Contacts of the strand formed by residues 910 - 913 (chain N) in PDB entry 5L4K
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 GLY 910 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254N GLU* 3.8 20.9 - - - -
338N HIS* 6.4 0.7 - - - -
751N ARG* 4.2 8.6 - - - +
786N THR* 5.3 0.4 - - - +
787N CYS 3.5 10.0 + - - +
788N VAL* 3.8 1.4 - - - -
789N ILE* 3.1 25.8 + - - -
908N ILE 3.8 0.8 + - - -
909N GLY* 1.3 76.9 - - - +
911N ILE* 1.3 66.5 + - - -
912N ILE* 3.3 3.0 + - - +
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Residues in contact with ILE 911 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250N PHE* 3.3 63.6 - - + +
253N TYR* 6.2 0.9 - - + -
254N GLU* 4.8 1.4 + - - -
334N ALA* 3.9 24.7 - - + -
337N LEU* 4.2 12.6 - - + -
338N HIS* 5.1 3.4 - - + +
789N ILE* 3.7 34.1 - - + +
791N LEU* 4.1 11.4 - - + -
904N LYS* 4.2 15.6 + - - +
910N GLY* 1.3 71.1 - - - -
912N ILE* 1.3 65.2 + - - +
913N ILE* 4.0 11.2 + - + +
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Residues in contact with ILE 912 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788N VAL* 3.8 28.5 - - + -
789N ILE 3.3 6.5 + - - +
790N GLY* 3.5 4.3 - - - -
791N LEU* 2.9 25.8 + - - +
902N PRO* 4.4 13.0 - - + -
904N LYS* 3.8 35.4 - - + +
905N PRO 4.1 17.9 - - - +
906N LEU* 5.0 9.4 - - + -
907N SER* 4.6 9.4 - - - +
909N GLY 4.0 16.2 - - - +
910N GLY 3.3 5.1 + - - +
911N ILE* 1.3 78.8 - - - +
913N ILE* 1.3 68.6 + - - +
914N LEU* 3.2 10.1 + - + -
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Residues in contact with ILE 913 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243N LEU* 3.4 34.3 - - + +
246N TYR* 4.1 25.1 - - + -
247N GLN* 4.1 22.4 - - + +
250N PHE* 3.4 35.0 - - + -
791N LEU* 3.6 15.9 - - + +
792N ASN 5.2 0.9 - - - +
793N LYS* 5.0 3.8 - - - -
795N LEU* 5.3 0.9 - - + -
903N PHE* 3.2 28.3 + - - +
904N LYS* 4.8 5.3 - - + +
911N ILE* 4.0 10.1 + - + +
912N ILE* 1.3 75.8 - - - +
914N LEU* 1.3 66.4 + - - +
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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