Contacts of the helix formed by residues 1037 - 1047 (chain A) in PDB entry 5XJY
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 MET1037 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1034A SER* 6.4 1.1 - - - -
1035A GLY 2.7 11.9 + - - +
1036A GLY* 1.3 68.7 - - - -
1038A GLN* 1.3 63.9 + - - +
1039A ARG* 3.2 2.9 - - - +
1040A LYS* 3.1 26.7 + - + +
1041A LEU* 3.2 11.6 + - - +
1066A TYR* 6.0 6.1 - - + -
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Residues in contact with GLN1038 (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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1031A SER 5.6 6.1 - - - +
1034A SER* 5.9 3.6 - - - +
1035A GLY* 4.3 7.9 - - - +
1036A GLY 3.1 11.7 - - - +
1037A MET* 1.3 77.0 - - - +
1039A ARG* 1.3 58.2 + - - +
1041A LEU* 3.0 11.7 + - - +
1042A SER* 2.9 23.4 + - - -
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Residues in contact with ARG1039 (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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1036A GLY 4.3 5.4 + - - +
1037A MET 3.2 0.4 - - - -
1038A GLN* 1.3 76.2 - - - +
1040A LYS* 1.3 60.2 + - - +
1042A SER* 3.3 11.3 - - - -
1043A VAL* 2.9 30.3 + - - +
1059A PRO* 4.6 15.3 - - + +
1061A ALA 6.3 0.4 - - - +
1062A GLY* 6.2 5.2 - - - +
1071A ILE* 6.1 2.6 - - + +
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Residues in contact with LYS1040 (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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1018A ASP 6.0 1.1 - - - +
1019A VAL* 6.0 9.0 - - + -
1037A MET* 3.1 25.0 + - + +
1039A ARG* 1.3 78.8 - - - +
1041A LEU* 1.3 49.9 + - - +
1043A VAL* 4.7 3.3 - - - +
1044A ALA* 2.7 38.3 + - - +
1070A GLY* 5.4 16.2 - - - -
1071A ILE* 6.2 2.0 - - - +
1074A LEU* 5.9 5.5 - - + +
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Residues in contact with LEU1041 (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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1019A VAL* 6.4 2.5 - - + -
1037A MET 3.2 8.2 + - - +
1038A GLN* 3.0 13.4 + - - +
1040A LYS* 1.3 74.5 - - - +
1042A SER* 1.3 61.1 + - - +
1044A ALA* 3.8 7.1 - - - +
1045A LEU* 2.9 28.6 + - - +
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Residues in contact with SER1042 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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978A CYS* 4.6 8.2 - - - +
979A PRO 6.0 1.6 - - - -
982A ASN* 5.2 17.0 - - - -
983A VAL 5.6 7.9 - - - -
1038A GLN 2.9 7.8 + - - -
1039A ARG* 3.0 20.6 + - - -
1041A LEU* 1.3 75.1 - - - +
1043A VAL* 1.3 61.9 + - - +
1045A LEU* 3.1 6.9 + - - +
1046A ALA* 2.9 26.0 + - - +
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Residues in contact with VAL1043 (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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978A CYS* 5.1 5.2 - - + -
1039A ARG 2.9 16.4 + - - +
1040A LYS* 4.7 3.1 - - - +
1042A SER* 1.3 75.0 - - - +
1044A ALA* 1.3 56.4 + - - +
1046A ALA* 3.7 7.6 - - - +
1047A PHE* 2.9 31.7 + - - +
1056A LEU* 6.0 5.4 - - + -
1059A PRO* 5.5 11.2 - - + -
1071A ILE* 5.7 8.1 - - + +
1074A LEU* 5.4 13.0 - - + -
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Residues in contact with ALA1044 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1015A MET* 5.6 7.0 - - + +
1018A ASP* 5.1 16.4 - - + -
1019A VAL* 5.9 6.5 - - + +
1040A LYS 2.7 24.3 + - - +
1041A LEU* 3.8 7.0 - - - -
1043A VAL* 1.3 76.9 - - - +
1045A LEU* 1.3 61.8 + - - +
1047A PHE* 3.5 3.5 + - - -
1048A VAL* 3.1 23.2 + - - +
1074A LEU* 5.9 3.5 - - + +
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Residues in contact with LEU1045 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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674A MET* 5.6 4.9 - - + +
983A VAL 5.8 3.8 - - - +
993A HIS* 5.5 4.3 - - + +
994A ILE* 5.9 5.8 - - - +
997A TYR* 4.5 25.5 - - + +
1041A LEU 2.9 20.7 + - - +
1042A SER* 3.1 6.3 + - - +
1044A ALA* 1.3 75.5 - - - +
1046A ALA* 1.3 62.3 + - - +
1048A VAL* 3.5 17.9 + - - +
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Residues in contact with ALA1046 (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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674A MET* 5.8 3.4 - - - -
976A GLY* 4.9 11.8 - - - -
977A VAL 3.3 29.4 - - - +
978A CYS* 3.7 18.8 - - + -
1042A SER 2.9 11.7 + - - +
1043A VAL* 3.7 6.3 - - - +
1045A LEU* 1.3 79.7 - - - +
1047A PHE* 1.3 58.2 + - - +
1048A VAL 3.1 11.7 + - - +
1051A SER* 4.9 4.9 - - - -
1054A VAL* 5.3 8.8 - - + +
1056A LEU* 6.0 2.5 - - + -
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Residues in contact with PHE1047 (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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1043A VAL 2.9 17.6 + - - +
1044A ALA* 3.8 4.9 - - - +
1046A ALA* 1.3 74.2 - - - +
1048A VAL* 1.3 63.1 + - - +
1049A GLY 3.5 9.1 - - - +
1051A SER* 4.4 15.9 - - - -
1054A VAL* 5.3 6.3 - - + -
1078A TYR* 5.1 15.7 - - + -
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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