Contacts of the strand formed by residues 787 - 791 (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 CYS 787 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338N HIS* 5.5 0.4 - - - -
341N PHE* 3.6 43.1 - - + -
785N PRO 2.7 16.2 + - - -
786N THR* 1.3 75.3 - - - +
788N VAL* 1.3 65.9 + - - +
789N ILE* 3.1 30.3 + - - +
881N PRO 4.4 1.1 - - - -
882N ALA 2.9 27.6 - - - +
883N ARG 3.7 0.4 - - - +
884N VAL* 4.0 1.8 - - - -
909N GLY* 3.8 5.6 - - - -
910N GLY 3.5 12.0 + - - +
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Residues in contact with VAL 788 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787N CYS* 1.3 68.7 - - - +
789N ILE* 1.3 54.4 + - - +
790N GLY 4.3 4.5 - - - +
802N TYR* 2.9 37.5 - - + +
880N ASN 2.3 24.1 - - - +
881N PRO* 3.2 2.1 - - - +
882N ALA* 2.9 30.7 + - + -
884N VAL* 3.8 28.2 - - + +
889N LEU* 5.0 4.9 - - + -
892N LEU* 6.3 1.3 - - + -
906N LEU* 4.8 7.9 - - + -
907N SER 4.7 5.4 - - - +
909N GLY* 4.2 9.4 - - - +
910N GLY 3.8 4.7 - - - -
912N ILE* 3.8 24.2 - - + -
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Residues in contact with ILE 789 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337N LEU* 3.8 38.1 - - + +
338N HIS* 3.2 41.3 - - + +
341N PHE* 5.8 2.0 - - + -
785N PRO 5.3 0.4 - - - +
787N CYS* 3.1 32.4 + - - +
788N VAL* 1.3 70.0 - - - +
790N GLY* 1.3 68.1 + - - +
791N LEU* 3.2 4.0 + - + -
880N ASN* 3.3 4.0 - - - +
881N PRO* 5.2 3.4 - - + -
910N GLY* 3.1 13.5 + - - +
911N ILE* 3.7 17.8 - - + +
912N ILE 3.3 17.5 + - - -
931N HIS* 6.1 3.4 - - + -
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Residues in contact with GLY 790 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788N VAL* 3.7 3.2 - - - +
789N ILE* 1.3 75.1 - - - +
791N LEU* 1.3 61.7 + - - +
798N PRO* 3.0 11.3 - - - +
802N TYR* 4.9 1.6 - - - -
880N ASN* 2.9 36.9 + - - +
912N ILE* 3.5 8.5 - - - -
914N LEU* 3.3 25.8 - - - -
931N HIS* 4.5 2.8 - - - -
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Residues in contact with LEU 791 (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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250N PHE* 4.2 18.2 - - + -
333N MET* 6.2 3.8 - - + -
337N LEU* 3.9 39.9 - - + -
789N ILE* 3.2 1.1 + - + +
790N GLY* 1.3 77.9 - - - +
792N ASN* 1.3 65.4 + - - +
795N LEU* 3.7 41.3 - - + +
796N LYS 3.0 26.7 - - - +
797N MET* 5.0 1.8 - - + -
798N PRO* 3.8 2.2 - - - +
911N ILE* 4.1 16.2 - - + -
912N ILE 2.9 8.9 + - - +
913N ILE* 3.6 9.2 - - + +
914N LEU* 3.0 22.8 + - - +
931N HIS* 6.4 0.4 - - + -
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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
------------------------------------------------------------
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