Contacts of the helix formed by residues 1136 - 1142 (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 SER1136 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1114D PHE* 4.5 19.4 - - - -
1132D ASN 4.2 5.3 + - - -
1133D LEU* 2.8 25.4 + - - -
1134D ALA 3.2 3.8 - - - +
1135D LYS* 1.3 82.0 - - - +
1137D ARG* 1.3 64.4 + - - +
1138D TRP* 3.4 16.3 + - - +
1139D TYR 3.5 6.2 + - - -
1140D ASN* 3.5 18.5 + - - +
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Residues in contact with ARG1137 (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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1136D SER* 1.3 73.9 - - - +
1138D TRP* 1.3 61.2 + - - +
1140D ASN* 3.2 10.3 - - - +
1141D GLN* 2.9 56.1 + - + +
2002D PO4 2.8 44.4 + - - -
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Residues in contact with TRP1138 (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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1101D ASN* 5.3 0.2 - - - -
1102D MET* 3.4 52.3 - - + -
1105D GLN* 3.0 33.9 + - - +
1106D MET* 3.9 31.2 - - + -
1114D PHE* 4.5 14.1 - + + -
1133D LEU* 5.0 10.8 - - + -
1136D SER* 3.4 9.8 + - - +
1137D ARG* 1.3 75.0 - - - +
1139D TYR* 1.3 72.2 + - - +
1141D GLN* 2.8 20.1 + - + +
1142D THR* 3.1 21.6 + - - -
1145D ARG* 5.0 2.4 - - + +
1146D ALA* 4.0 33.3 - - + +
1149D VAL* 4.1 17.7 - - + -
1150D ILE* 4.6 13.2 - - + -
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Residues in contact with TYR1139 (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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1133D LEU 3.5 18.8 - - - +
1134D ALA* 3.5 37.7 - - + +
1136D SER* 3.5 3.3 + - - +
1138D TRP* 1.3 79.6 - - + +
1140D ASN* 1.3 62.7 + - + +
1143D PRO* 3.0 46.8 - - + +
1146D ALA* 3.8 27.4 - - + -
1147D LYS* 3.8 38.0 + - + -
1150D ILE* 4.2 10.8 - - + -
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Residues in contact with ASN1140 (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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1136D SER 3.5 13.8 + - - +
1137D ARG* 3.2 15.8 + - - +
1138D TRP 2.9 0.2 + - - -
1139D TYR* 1.3 85.5 - - + +
1141D GLN* 1.3 74.4 + - - +
1143D PRO* 4.3 5.4 - - - +
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Residues in contact with GLN1141 (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* 3.5 27.2 + - - +
1137D ARG* 2.9 47.5 + - + +
1138D TRP* 2.8 16.5 + - + +
1140D ASN* 1.3 82.2 - - - +
1142D THR* 1.3 69.4 + - + +
1143D PRO* 3.9 3.7 - - - +
2002D PO4 4.7 6.3 + - - -
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Residues in contact with THR1142 (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 ASP* 5.8 0.2 - - - +
1021D THR* 4.1 18.4 - - + +
1022D GLU* 3.8 22.2 + - + +
1105D GLN* 4.2 11.5 + - - +
1138D TRP* 3.1 21.6 + - - +
1139D TYR 3.4 3.4 - - - -
1141D GLN* 1.3 87.5 - - + +
1143D PRO* 1.3 67.2 - - - +
1144D ASN* 3.3 3.7 + - - -
1145D ARG* 3.8 8.8 + - - +
1146D ALA* 3.5 19.1 + - - +
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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