Contacts of the helix formed by residues 1131 - 1137 (chain D) in PDB entry 5NPK
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 ILE1131 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1101D TYR* 4.0 29.4 - - + +
1102D PRO 3.6 12.6 - - - +
1103D LEU* 4.3 12.3 - - + -
1129D THR* 3.6 13.6 - - - +
1130D LYS* 1.3 78.7 - - - +
1132D THR* 1.3 60.9 + - - +
1134D GLU* 3.0 29.4 + - + +
1164D PHE* 3.5 28.6 - - + -
1188D LEU* 4.1 24.5 - - + -
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Residues in contact with THR1132 (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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1050D LEU* 4.1 21.3 - - + -
1103D LEU* 2.6 45.1 + - - +
1128D MET* 3.9 25.1 - - + -
1129D THR* 3.2 12.8 + - - -
1130D LYS 3.2 0.6 - - - -
1131D ILE* 1.3 78.3 - - - +
1133D LEU* 1.3 60.0 + - - +
1135D LEU* 2.9 28.3 + - + +
1136D LEU* 3.3 19.3 + - + +
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Residues in contact with LEU1133 (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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1054D ASN* 5.4 4.0 - - - +
1059D THR* 4.0 26.9 - - + -
1060D PRO* 3.7 27.8 - - + -
1128D MET* 4.3 10.3 - - + -
1129D THR 3.6 1.7 + - - +
1130D LYS* 3.1 23.1 + - + +
1132D THR* 1.3 78.5 - - - +
1134D GLU* 1.3 63.1 + - - +
1136D LEU* 3.4 4.9 + - + +
1137D ARG* 2.9 29.1 + - - +
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Residues in contact with GLU1134 (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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1130D LYS 4.4 2.5 - - - +
1131D ILE* 3.0 25.9 + - + +
1133D LEU* 1.3 83.8 - - - +
1135D LEU* 1.3 62.6 + - - +
1137D ARG* 3.0 40.2 + - - -
1163D ARG* 2.9 42.0 + - + +
1164D PHE* 4.0 14.4 - - + -
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Residues in contact with LEU1135 (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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1040D ASP* 4.8 2.7 - - + +
1042D LEU* 4.8 4.3 - - + -
1050D LEU* 3.7 28.0 - - + -
1103D LEU* 3.9 26.0 - - + -
1131D ILE 3.6 0.4 + - - -
1132D THR* 2.9 15.6 + - + +
1134D GLU* 1.3 78.3 - - - +
1136D LEU* 1.3 59.8 + - + +
1137D ARG 3.5 0.4 + - - -
1160D LEU* 3.4 15.9 - - + +
1161D PRO* 3.3 11.6 - - - +
1162D ALA* 3.0 41.8 + - + +
1164D PHE* 3.6 29.2 - - + +
1166D ASN* 3.9 23.6 - - + +
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Residues in contact with LEU1136 (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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1050D LEU* 3.7 17.5 - - + +
1051D TYR* 4.3 4.9 - - - -
1054D ASN* 3.4 46.6 + - + +
1128D MET* 3.7 20.6 - - - -
1132D THR* 3.3 19.0 + - + +
1133D LEU* 3.7 5.2 - - + +
1135D LEU* 1.3 79.0 - - + +
1137D ARG* 1.3 67.0 + - - +
1138D ASP 3.2 0.3 + - - -
1139D ILE* 3.0 43.2 + - + +
1160D LEU* 4.0 23.1 - - + -
1161D PRO* 4.4 3.1 - - - -
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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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1133D LEU 2.9 16.6 + - - +
1134D GLU* 3.0 38.6 + - - +
1135D LEU 3.5 1.4 - - - -
1136D LEU* 1.3 73.9 - - - +
1138D ASP* 1.3 83.5 + - - +
1161D PRO* 3.2 23.4 - - - +
1163D ARG* 3.8 34.4 - - + +
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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