Contacts of the helix formed by residues 1021 - 1036 (chain D) in PDB entry 6PUO
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 PRO1021 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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964A ASP* 5.5 11.0 - - + -
1020D PHE* 1.3 87.7 - - - +
1022D GLU* 1.3 61.3 + - + +
1023D TRP 3.5 0.7 - - - -
1024D LEU* 4.0 7.4 - - + -
1025D THR* 2.9 37.1 + - - -
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Residues in contact with GLU1022 (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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964A ASP* 6.5 0.9 - - + -
968A ARG* 6.0 7.0 - - + -
1020D PHE 3.3 3.1 - - - -
1021D PRO* 1.3 82.8 - - + +
1023D TRP* 1.3 58.4 + - - +
1025D THR* 4.2 2.1 - - - -
1026D VAL* 2.9 33.2 + - - +
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Residues in contact with TRP1023 (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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1020D PHE 4.3 5.4 + - - +
1022D GLU* 1.3 78.0 - - - +
1024D LEU* 1.3 57.5 + - - +
1026D VAL* 3.5 4.8 + - - +
1027D LEU* 2.9 31.1 + - - +
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Residues in contact with LEU1024 (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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956D LEU* 6.2 4.7 - - + -
1020D PHE 4.5 3.7 + - - +
1021D PRO* 3.7 12.2 + - + +
1022D GLU 3.4 0.4 - - - -
1023D TRP* 1.3 80.9 - - - +
1025D THR* 1.3 57.5 + - - +
1027D LEU* 3.3 6.1 + - - +
1028D LEU* 3.0 29.5 + - - +
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Residues in contact with THR1025 (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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1021D PRO* 2.9 23.7 + - - -
1022D GLU* 4.2 2.0 - - - -
1024D LEU* 1.3 73.6 - - - +
1026D VAL* 1.3 60.3 + - - +
1028D LEU* 3.5 4.9 + - - +
1029D LEU* 2.9 43.2 + - - +
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Residues in contact with VAL1026 (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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1022D GLU 2.9 21.0 + - - +
1023D TRP* 3.8 5.2 - - - +
1025D THR* 1.3 76.3 - - - +
1027D LEU* 1.3 57.9 + - - +
1029D LEU* 4.1 4.7 - - - +
1030D CYS* 2.9 34.9 + - - +
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Residues in contact with LEU1027 (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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1023D TRP 2.9 18.6 + - - +
1024D LEU* 3.6 7.0 - - - +
1026D VAL* 1.3 74.8 - - - +
1028D LEU* 1.3 60.1 + - - +
1030D CYS* 3.2 12.6 - - - -
1031D LEU* 2.9 30.3 + - - +
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Residues in contact with LEU1028 (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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948D PHE* 5.5 1.6 - - - -
952D LYS* 6.4 1.6 - - + -
1024D LEU 3.0 17.1 + - - +
1025D THR* 4.0 5.6 - - - +
1027D LEU* 1.3 75.0 - - - +
1029D LEU* 1.3 60.4 + - + +
1031D LEU* 3.3 7.1 + - - +
1032D TYR* 3.0 28.4 + - - +
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Residues in contact with LEU1029 (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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975A TYR* 4.7 20.0 - - + -
1025D THR* 2.9 28.5 + - - +
1026D VAL* 4.1 4.5 - - - +
1028D LEU* 1.3 77.5 - - + +
1030D CYS* 1.3 59.1 + - - +
1032D TYR* 3.4 6.6 + - + +
1033D LEU* 2.9 44.0 + - + +
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Residues in contact with CYS1030 (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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938A LEU* 5.2 1.7 - - - +
1026D VAL 2.9 18.4 + - - +
1027D LEU* 3.2 24.5 - - - -
1029D LEU* 1.3 73.9 - - - +
1031D LEU* 1.3 62.1 + - - +
1033D LEU* 3.8 6.4 - - - +
1034D LEU* 2.8 32.8 + - - +
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Residues in contact with LEU1031 (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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948D PHE* 4.6 17.0 - - + -
1027D LEU 2.9 19.4 + - - +
1028D LEU* 3.6 7.9 - - - +
1029D LEU 3.3 0.2 - - - -
1030D CYS* 1.3 80.2 - - - +
1032D TYR* 1.3 57.7 + - - +
1034D LEU* 3.4 8.6 + - - +
1035D PHE* 3.0 40.7 + - + -
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Residues in contact with TYR1032 (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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948D PHE* 4.7 12.7 - - + -
977D THR* 6.6 0.2 - - - -
1028D LEU 3.0 16.4 + - - +
1029D LEU* 3.7 10.1 - - + +
1031D LEU* 1.3 77.0 - - - +
1033D LEU* 1.3 60.2 + - + +
1036D THR* 2.7 52.2 + - + +
1037D ASN* 3.9 0.7 - - - -
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Residues in contact with LEU1033 (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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938A LEU* 5.1 2.8 - - - +
941A LEU* 6.4 3.8 - - + -
978A ILE* 4.7 23.8 - - + +
979A PHE* 5.7 4.3 - - + -
1029D LEU* 2.9 35.6 + - + +
1030D CYS* 4.0 7.2 - - - +
1032D TYR* 1.3 78.3 - - + +
1034D LEU* 1.3 65.0 + - - +
1037D ASN* 3.3 47.6 - - + +
1038D ILE* 3.8 8.7 - - - +
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Residues in contact with LEU1034 (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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934A VAL* 5.3 3.8 - - + +
935A PHE* 5.1 12.6 - - + -
938A LEU* 3.7 36.3 - - + +
1030D CYS* 2.8 20.1 + - - +
1031D LEU* 3.5 7.6 - - - +
1032D TYR 3.2 0.2 - - - -
1033D LEU* 1.3 79.6 - - - +
1035D PHE* 1.3 99.3 + - + +
1038D ILE* 3.4 12.7 - - - +
1039D LEU* 3.3 20.8 - - + +
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Residues in contact with PHE1035 (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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908A LEU* 5.8 11.2 - - + -
944D TRP* 3.5 41.7 - + + -
948D PHE* 4.4 10.8 - + - -
1031D LEU* 3.0 27.7 + - + +
1034D LEU* 1.3 101.5 - - + +
1036D THR* 1.3 66.2 + - + +
1039D LEU* 3.5 36.0 + - + +
1040D LEU* 4.5 5.2 + - - +
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Residues in contact with THR1036 (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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944D TRP* 3.7 34.8 - - + +
945D VAL* 6.2 0.7 - - + -
948D PHE* 5.7 1.3 - - + -
977D THR 5.7 3.1 + - - +
1032D TYR* 2.7 24.3 + - + +
1035D PHE* 1.3 77.1 - - - +
1037D ASN* 1.3 89.0 + - - +
1038D ILE 3.1 2.4 + - - -
1039D LEU 4.4 0.3 + - - -
1040D LEU* 4.8 9.6 + - - +
1041D LEU* 3.3 14.0 - - - +
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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