Contacts of the helix formed by residues 1032 - 1046 (chain A) in PDB entry 3AVR
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 ILE1032 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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989A LEU* 3.7 30.5 - - + +
990A VAL* 4.2 12.6 - - + -
993A ASN 2.9 30.5 - - - +
994A ASN* 3.3 9.6 - - - +
996A HIS* 2.9 18.4 + - + +
998A VAL* 3.6 16.8 - - + +
1031A THR* 1.3 73.6 - - - +
1033A ALA* 1.3 60.2 + - - +
1035A TYR* 4.2 1.5 - - - +
1036A ALA* 2.8 32.4 + - - +
1088A ILE* 5.2 3.1 - - + -
1096A TRP* 4.6 10.5 - - + -
1134A LEU* 4.3 10.1 - - + -
1136A MET* 3.8 29.8 - - + -
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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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990A VAL* 4.2 12.3 - - + -
994A ASN* 3.1 49.0 + - - +
995A GLU* 4.7 1.8 - - - +
1031A THR* 3.2 4.7 - - - +
1032A ILE* 1.3 78.5 - - - +
1034A LYS* 1.3 64.2 + - + +
1036A ALA* 3.5 3.1 + - - +
1037A GLN* 3.2 33.0 + - - +
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Residues in contact with LYS1034 (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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6A EDO 3.3 9.2 + - - +
1030A THR* 3.3 20.2 - - - +
1031A THR* 3.1 18.2 + - + +
1033A ALA* 1.3 77.1 - - + +
1035A TYR* 1.3 66.1 + - - +
1037A GLN* 3.2 21.2 + - - +
1038A TYR* 3.2 18.4 + - - +
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Residues in contact with TYR1035 (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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6A EDO 3.3 21.2 + - - -
998A VAL* 4.4 7.6 - - + -
1000A VAL* 4.7 2.9 - - + -
1030A THR* 4.0 11.2 - - + -
1031A THR 2.9 15.9 + - - +
1032A ILE* 4.2 4.3 - - - +
1034A LYS* 1.3 76.0 - - - +
1036A ALA* 1.3 58.8 + - - +
1038A TYR* 3.0 20.9 + + - +
1039A GLN* 2.9 37.6 + - + -
1083A LYS* 2.6 36.6 + - + -
1084A PHE* 3.6 1.5 - - - -
1085A GLY* 3.5 17.9 - - - -
1136A MET* 3.1 56.9 + - + -
1137A LYS 4.4 0.2 - - - -
1138A VAL* 3.7 16.2 + - + +
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Residues in contact with ALA1036 (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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986A THR* 3.3 32.8 - - + +
990A VAL* 3.3 16.4 - - + -
1032A ILE 2.8 20.1 + - - +
1033A ALA 3.6 5.2 - - - +
1035A TYR* 1.3 78.2 - - - +
1037A GLN* 1.3 56.8 + - + +
1039A GLN* 3.8 2.7 - - - +
1040A ALA* 2.9 33.9 + - - +
1136A MET* 4.4 3.8 - - + +
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Residues in contact with GLN1037 (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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1033A ALA* 3.2 23.9 + - - +
1034A LYS* 3.2 22.4 + - - +
1036A ALA* 1.3 75.7 - - - +
1038A TYR* 1.3 58.3 + - - +
1040A ALA* 4.2 3.8 - - - +
1041A SER* 3.0 34.0 + - - -
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Residues in contact with TYR1038 (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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6A EDO 4.8 6.7 - - - +
1034A LYS 3.2 8.6 + - - +
1035A TYR* 3.0 30.2 + + + +
1037A GLN* 1.3 80.3 - - - +
1039A GLN* 1.3 60.5 + - - +
1041A SER* 3.3 7.5 + - - -
1042A SER* 2.9 37.4 + - - -
1080A LYS* 6.0 0.9 - - - -
1081A THR 4.4 1.9 + - - -
1082A ILE* 3.4 16.1 - - - +
1083A LYS* 3.0 69.4 + - + +
1138A VAL* 3.7 18.5 - - + +
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Residues in contact with GLN1039 (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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5A EDO 2.9 29.9 + - - +
986A THR* 2.6 29.6 + - - +
1035A TYR* 2.9 26.8 + - + +
1036A ALA 3.8 2.9 - - - +
1038A TYR* 1.3 76.2 - - - +
1040A ALA* 1.3 62.3 + - - +
1042A SER* 3.2 3.8 - - - -
1043A PHE* 3.0 23.2 + - - +
1136A MET* 3.9 5.0 - - - +
1137A LYS 3.0 36.1 + - - +
1138A VAL* 4.1 11.7 - - + -
1233A TRP* 3.6 6.6 - - + -
1234A CYS 3.6 2.0 + - - -
1235A ASN* 3.1 22.6 + - - -
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Residues in contact with ALA1040 (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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5A EDO 3.7 20.4 + - - +
986A THR* 6.0 0.9 - - + -
1036A ALA 2.9 18.7 + - - +
1037A GLN* 4.2 4.0 - - - +
1039A GLN* 1.3 77.0 - - - +
1041A SER* 1.3 58.3 + - - +
1043A PHE* 3.3 4.3 + - - +
1044A GLN* 2.7 32.6 - - - +
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Residues in contact with SER1041 (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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1037A GLN 3.0 22.8 + - - -
1038A TYR* 3.3 9.4 + - - -
1040A ALA* 1.3 73.6 - - - +
1042A SER* 1.3 68.4 + - - +
1044A GLN* 3.0 10.4 + - - +
1045A GLU* 2.9 24.0 + - - +
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Residues in contact with SER1042 (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 TYR* 2.9 28.9 + - - -
1039A GLN* 3.2 9.6 - - - -
1041A SER* 1.3 71.9 + - - +
1043A PHE* 1.3 56.8 + - - +
1044A GLN 2.9 10.8 + - - -
1045A GLU* 3.3 16.4 + - - +
1046A SER* 3.2 21.3 + - - -
1138A VAL* 3.9 13.5 - - - +
1139A PRO* 5.0 0.2 - - - +
1233A TRP* 3.0 24.5 + - - -
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Residues in contact with PHE1043 (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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5A EDO 4.0 16.8 - - - -
1039A GLN 3.0 8.8 + - - +
1040A ALA 3.4 6.7 - - - +
1041A SER 3.2 0.2 - - - -
1042A SER* 1.3 77.5 - - - +
1044A GLN* 1.3 83.5 + - - +
1046A SER* 3.9 8.3 + - - -
1047A LEU* 3.7 26.6 - - + +
1161A PRO* 4.4 20.9 - - + -
1233A TRP* 3.5 45.9 - + + +
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Residues in contact with GLN1044 (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 ALA* 2.7 18.5 + - - +
1041A SER* 3.0 11.4 + - - +
1042A SER 2.9 0.6 - - - -
1043A PHE* 1.3 102.5 - - - +
1045A GLU* 1.3 67.7 + - - +
1046A SER 3.3 1.6 - - - -
1047A LEU* 3.0 30.2 + - + +
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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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1041A SER 2.9 14.5 + - - +
1042A SER* 3.7 15.1 + - - +
1044A GLN* 1.3 76.1 - - - +
1046A SER* 1.3 62.9 + - - +
1047A LEU 3.1 3.6 + - - -
1080A LYS* 3.9 27.3 + - - -
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Residues in contact with SER1046 (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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1042A SER 3.2 3.4 + - - -
1043A PHE 3.9 5.0 + - - -
1045A GLU* 1.3 80.7 - - - +
1047A LEU* 1.3 67.9 + - - +
1233A TRP* 3.1 41.0 - - - -
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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