Contacts of the helix formed by residues 1027 - 1036 (chain D) in PDB entry 6DV9
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 GLY1027 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1010D LEU* 4.1 3.4 - - - -
1011D THR* 3.5 28.8 - - - -
1026D GLY* 1.3 73.2 - - - -
1028D LEU* 1.3 66.1 + - - -
1029D PRO 3.5 1.1 - - - -
1030D ARG* 3.2 11.3 + - - +
1031D VAL* 3.3 15.4 - - - +
1141D VAL* 3.4 17.6 - - - +
1145D GLN* 5.5 1.1 - - - -
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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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866D ARG* 4.0 30.5 - - + +
869D ASP* 3.8 28.7 - - + -
870D SER* 4.1 9.6 - - - +
873D LEU* 3.9 25.4 - - + -
1007D GLY* 4.5 10.3 - - - +
1010D LEU* 3.6 36.0 - - + +
1011D THR 4.0 3.1 - - - -
1027D GLY* 1.3 69.2 - - - -
1029D PRO* 1.3 75.7 - - + +
1031D VAL* 3.0 16.1 + - + +
1032D GLN* 3.1 18.1 + - - +
1142D TYR* 5.9 0.4 - - - +
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Residues in contact with PRO1029 (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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1011D THR 4.7 9.0 - - - +
1026D GLY 4.6 4.3 - - - +
1027D GLY* 3.7 4.7 - - - -
1028D LEU* 1.3 97.2 - - + +
1030D ARG* 1.3 54.8 + - - +
1032D GLN* 3.3 14.0 + - + +
1033D GLU* 2.9 36.0 + - + +
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Residues in contact with ARG1030 (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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1026D GLY* 3.6 28.3 + - - +
1027D GLY 3.2 11.1 + - - +
1028D LEU 3.1 0.8 - - - -
1029D PRO* 1.3 78.6 - - - +
1031D VAL* 1.3 63.2 + - - +
1033D GLU* 3.2 30.5 + - - +
1034D LEU* 3.3 39.8 + - + +
1040D PRO* 3.7 20.6 - - - +
1041D ARG* 6.0 3.1 - - - +
1115D SER* 3.1 40.9 + - - +
1116D ALA 5.3 1.8 + - - -
1133D HIS* 5.2 3.6 + - - -
1137D GLU* 3.2 34.7 + - - +
1141D VAL* 3.9 20.4 - - + -
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Residues in contact with VAL1031 (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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873D LEU* 4.2 13.2 - - + -
1010D LEU* 4.1 14.4 - - + -
1027D GLY 3.3 15.9 - - - +
1028D LEU* 3.0 8.4 + - + +
1030D ARG* 1.3 76.5 - - - +
1032D GLN* 1.3 60.7 + - - +
1034D LEU* 3.4 7.4 + - - +
1035D PHE* 3.1 57.5 + - + -
1138D VAL* 4.5 2.7 - - + -
1141D VAL* 3.7 24.2 - - + -
1142D TYR* 3.6 26.0 - - + +
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Residues in contact with GLN1032 (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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869D ASP* 3.8 35.7 + - - +
872D TYR* 5.7 0.7 - - - -
873D LEU* 4.1 16.6 - - + +
876D ARG* 3.5 32.7 + - - +
1028D LEU* 3.1 22.9 + - - +
1029D PRO* 3.7 12.5 - - + +
1030D ARG 3.2 0.2 - - - -
1031D VAL* 1.3 74.8 - - - +
1033D GLU* 1.3 64.6 + - - +
1035D PHE* 4.6 0.7 - - - +
1036D GLU* 3.1 36.4 + - + +
1038D ARG* 4.6 3.7 + - - +
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Residues in contact with GLU1033 (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 PRO* 2.9 17.6 + - + +
1030D ARG* 3.2 42.2 + - - +
1032D GLN* 1.3 75.9 - - - +
1034D LEU* 1.3 60.3 + - - +
1037D ALA* 3.5 1.0 + - - -
1038D ARG* 3.1 47.9 + - + +
1039D VAL 5.0 0.2 - - - +
1040D PRO* 3.7 10.6 - - + +
1041D ARG* 3.1 42.9 + - - +
1118D PRO* 5.4 1.7 - - - +
19H C 5.7 3.5 + - - +
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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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1030D ARG* 3.3 53.4 + - + +
1031D VAL* 3.8 6.3 - - - +
1032D GLN 3.1 0.6 - - - -
1033D GLU* 1.3 75.6 - - - +
1035D PHE* 1.3 65.4 + - - +
1036D GLU 3.2 1.6 - - - -
1037D ALA* 3.2 12.5 + - - +
1040D PRO* 6.1 0.2 - - + -
1118D PRO* 4.5 11.6 - - + +
1133D HIS* 5.5 2.0 - - - +
1134D LEU* 4.0 32.7 - - + +
1137D GLU* 3.7 27.6 - - + +
1138D VAL* 3.6 35.4 - - + +
1141D VAL* 4.9 0.7 - - + -
1161D MET* 3.7 9.5 - - - +
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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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873D LEU* 4.6 9.0 - - + -
877D LEU* 3.5 24.0 - - + -
1003D ILE* 4.2 22.9 - - + -
1031D VAL* 3.1 47.4 + - + +
1032D GLN 4.6 1.3 - - - +
1034D LEU* 1.3 79.7 - - - +
1036D GLU* 1.3 59.5 + - + +
1037D ALA 3.4 0.2 - - - -
1138D VAL* 3.6 31.6 - - + -
1154D ILE* 4.4 9.6 - - + -
1157D ILE* 3.5 34.3 - - + -
1158D VAL* 5.6 2.9 - - + -
1161D MET* 3.3 18.1 - - - +
1210D ILE* 3.0 38.8 + - + +
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Residues in contact with GLU1036 (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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873D LEU* 6.0 0.7 - - + -
876D ARG* 2.9 30.9 + - - +
1032D GLN* 3.1 24.3 + - + +
1035D PHE* 1.3 74.8 - - - +
1037D ALA* 1.3 71.0 + - - +
1038D ARG* 3.2 41.3 + - + +
1209D GLY* 3.3 14.5 + - - -
1210D ILE* 3.5 14.5 + - + +
1211D THR* 2.5 44.5 + - - -
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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