Contacts of the helix formed by residues 1030 - 1039 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1026D ALA* 2.9 35.2 - - + +
1027D ASP 4.6 2.0 - - - +
1028D LYS 2.8 23.3 - - - +
1029D VAL* 1.3 74.5 - - - +
1031D LYS* 1.3 58.9 + - - +
1033D ALA* 4.2 5.2 - - + -
1034D GLU* 2.8 34.1 + - - +
1086D GLU* 3.2 16.2 - - - +
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Residues in contact with LYS1031 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1030D PRO* 1.3 78.8 - - - +
1032D THR* 1.3 59.8 + - - +
1034D GLU* 4.7 0.7 - - - -
1035D ASN* 3.8 6.8 + - - +
1079D TYR* 3.0 44.1 + - + +
1083D PHE* 4.2 30.0 - - + +
1084D GLU* 4.5 26.0 + - - +
1086D GLU* 3.2 27.3 + - + +
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Residues in contact with THR1032 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029D VAL* 3.6 17.4 + - - +
1030D PRO 3.2 0.4 - - - -
1031D LYS* 1.3 79.0 - - - +
1033D ALA* 1.3 63.9 + - - +
1035D ASN* 3.4 5.0 + - - +
1036D PHE 3.3 16.5 + - - -
1083D PHE* 4.3 16.7 - - + -
1085D ASP* 5.4 0.3 - - - -
1086D GLU* 3.7 23.4 + - - +
1100D MET* 3.5 36.6 - - + -
1108D ASN* 5.8 0.7 - - - +
1127D VAL* 4.4 11.9 - - + +
1129D PHE* 3.5 21.4 - - + -
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Residues in contact with ALA1033 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004D PRO* 6.0 0.9 - - + -
1024D LEU* 3.4 32.5 - - + +
1025D PHE 4.1 11.4 - - - +
1026D ALA* 4.4 4.5 - - + +
1029D VAL 2.8 23.6 + - - +
1030D PRO* 4.0 4.3 - - + +
1032D THR* 1.3 76.9 - - - +
1034D GLU* 1.3 50.8 + - - +
1035D ASN 3.1 0.3 + - - -
1036D PHE* 3.2 2.3 + - - +
1037D ARG* 2.8 36.8 + - - +
1129D PHE* 4.1 12.0 - - - +
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Residues in contact with GLU1034 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004D PRO* 5.6 3.5 - - - +
1030D PRO 2.8 20.4 + - - +
1031D LYS* 4.7 0.9 - - - -
1032D THR 3.3 0.4 - - - -
1033D ALA* 1.3 75.8 - - - +
1035D ASN* 1.3 56.3 + - - +
1037D ARG* 2.7 43.7 + - - +
1038D ALA* 3.1 22.9 + - - +
1044D LYS* 5.9 1.0 - - - -
1078D ILE* 3.3 11.0 - - + +
1079D TYR* 3.7 15.5 - - + +
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Residues in contact with ASN1035 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031D LYS 3.8 4.0 + - - +
1032D THR 3.4 8.7 + - - +
1033D ALA 3.1 0.4 - - - -
1034D GLU* 1.3 75.0 - - - +
1036D PHE* 1.3 65.6 + - - +
1037D ARG 3.0 1.3 - - - -
1038D ALA 3.5 0.7 + - - -
1039D LEU* 2.9 42.8 + - - +
1048D TYR* 4.7 0.8 + - - -
1077D SER* 3.3 9.0 - - - -
1078D ILE* 3.2 37.8 + - - +
1079D TYR* 3.6 15.2 + - + -
1083D PHE* 3.7 17.5 - - + -
1100D MET* 4.1 11.1 - - - +
1109D GLY 3.1 22.0 + - - -
1110D SER* 4.3 1.2 - - - +
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Residues in contact with PHE1036 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006D VAL* 3.6 23.8 - - + -
1008D PHE* 3.6 25.6 - + - -
1022D PHE* 3.9 8.7 - + - -
1024D LEU* 3.4 18.4 - - + -
1032D THR 3.3 1.6 + - - +
1033D ALA 3.2 7.1 + - - +
1035D ASN* 1.3 80.9 - - - +
1037D ARG* 1.3 56.5 + - - +
1039D LEU* 3.7 5.0 - - - +
1040D SER* 3.1 39.2 + - - -
1048D TYR* 4.1 17.6 - + - -
1098D LEU* 3.6 29.4 - - + -
1100D MET* 5.4 0.7 - - - -
1112D PHE* 3.8 30.7 - + + -
1129D PHE* 3.3 35.0 - + + -
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Residues in contact with ARG1037 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004D PRO* 4.0 11.9 - - + -
1006D VAL* 4.2 8.5 - - + +
1024D LEU* 3.3 24.2 - - + -
1033D ALA 2.8 16.0 + - - +
1034D GLU* 2.7 43.3 + - - +
1035D ASN 3.0 0.6 - - - -
1036D PHE* 1.3 73.2 - - - +
1038D ALA* 1.3 65.2 + - - +
1039D LEU 3.0 8.5 + - - -
1040D SER* 3.1 12.0 + - - -
1041D THR* 3.7 23.4 + - - +
1043D GLU* 2.6 43.2 + - - -
1044D LYS* 5.8 0.2 - - - +
1163D GLN* 3.6 37.7 + - - +
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Residues in contact with ALA1038 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034D GLU* 3.1 8.3 + - - +
1035D ASN 4.0 0.2 - - - -
1037D ARG* 1.3 82.3 - - - +
1039D LEU* 1.3 61.3 + - - +
1041D THR* 4.1 2.0 - - - -
1042D GLY* 3.7 14.0 + - - -
1043D GLU* 3.7 37.4 + - + +
1044D LYS* 3.7 20.1 + - + +
1046D PHE 5.0 0.9 - - - +
1078D ILE* 3.5 28.3 - - + -
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Residues in contact with LEU1039 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035D ASN* 2.9 36.8 + - - +
1036D PHE 3.7 0.4 - - - +
1037D ARG 3.0 0.8 - - - -
1038D ALA* 1.3 77.6 - - - +
1040D SER* 1.3 59.2 + - - +
1041D THR 3.1 9.4 + - - -
1042D GLY 3.8 3.8 + - - -
1044D LYS* 5.6 0.4 - - + -
1046D PHE* 3.5 28.3 - - + -
1047D GLY* 3.1 26.7 - - - -
1048D TYR* 3.2 48.4 + - + +
1049D LYS 5.0 0.2 + - - -
1067D PHE* 4.4 1.6 - - + -
1076D LYS 4.2 3.8 - - - +
1078D ILE* 3.3 26.7 - - + -
1110D SER* 3.7 20.4 - - - -
1161D CYS* 5.1 0.2 - - - -
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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