Contacts of the helix formed by residues 1038 - 1049 (chain A) in PDB entry 5IYB
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 THR1038 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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894A ASP 5.6 0.2 - - - +
1020A LEU* 4.6 6.1 - - + +
1022A ILE* 3.9 30.3 - - + -
1034A GLN* 3.4 26.7 + - - +
1035A GLU* 4.1 3.3 + - - -
1036A ASN 3.1 0.4 - - - -
1037A ALA* 1.3 83.5 - - - +
1039A LEU* 1.3 53.9 + - - +
1040A LEU 3.4 2.9 - - - -
1041A PHE* 3.3 13.7 + - - +
1042A ASN* 2.7 44.5 + - - +
1076A PHE* 4.7 10.1 - - + -
200E ALA* 4.5 1.3 - - - +
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Residues in contact with LEU1039 (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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962A ASP* 5.0 5.6 - - - +
965A VAL* 4.6 12.1 - - + -
969A ILE* 4.5 20.6 - - + -
1035A GLU* 3.3 16.9 + - + +
1036A ASN* 3.3 16.8 + - - +
1038A THR* 1.3 77.7 - - - +
1040A LEU* 1.3 60.2 + - - +
1042A ASN* 3.7 6.0 - - + +
1043A ILE* 3.0 49.2 + - + +
1046A ARG* 5.4 1.6 - - - +
200E ALA 3.7 1.8 + - - +
202E ARG* 4.1 42.0 - - + +
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Residues in contact with LEU1040 (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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906A LEU* 3.8 26.5 - - + -
966A LEU* 4.2 9.4 - - + -
969A ILE* 5.3 4.9 - - + -
970A PHE* 4.1 17.9 - - + -
977A VAL* 4.2 14.1 - - + -
978A VAL 5.3 0.4 - - - +
979A LEU* 4.7 11.4 - - + -
1038A THR 3.4 0.4 - - - -
1039A LEU* 1.3 74.0 - - - +
1041A PHE* 1.3 62.7 + - - +
1043A ILE* 3.5 16.2 - - + +
1044A HIS* 3.2 22.2 + - - +
198E GLU 4.1 13.7 - - - +
199E THR* 3.2 23.6 - - - +
200E ALA 2.9 24.1 + - - +
201E GLY* 4.2 5.8 - - - +
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Residues in contact with PHE1041 (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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979A LEU* 4.1 31.9 - - + +
980A PRO* 3.7 27.8 - - + -
981A CYS* 4.6 3.8 - - - -
983A LEU* 4.8 15.0 - - + -
1020A LEU* 3.4 31.9 - - + -
1038A THR* 3.3 16.1 + - - +
1040A LEU* 1.3 78.9 - - - +
1042A ASN* 1.3 61.1 + - - +
1044A HIS* 3.4 7.0 + + - +
1045A LEU* 2.8 41.4 + - + +
1072A ILE* 4.4 16.4 - - + -
1076A PHE* 3.7 29.4 - + + -
199E THR 4.7 1.4 + - - +
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Residues in contact with ASN1042 (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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1017A SER* 3.0 36.2 + - - +
1020A LEU* 6.1 1.4 - - - +
1035A GLU 5.8 0.4 - - - +
1038A THR* 2.7 30.9 + - - +
1039A LEU* 3.7 7.9 - - + +
1041A PHE* 1.3 75.7 - - + +
1043A ILE* 1.3 60.8 + - - +
1045A LEU* 3.3 8.6 + - - +
1046A ARG* 2.8 66.9 + - - +
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Residues in contact with ILE1043 (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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906A LEU* 5.2 2.7 - - + -
908A THR* 5.5 5.2 - - + +
959A MET* 4.6 1.8 - - - +
962A ASP* 3.8 27.8 - - + +
965A VAL* 6.3 2.2 - - + -
966A LEU* 3.8 46.9 - - + +
969A ILE* 5.5 4.0 - - + -
1039A LEU* 3.0 28.1 + - + +
1040A LEU* 3.5 20.4 - - + +
1042A ASN* 1.3 71.6 - - - +
1044A HIS* 1.3 65.3 + - + +
1046A ARG* 3.3 23.7 - - - +
1047A SER* 2.8 36.2 + - - +
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Residues in contact with HIS1044 (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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904A GLN* 3.2 28.3 + - + +
905A ASN 3.2 25.4 - - - -
906A LEU* 3.1 24.6 - - + +
907A ALA* 5.3 2.4 + - + -
979A LEU* 3.7 21.3 - - + -
983A LEU* 3.7 21.1 - - + +
984A LEU* 6.3 3.1 - - + +
1040A LEU 3.2 15.8 + - - +
1041A PHE* 3.5 8.7 - + - +
1043A ILE* 1.3 84.0 - - - +
1045A LEU* 1.3 61.6 + - - +
1047A SER* 3.6 5.4 + - - -
1048A THR* 2.8 48.6 + - + -
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Residues in contact with LEU1045 (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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983A LEU* 3.6 33.0 - - + -
1013A VAL* 4.7 12.1 - - + -
1016A LEU* 3.9 25.8 - - + -
1017A SER* 4.6 14.1 - - - +
1020A LEU* 4.6 14.8 - - + -
1041A PHE* 2.8 27.8 + - + +
1042A ASN* 3.5 9.2 - - - +
1043A ILE 3.2 0.2 - - - -
1044A HIS* 1.3 78.1 - - - +
1046A ARG* 1.3 54.3 + - + +
1048A THR* 3.8 0.2 - - - -
1049A LEU* 2.7 50.4 + - + +
1072A ILE* 4.3 14.8 - - + -
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Residues in contact with ARG1046 (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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955A GLU* 4.5 2.1 - - - +
958A ARG* 4.3 20.1 - - - +
959A MET* 3.5 31.4 - - + +
962A ASP* 3.0 31.4 + - - -
1013A VAL* 3.5 31.0 - - + -
1014A LYS* 6.4 2.0 - - - -
1017A SER* 5.0 2.0 - - - -
1039A LEU* 5.4 1.6 - - - +
1042A ASN* 2.8 39.7 + - - +
1043A ILE* 3.3 26.6 - - - +
1045A LEU* 1.3 76.1 - - + +
1047A SER* 1.3 62.9 + - - +
1049A LEU 3.6 3.0 - - - +
1050A CYS* 3.3 19.6 + - - -
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Residues in contact with SER1047 (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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907A ALA* 5.2 3.9 + - - +
908A THR* 2.9 33.3 + - - -
920A PHE* 3.4 18.8 - - - -
959A MET* 3.7 20.5 - - - -
1043A ILE 2.8 27.4 + - - -
1044A HIS* 3.3 11.3 + - - -
1046A ARG* 1.3 73.9 - - - +
1048A THR* 1.3 63.4 + - - +
1050A CYS* 4.0 1.7 + - - +
1053A ARG* 3.0 20.9 + - - +
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Residues in contact with THR1048 (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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907A ALA* 5.6 4.0 - - - +
983A LEU* 4.3 12.1 - - + -
984A LEU* 4.1 21.8 - - + -
987A ILE* 4.1 14.6 - - + -
1044A HIS* 2.8 43.6 + - + -
1045A LEU 3.9 1.3 - - - -
1047A SER* 1.3 79.0 + - - +
1049A LEU* 1.3 71.2 + - + +
1050A CYS 3.2 5.2 + - - -
1053A ARG* 3.3 32.2 + - - +
1058A PHE* 3.9 8.2 - - + -
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Residues in contact with LEU1049 (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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955A GLU* 4.7 1.7 - - - +
983A LEU* 4.5 7.0 - - + -
987A ILE* 3.8 24.2 - - + -
1009A VAL* 3.6 16.1 - - - +
1013A VAL* 4.0 20.2 - - + +
1016A LEU* 5.1 0.7 - - + -
1045A LEU* 2.7 37.0 + - + +
1046A ARG* 3.6 6.4 - - - +
1048A THR* 1.3 80.3 - - + +
1050A CYS* 1.3 61.6 + - - -
1054A MET* 3.7 17.7 - - + -
1065A PHE* 4.0 18.4 - - + -
1068A LEU* 4.0 20.0 - - + -
1069A LEU* 4.8 4.9 - - + -
1072A ILE* 4.2 15.3 - - + -
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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