Contacts of the strand formed by residues 1009 - 1015 (chain K) in PDB entry 5ANC
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 ARG1009 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96D LYS* 3.7 39.8 + - - +
1000K TYR* 5.1 8.3 - - - +
1003K LEU* 5.5 4.5 - - - +
1008K GLY* 1.3 76.1 - - - +
1010K VAL* 1.3 69.8 + - - +
1011K LEU* 3.5 29.8 + - + +
1026K ALA* 3.6 4.1 - - - -
1027K VAL* 3.3 37.1 + - + +
1475N A 4.7 2.4 + - - -
1476N U 3.0 36.8 + - - +
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Residues in contact with VAL1010 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D LYS* 4.3 0.2 + - - -
1000K TYR* 3.3 41.1 - - + +
1003K LEU* 5.2 1.7 - - + +
1009K ARG* 1.3 82.7 + - + +
1011K LEU* 1.3 62.8 + - - +
1012K GLN 4.4 4.5 - - - +
1024K ILE* 3.4 26.9 - - + -
1025K LYS 3.3 15.7 - - - +
1026K ALA* 3.8 10.5 - - + +
1476N U 4.0 14.1 + - - +
1477N G 3.3 34.0 + - - +
1478N G 4.7 2.0 - - - +
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Residues in contact with LEU1011 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D GLY* 5.6 0.7 - - - -
26D SER* 4.8 1.0 + - - -
96D LYS* 3.6 26.5 + - - -
986K THR* 5.2 4.0 - - - +
1009K ARG* 3.5 36.1 + - + +
1010K VAL* 1.3 72.2 - - - +
1012K GLN* 1.3 80.4 + - + +
1025K LYS* 3.3 11.9 + - + +
1026K ALA* 5.0 4.9 - - - +
1027K VAL* 3.9 31.2 - - + +
1477N G 3.6 2.1 + - - +
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Residues in contact with GLN1012 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D SER* 3.3 25.8 + - - +
1010K VAL* 3.7 3.9 - - - -
1011K LEU* 1.3 94.7 - - + +
1013K GLU* 1.3 62.2 + - - +
1024K ILE* 4.3 1.7 - - - +
1025K LYS* 3.1 44.0 + - + +
1477N G 3.9 12.3 - - - -
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Residues in contact with GLU1013 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D SER* 3.7 9.7 - - - -
27D THR* 3.3 20.4 + - - -
996K LEU* 3.8 14.9 - - - +
1012K GLN* 1.3 78.6 - - - +
1014K GLU* 1.3 62.2 - - - +
1015K MET* 3.8 19.1 - - - +
1022K PHE* 3.8 15.0 - - - +
1023K ILE 3.8 12.8 - - - +
1024K ILE* 3.6 24.9 - - + +
1025K LYS* 5.4 0.4 - - - -
1477N G 3.1 69.9 + - + +
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Residues in contact with GLU1014 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D THR* 3.9 5.8 - - - +
41D LYS* 3.4 28.3 + - - +
1013K GLU* 1.3 74.4 - - - +
1015K MET* 1.3 59.4 + - - +
1016K LYS* 5.7 2.5 + - + -
1022K PHE* 3.9 1.4 - - - +
1023K ILE* 2.8 58.7 + - + +
1025K LYS* 4.5 17.2 + - + +
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Residues in contact with MET1015 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D THR* 3.2 41.6 - - + +
28D LEU* 3.8 14.1 - - - -
29D ALA 3.5 14.4 - - - +
33D GLY* 3.5 26.5 - - - +
34D PRO* 5.5 0.2 - - + -
40D LYS* 4.6 10.1 - - + +
41D LYS* 3.5 22.3 + - - -
1013K GLU* 3.8 11.0 - - - +
1014K GLU* 1.3 78.4 - - - +
1016K LYS* 1.3 68.3 + - - +
1017K GLU 3.7 1.7 + - - -
1022K PHE* 3.6 24.7 - - + -
1477N G 3.3 31.2 - - + +
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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