 3.5 10.6 + - - +
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Residues in contact with LEU1039 (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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1017B ILE* 4.1 27.6 - - + -
1025B TYR* 4.3 31.6 - - + +
1037B PRO 3.5 3.4 + - - -
1038B SER* 1.3 69.6 + - - +
1040B ASN* 1.3 66.1 + - - +
1041B ALA 3.1 2.0 - - - -
1042B ALA* 3.2 5.1 + - + +
1043B LYS* 2.9 30.4 + - + +
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Residues in contact with ASN1040 (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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1038B SER* 3.4 9.5 + - - +
1039B LEU* 1.3 78.8 - - - +
1041B ALA* 1.3 57.5 + - - +
1043B LYS* 3.6 7.3 + - - +
1044B SER* 2.9 28.8 + - - -
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Residues in contact with ALA1041 (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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1034B THR* 4.2 5.8 - - + +
1036B SER* 3.4 25.8 - - - +
1038B SER* 3.6 13.2 + - - +
1039B LEU 3.1 0.6 - - - -
1040B ASN* 1.3 76.2 - - - +
1042B ALA* 1.3 64.9 - - - +
1044B SER* 3.0 8.8 + - - -
1045B GLU* 2.9 26.6 + - + +
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Residues in contact with ALA1042 (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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1017B ILE* 5.5 0.7 - - + -
1025B TYR* 3.8 29.4 - - + -
1033B LEU* 3.7 27.4 - - + +
1034B THR* 3.7 17.8 - - + +
1038B SER 3.5 2.3 + - - +
1039B LEU* 3.2 13.8 + - + +
1041B ALA* 1.3 78.1 - - - +
1043B LYS* 1.3 58.1 + - - +
1045B GLU* 3.2 5.8 + - - +
1046B LEU* 2.9 26.3 + - - +
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Residues in contact with LYS1043 (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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1017B ILE* 4.9 11.9 - - + +
1039B LEU* 2.9 24.3 + - + +
1040B ASN* 3.9 6.5 - - - +
1042B ALA* 1.3 76.0 - - - +
1044B SER* 1.3 57.5 + - - +
1046B LEU* 3.2 9.6 + - + +
1047B ASP* 2.9 47.9 + - - +
1053B ASN* 5.3 2.5 - - - +
1054B THR* 4.7 7.2 - - - +
1055B ASN* 3.4 49.5 + - - +
1056B GLY* 4.6 5.8 - - - +
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Residues in contact with SER1044 (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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1040B ASN 2.9 16.1 + - - -
1041B ALA* 3.0 12.8 + - - -
1043B LYS* 1.3 74.9 - - - +
1045B GLU* 1.3 60.0 + - - +
1047B ASP* 3.2 13.4 + - - +
1048B LYS* 2.9 26.7 + - - +
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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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1033B LEU* 4.2 32.6 - - + +
1034B THR* 4.8 7.0 - - - -
1041B ALA* 2.9 17.1 + - + +
1042B ALA 3.6 7.9 - - - +
1044B SER* 1.3 76.3 - - - +
1046B LEU* 1.3 57.5 + - - +
1048B LYS* 3.2 13.5 + - - +
1049B ALA* 2.9 29.5 + - - +
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Residues in contact with LEU1046 (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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1017B ILE* 4.2 18.8 - - + -
1027B ILE* 3.7 40.6 - - + -
1031B HIS* 5.8 1.1 - - + -
1033B LEU* 4.8 11.8 - - + +
1042B ALA 2.9 13.8 + - - +
1043B LYS* 3.3 11.7 - - - +
1045B GLU* 1.3 77.6 - - - +
1047B ASP* 1.3 55.9 + - - +
1049B ALA* 4.5 4.7 - - + +
1050B ILE* 2.9 48.1 + - + +
1052B ARG 4.9 0.2 - - - -
1054B THR* 3.0 33.0 - - + +
1056B GLY* 4.8 2.9 - - - -
1058B ILE* 4.5 2.5 - - + -
1066B LEU* 5.0 6.3 - - + -
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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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1043B LYS* 2.9 35.7 + - - +
1044B SER* 3.2 9.9 + - - +
1046B LEU* 1.3 74.0 - - - +
1048B LYS* 1.3 59.2 + - - +
1051B GLY* 2.8 29.6 + - - -
1052B ARG 3.2 21.9 + - - +
1053B ASN* 3.5 22.7 + - - +
1054B THR* 3.4 20.4 + - - -
1055B ASN 4.6 0.5 + - - -
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Residues in contact with LYS1048 (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 SER 2.9 12.8 + - - +
1045B GLU* 3.2 21.3 + - - +
1047B ASP* 1.3 78.9 - - - +
1049B ALA* 1.3 61.0 + - - +
1051B GLY* 3.8 6.1 + - - -
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Residues in contact with ALA1049 (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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1031B HIS* 4.7 17.0 - - + +
1033B LEU* 6.3 0.4 - - + -
1045B GLU 2.9 16.1 + - - +
1046B LEU* 4.0 6.3 - - + +
1048B LYS* 1.3 77.0 - - - +
1050B ILE* 1.3 68.3 + - + +
1051B GLY* 4.5 0.3 - - - -
1066B LEU* 4.9 14.3 - - + +
1069B GLN* 5.4 8.9 + - - +
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Residues in contact with ILE1050 (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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1046B LEU* 2.9 36.5 + - + +
1049B ALA* 1.3 77.4 - - - +
1051B GLY* 1.3 58.7 + - - +
1052B ARG* 3.7 25.5 - - + +
1054B THR* 3.7 17.9 - - + -
1058B ILE* 4.7 2.5 - - + -
1062B GLU* 3.4 38.4 - - + +
1066B LEU* 3.9 30.1 - - + -
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Residues in contact with GLY1051 (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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522A LYS* 5.4 5.5 + - - -
1047B ASP 2.8 15.9 + - - -
1048B LYS 4.2 6.1 - - - -
1049B ALA 3.3 1.4 - - - -
1050B ILE* 1.3 78.3 - - - +
1052B ARG* 1.3 59.6 + - - +
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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