Contacts of the helix formed by residues 1083 - 1090 (chain D) in PDB entry 4DAJ
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 LYS1083 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1081D ASN* 2.5 18.0 + - - +
1082D ALA* 1.3 75.6 - - + +
1084D LEU* 1.3 64.4 + - + +
1086D PRO* 3.3 10.9 - - - +
1087D VAL* 3.7 17.8 - - - +
1112D ALA* 3.1 34.4 + - + +
1113D GLY* 5.2 0.8 - - - -
1115D THR* 3.5 25.1 - - + +
1118D LEU* 4.6 12.0 - - + +
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Residues in contact with LEU1084 (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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1077D GLY 3.6 19.5 - - - +
1078D ILE* 3.5 23.0 - - + +
1081D ASN* 2.8 20.7 + - + +
1083D LYS* 1.3 74.9 - - + +
1085D LYS* 1.3 60.6 + - - +
1087D VAL* 3.5 6.3 + - - +
1088D TYR* 2.9 28.4 + - - +
1099D LEU* 4.3 6.2 - - + +
1103D VAL* 3.8 25.8 - - + -
1108D GLU* 3.7 22.4 - - + +
1111D VAL* 4.0 32.8 - - + +
1112D ALA* 4.5 3.1 - - - -
1118D LEU* 4.3 15.5 - - + -
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Residues in contact with LYS1085 (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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1078D ILE 3.0 18.5 + - - +
1079D LEU* 3.8 32.5 - - + +
1081D ASN 3.3 9.1 + - - +
1082D ALA* 4.9 0.7 - - - +
1084D LEU* 1.3 72.3 - - - +
1086D PRO* 1.3 75.7 - - + +
1087D VAL 3.0 1.6 - - - -
1088D TYR* 3.0 4.6 + - - -
1089D ASP* 2.9 60.9 + - - +
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Residues in contact with PRO1086 (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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1082D ALA 3.0 25.4 - - - +
1083D LYS* 3.3 10.3 - - - +
1085D LYS* 1.3 98.0 - - + +
1087D VAL* 1.3 58.2 + - + +
1089D ASP* 3.9 6.6 + - + +
1090D SER* 3.1 21.3 + - - -
1122D GLN* 3.6 25.3 + - - +
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Residues in contact with VAL1087 (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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1083D LYS 3.7 14.8 - - - +
1084D LEU 3.5 6.7 + - - +
1085D LYS 3.0 0.6 - - - -
1086D PRO* 1.3 78.9 - - + +
1088D TYR* 1.3 63.1 + - - +
1090D SER* 2.9 18.4 + - - -
1091D LEU* 3.2 18.4 - - + +
1099D LEU* 4.5 11.0 - - + -
1118D LEU* 3.7 52.0 - - + +
1121D LEU* 4.2 17.3 - - + -
1122D GLN* 4.2 13.9 - - + +
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Residues in contact with TYR1088 (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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1075D VAL* 5.2 8.7 - - + +
1078D ILE* 3.3 29.4 - - + -
1079D LEU* 4.3 16.4 - - + -
1084D LEU 2.9 19.7 + - - +
1085D LYS* 3.0 4.7 + - - +
1087D VAL* 1.3 73.5 - - - +
1089D ASP* 1.3 77.9 + - - +
1090D SER 3.0 1.6 - - - -
1091D LEU* 2.9 14.9 + - - +
1096D ARG* 3.5 45.5 + - + +
1099D LEU* 3.7 16.5 - - + +
1100D ILE* 3.3 39.7 - - + +
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Residues in contact with ASP1089 (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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1079D LEU* 4.6 3.6 - - - +
1085D LYS* 2.9 51.5 + - - +
1086D PRO* 3.9 6.1 - - + +
1088D TYR* 1.3 86.4 - - - +
1090D SER* 1.3 58.5 + - - +
1091D LEU 4.0 0.2 - - - +
1096D ARG* 3.3 22.1 + - - +
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Residues in contact with SER1090 (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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1086D PRO 3.1 14.7 + - - -
1087D VAL* 2.9 18.4 + - - -
1088D TYR 3.0 0.2 - - - -
1089D ASP* 1.3 77.9 - - - +
1091D LEU* 1.3 61.3 - - - +
1092D ASP 4.2 0.5 + - - -
1121D LEU 5.2 3.1 - - - +
1122D GLN* 3.4 35.2 - - - +
1126D TRP* 5.6 3.3 - - - -
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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