Contacts of the helix formed by residues 1038 - 1051 (chain A) in PDB entry 3RZE
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1025A TYR* 3.5 12.8 - - - -
1036A SER 3.7 0.9 - - - +
1037A PRO* 1.4 80.3 - - - +
1039A LEU* 1.4 64.2 + - - +
1040A ASN* 3.5 9.1 + - - +
1041A ALA* 3.2 28.6 + - - +
1042A ALA 3.2 9.2 + - - -
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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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1017A ILE* 3.9 32.8 - - + +
1025A TYR* 3.2 26.2 + - + +
1038A SER* 1.4 72.7 - - - +
1040A ASN* 1.3 55.0 + - - +
1042A ALA* 3.2 2.9 + - - +
1043A LYS* 2.8 71.1 + - + +
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Residues in contact with ASN1040 (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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1038A SER* 3.3 8.2 + - - +
1039A LEU* 1.3 83.7 - - - +
1041A ALA* 1.4 54.7 + - - +
1043A LYS* 3.8 21.5 + - - +
1044A SER* 3.0 28.4 + - - -
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Residues in contact with ALA1041 (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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1035A LYS 4.8 2.2 - - - +
1036A SER* 3.9 18.6 + - - -
1037A PRO* 3.9 13.7 - - + -
1038A SER* 3.2 22.6 + - - +
1040A ASN* 1.4 74.6 - - - +
1042A ALA* 1.4 59.0 + - - +
1044A SER* 3.3 7.5 + - - -
1045A GLU* 3.0 28.6 + - - +
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Residues in contact with ALA1042 (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 ILE* 4.0 7.1 - - + +
1025A TYR* 3.5 41.1 - - + -
1033A LEU* 4.0 10.3 - - + +
1036A SER* 3.3 19.8 + - - +
1038A SER 3.2 3.2 + - - +
1039A LEU 3.4 8.5 - - - +
1041A ALA* 1.4 75.2 - - - +
1043A LYS* 1.4 63.0 + - - +
1045A GLU* 3.4 2.6 + - - +
1046A LEU* 3.1 25.5 + - - +
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Residues in contact with LYS1043 (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 ILE* 4.0 13.0 - - + -
1039A LEU* 2.8 56.9 + - + +
1040A ASN* 3.8 22.3 + - - +
1042A ALA* 1.4 70.7 - - - +
1044A SER* 1.4 57.6 + - - +
1046A LEU* 3.3 4.3 + - - +
1047A ASP* 2.9 41.2 + - - +
1055A ASN* 3.4 40.8 + - - -
1056A GLY* 4.0 9.6 - - - +
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Residues in contact with SER1044 (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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1040A ASN 3.0 18.1 + - - -
1041A ALA* 3.3 7.8 + - - -
1043A LYS* 1.4 74.8 - - - +
1045A GLU* 1.3 61.3 + - - +
1047A ASP* 4.0 8.3 - - - +
1048A LYS* 3.4 21.0 + - - +
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Residues in contact with GLU1045 (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 HIS* 5.1 3.5 + - - -
1032A LEU 4.8 0.9 - - - +
1033A LEU* 3.2 20.0 - - + +
1034A THR* 2.8 43.2 + - - +
1035A LYS 4.7 0.5 - - - +
1036A SER* 2.8 16.9 + - - +
1041A ALA 3.0 14.4 + - - +
1042A ALA 3.8 4.0 - - - +
1043A LYS 3.3 0.4 - - - -
1044A SER* 1.3 75.5 - - - +
1046A LEU* 1.4 58.7 + - - +
1048A LYS* 3.2 9.7 + - + +
1049A ALA* 3.0 27.7 + - + +
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Residues in contact with LEU1046 (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 ILE* 3.6 28.9 - - + -
1027A ILE* 3.7 26.2 - - + -
1033A LEU* 4.2 12.0 - - + +
1042A ALA 3.1 17.0 + - - +
1043A LYS* 3.6 2.9 - - - +
1045A GLU* 1.4 76.3 - - - +
1047A ASP* 1.4 51.8 + - - +
1049A ALA* 3.2 5.9 + - + +
1050A ILE* 2.8 69.3 + - + +
1054A THR* 3.3 25.6 - - - +
1056A GLY* 3.9 11.4 - - - -
1058A ILE* 4.1 8.7 - - + -
1066A LEU* 4.4 3.8 - - + -
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Residues in contact with ASP1047 (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 LYS* 2.9 24.8 + - - +
1044A SER* 4.1 8.4 - - - +
1045A GLU 3.3 0.2 - - - -
1046A LEU* 1.4 73.7 - - - +
1048A LYS* 1.4 56.3 + - - +
1051A GLY* 3.0 24.1 + - - -
1052A ARG 3.2 25.3 + - - +
1053A ASN* 3.5 20.5 + - - -
1054A THR* 2.4 39.6 + - - -
1055A ASN 3.9 2.1 + - - -
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Residues in contact with LYS1048 (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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1044A SER 3.4 12.2 + - - +
1045A GLU* 3.2 12.9 + - + +
1047A ASP* 1.4 79.9 - - - +
1049A ALA* 1.3 62.8 + - - +
1051A GLY* 3.7 7.1 + - - -
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Residues in contact with ALA1049 (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 HIS* 5.6 3.6 - - - +
1033A LEU* 6.0 1.3 - - + -
1045A GLU* 3.0 13.0 + - + +
1046A LEU* 3.4 11.0 - - + +
1048A LYS* 1.3 77.8 - - - +
1050A ILE* 1.3 61.9 + - + +
1065A LYS* 3.0 22.4 + - - -
1066A LEU* 4.3 24.2 - - + -
1069A GLN* 4.9 6.8 + - - +
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Residues in contact with ILE1050 (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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1046A LEU* 2.8 49.4 + - + +
1047A ASP 4.8 0.2 - - - +
1049A ALA* 1.3 76.5 - - + +
1051A GLY* 1.3 57.1 + - - +
1052A ARG* 3.6 27.5 - - + +
1054A THR* 3.8 9.0 - - + -
1058A ILE* 3.7 13.2 - - + -
1062A GLU* 3.7 33.4 - - + +
1065A LYS* 3.8 17.8 + - + +
1066A LEU* 3.6 25.4 - - + -
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Residues in contact with GLY1051 (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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1047A ASP 3.0 11.4 + - - -
1048A LYS 4.1 6.3 - - - -
1049A ALA 3.4 2.0 - - - -
1050A ILE* 1.3 77.9 - - - +
1052A ARG* 1.4 63.0 + - - +
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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