Contacts of the helix formed by residues 1030 - 1040 (chain A) in PDB entry 1AWV
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 PRO1030 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1026A ALA* 3.3 29.1 - - + +
1027A ASP 5.3 0.9 - - - -
1028A LYS 3.4 9.0 - - - +
1029A VAL* 1.3 87.3 - - - +
1031A LYS* 1.3 53.2 + - - +
1033A ALA* 3.6 0.5 - - - +
1034A GLU* 2.6 40.4 + - - +
1086A GLU* 3.3 12.6 - - - +
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Residues in contact with LYS1031 (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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1030A PRO* 1.3 79.3 - - - +
1032A THR* 1.3 62.2 - - - +
1034A GLU* 4.3 3.1 - - - -
1035A ASN* 3.2 11.6 + - - +
1079A TYR* 2.8 67.0 + - + +
1083A PHE* 4.2 14.0 - - + +
1084A GLU* 2.8 33.8 + - - +
1086A GLU* 3.1 17.6 + - + +
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Residues in contact with THR1032 (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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1029A VAL* 3.3 11.3 + - - +
1030A PRO 3.2 0.6 - - - -
1031A LYS* 1.3 80.2 - - - +
1033A ALA* 1.3 62.0 + - - +
1035A ASN* 3.7 6.6 + - - +
1036A PHE* 3.6 11.8 + - - +
1083A PHE* 4.1 21.0 - - + -
1086A GLU* 2.6 34.6 + - - +
1100A MET* 3.7 30.5 - - + +
1108A ASN* 5.7 0.9 - - - +
1127A VAL* 4.4 11.8 - - + +
1129A PHE* 3.8 23.8 - - + -
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Residues in contact with ALA1033 (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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1004A PRO* 6.1 0.9 - - + -
1024A LEU* 3.6 29.5 - - + +
1025A PHE 4.4 3.4 - - - +
1026A ALA* 4.1 19.1 - - + +
1029A VAL 2.7 23.6 + - - +
1030A PRO 3.7 2.0 - - - +
1032A THR* 1.3 71.0 - - - +
1034A GLU* 1.3 65.9 + - - +
1036A PHE* 3.1 7.1 + - - +
1037A ARG* 3.0 18.1 + - - -
1129A PHE* 3.9 14.5 - - - +
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Residues in contact with GLU1034 (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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1004A PRO* 6.0 0.5 - - - +
1030A PRO 2.6 23.3 + - - +
1031A LYS* 3.9 5.8 - - - +
1033A ALA* 1.3 72.4 - - - +
1035A ASN* 1.3 62.8 + - - +
1037A ARG* 2.9 46.4 + - - +
1038A ALA* 2.9 28.4 + - - +
1043A GLU* 4.6 1.6 - - - +
1044A LYS* 6.1 0.5 - - - -
1078A ILE* 4.3 8.4 - - + +
1079A TYR* 4.2 9.4 - - + +
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Residues in contact with ASN1035 (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 LYS 3.2 16.6 + - - +
1032A THR 3.7 6.0 + - - +
1033A ALA 3.2 0.4 + - - -
1034A GLU* 1.3 77.8 - - - +
1036A PHE* 1.3 63.7 + - - +
1038A ALA* 3.4 1.0 + - - +
1039A LEU* 3.0 40.9 + - - +
1048A TYR* 5.2 1.4 + - - -
1077A SER* 3.4 29.7 - - - -
1078A ILE* 3.5 13.8 + - - -
1079A TYR* 3.7 11.8 + - + +
1083A PHE* 3.5 14.1 - - + -
1100A MET* 4.1 11.7 - - - +
1109A GLY 3.2 19.2 + - - -
1110A SER* 4.6 4.6 - - - +
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Residues in contact with PHE1036 (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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1006A VAL* 3.4 20.9 - - + -
1008A PHE* 3.5 26.7 - + - -
1022A PHE* 4.5 4.9 - + - -
1024A LEU* 3.6 17.0 - - + -
1032A THR 3.6 1.7 + - - +
1033A ALA 3.1 7.2 + - - +
1035A ASN* 1.3 82.5 - - - +
1037A ARG* 1.3 54.4 + - - +
1039A LEU* 3.4 6.0 + - - +
1040A SER* 2.7 49.4 + - - -
1048A TYR* 3.3 31.6 - + - -
1098A LEU* 3.7 31.2 - - + -
1100A MET* 5.7 0.9 - - - -
1112A PHE* 4.0 11.0 - + + -
1129A PHE* 3.2 35.7 - + + -
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Residues in contact with ARG1037 (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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1004A PRO* 4.1 14.1 - - + -
1006A VAL* 4.0 14.1 - - + -
1024A LEU* 3.7 17.4 - - + +
1033A ALA 3.0 6.7 + - - +
1034A GLU* 2.9 49.1 + - - +
1036A PHE* 1.3 74.2 - - - +
1038A ALA* 1.3 57.7 + - - +
1039A LEU 3.0 8.5 + - - -
1040A SER* 3.3 6.4 + - - -
1041A THR* 3.1 31.7 - - - +
1043A GLU* 3.0 37.9 + - - -
1163A GLN* 3.1 45.4 + - + +
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Residues in contact with ALA1038 (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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1034A GLU* 2.9 20.7 + - - +
1035A ASN 3.7 0.9 - - - +
1037A ARG* 1.3 76.7 - - - +
1039A LEU* 1.3 61.4 + - - +
1041A THR* 4.0 2.7 - - - -
1042A GLY* 3.7 13.9 + - - -
1043A GLU* 3.8 38.1 + - + +
1044A LYS* 4.5 8.1 + - - +
1046A PHE 4.4 2.4 - - - +
1078A ILE* 4.0 30.2 - - + +
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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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1035A ASN* 3.0 35.8 + - - +
1036A PHE* 3.6 1.8 - - - +
1037A ARG 3.0 1.0 - - - -
1038A ALA* 1.3 79.6 - - - +
1040A SER* 1.3 61.1 + - - +
1041A THR 3.3 2.2 + - - -
1042A GLY* 4.1 2.7 + - - -
1046A PHE* 3.8 11.2 - - + +
1047A GLY* 3.2 20.0 - - - -
1048A TYR* 3.1 53.6 + - + +
1049A LYS 5.0 0.2 + - - -
1067A PHE* 3.3 36.6 - - + -
1076A LYS 4.1 6.7 - - - +
1078A ILE* 3.3 31.2 - - + +
1110A SER* 4.4 6.1 - - - -
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Residues in contact with SER1040 (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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1006A VAL* 4.1 20.2 - - - -
1007A PHE 4.6 0.2 - - - -
1008A PHE* 3.7 12.0 - - - -
1036A PHE* 2.7 40.2 + - - -
1037A ARG 3.3 4.4 + - - -
1039A LEU* 1.3 77.6 - - - +
1041A THR* 1.3 60.3 + - - +
1048A TYR* 3.5 13.2 - - - -
1161A CYS* 3.1 37.9 - - - +
1162A GLY* 4.1 5.6 - - - -
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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