Contacts of the helix formed by residues 1030 - 1040 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1025B PHE 3.2 8.0 - - - +
1026B ALA* 3.1 31.4 - - + +
1027B ASP 4.3 2.7 - - - +
1028B LYS 3.2 13.2 - - - +
1029B VAL* 1.3 78.9 - - - +
1031B LYS* 1.3 61.2 + - - +
1033B ALA* 4.5 0.2 - - + -
1034B GLU* 2.9 38.6 + - + +
1086B GLU* 3.3 11.7 - - - +
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Residues in contact with LYS1031 (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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1030B PRO* 1.3 80.7 - - - +
1032B THR* 1.3 67.5 + - - +
1034B GLU* 3.2 3.6 - - - +
1035B ASN 3.5 0.2 + - - -
1079B TYR* 2.6 60.2 + - + +
1083B PHE* 3.8 31.2 - - + +
1084B GLU* 3.2 38.8 + - - +
1086B GLU* 3.2 17.9 + - + +
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Residues in contact with THR1032 (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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1029B VAL* 3.5 23.6 - - - +
1031B LYS* 1.3 75.6 - - - +
1033B ALA* 1.3 66.4 + - - +
1035B ASN* 2.9 21.5 + - - +
1083B PHE* 4.4 19.3 - - + -
1085B ASP* 4.7 0.5 - - - -
1086B GLU* 3.4 21.8 + - - +
1100B MET* 3.7 23.3 - - + -
1127B VAL* 4.3 13.0 - - + +
1129B PHE* 3.4 29.1 - - + -
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Residues in contact with ALA1033 (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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1024B LEU* 3.5 17.7 - - + +
1025B PHE* 3.0 35.4 - - + +
1029B VAL 2.9 24.2 + - - +
1030B PRO* 4.2 0.7 - - + +
1032B THR* 1.3 72.4 - - - +
1034B GLU* 1.3 57.6 + - - +
1036B PHE* 2.8 23.2 + - - +
1037B ARG 2.9 8.5 + - - -
1129B PHE* 3.8 16.7 - - - +
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Residues in contact with GLU1034 (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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1004B PRO* 5.7 2.1 - - - +
1030B PRO* 2.9 23.8 + - + +
1031B LYS* 3.2 0.4 - - - +
1032B THR 3.1 0.4 - - - -
1033B ALA* 1.3 76.9 - - - +
1035B ASN* 1.3 55.0 + - - +
1037B ARG* 2.7 53.8 + - - +
1038B ALA* 2.8 36.0 + - - +
1078B ILE* 4.4 4.9 - - + +
1079B TYR* 2.9 27.4 + - + +
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Residues in contact with ASN1035 (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 LYS 3.5 3.5 + - - +
1032B THR 2.9 13.4 + - - +
1034B GLU* 1.3 76.0 - - - +
1036B PHE* 1.3 59.4 + - - +
1039B LEU* 2.9 55.6 + - - +
1048B TYR* 3.6 18.0 + - - -
1077B SER* 4.2 8.8 - - - -
1078B ILE* 4.4 13.3 + - + -
1079B TYR* 4.0 2.6 + - + -
1083B PHE* 4.2 17.7 - - + -
1100B MET* 3.4 31.5 - - + +
1109B GLY 3.3 17.7 + - - +
1110B SER* 3.9 1.8 - - - +
1129B PHE* 4.7 1.6 - - - -
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Residues in contact with PHE1036 (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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1006B VAL* 3.7 10.0 - - + +
1008B PHE* 3.6 25.8 - + - -
1022B PHE* 3.6 23.3 - + - -
1024B LEU* 3.4 29.4 - - + +
1032B THR 3.7 0.8 + - - -
1033B ALA 2.8 9.7 + - - +
1035B ASN* 1.3 79.9 - - - +
1037B ARG* 1.3 61.2 + - - +
1040B SER* 2.8 31.0 + - - -
1048B TYR* 3.6 17.3 - + - -
1098B LEU* 3.4 28.9 - - + -
1112B PHE* 3.5 31.9 - + - -
1129B PHE* 3.4 30.7 - + + -
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Residues in contact with ARG1037 (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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1004B PRO* 4.3 16.8 - - + -
1006B VAL* 4.3 3.4 - - + -
1024B LEU* 3.2 24.3 - - + +
1033B ALA 2.9 5.3 + - - +
1034B GLU* 2.7 51.4 + - - +
1036B PHE* 1.3 73.0 - - - +
1038B ALA* 1.3 80.1 + - - +
1039B LEU 2.8 14.6 + - - -
1040B SER* 2.9 13.5 + - - -
1041B THR* 3.1 30.2 + - + +
1043B GLU* 2.6 31.7 + - - -
1044B LYS* 4.9 4.2 - - - +
1163B GLN* 4.0 17.9 - - - +
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Residues in contact with ALA1038 (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 GLU 2.8 4.5 + - - +
1037B ARG* 1.3 109.4 - - - +
1039B LEU* 1.3 61.3 + - - +
1041B THR* 3.5 11.9 + - - -
1042B GLY* 4.5 0.2 - - - -
1043B GLU* 3.7 11.1 + - - +
1044B LYS* 3.8 27.6 + - + +
1046B PHE 5.6 0.2 - - - +
1078B ILE* 3.5 29.4 - - + -
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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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1035B ASN* 2.9 44.2 + - - +
1037B ARG 2.8 2.6 + - - -
1038B ALA* 1.3 78.2 - - - +
1040B SER* 1.3 62.4 + - - +
1042B GLY 3.5 7.6 + - - -
1044B LYS* 5.3 0.9 - - + -
1046B PHE* 3.3 41.7 - - + +
1047B GLY* 2.9 29.7 - - - -
1048B TYR* 3.6 34.5 + - + +
1067B PHE* 4.2 4.3 - - + -
1076B LYS 4.4 2.0 - - - +
1078B ILE* 3.5 14.4 - - + -
1110B SER* 3.8 17.7 - - - -
1161B CYS* 5.0 0.2 - - - -
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Residues in contact with SER1040 (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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1006B VAL* 4.4 20.4 - - - +
1007B PHE 5.1 0.2 - - - -
1008B PHE* 3.6 21.5 - - - -
1036B PHE* 2.8 21.4 + - - -
1037B ARG 2.9 4.2 + - - -
1039B LEU* 1.3 78.2 - - - +
1041B THR* 1.3 60.9 + - - +
1042B GLY* 3.2 1.6 + - - -
1048B TYR* 3.8 7.9 - - - -
1161B CYS* 3.1 49.7 - - - +
1162B GLY* 4.5 4.0 - - - -
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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