Contacts of the helix formed by residues 777 - 781 (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 HIS 777 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371N ILE* 3.7 26.2 - - + -
374N SER* 3.1 24.6 + - - -
375N PHE* 4.2 6.3 - - - -
403N THR* 4.2 22.1 + - + +
406N ALA* 3.6 20.5 - - + +
407N SER* 4.4 7.0 - - - -
410N VAL* 3.9 17.1 - - + +
444N TYR* 3.5 37.9 + + - +
448N LEU* 4.1 6.6 - - + +
774N PRO 4.3 7.0 - - - -
775N LEU 3.4 1.2 - - - -
776N SER* 1.3 88.5 + - - +
778N PHE* 1.3 59.0 + - - +
779N LEU 2.8 12.7 + - - +
780N SER* 3.0 23.2 + - - -
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Residues in contact with PHE 778 (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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444N TYR* 3.9 24.0 - + - -
448N LEU* 5.3 2.0 - - + -
479N LEU* 4.9 8.3 - - + -
483N LEU* 4.1 35.2 - - + -
514N LEU* 4.3 17.7 - - + -
518N LEU* 4.6 9.2 - - + -
761N VAL* 4.3 3.4 - - + +
762N GLY* 2.8 32.1 - - - +
765N VAL* 3.3 52.0 - - + -
766N PHE* 4.3 0.6 - - - +
775N LEU* 3.7 33.7 + - + -
776N SER 3.9 0.2 - - - -
777N HIS* 1.3 75.5 - - - +
779N LEU* 1.3 57.8 + - - +
780N SER 3.2 3.6 + - - -
781N LEU* 3.5 19.5 + - + +
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Residues in contact with LEU 779 (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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375N PHE* 3.6 19.3 - - + -
693N LEU* 4.1 18.4 - - + -
736N ILE* 3.8 30.1 - - + -
746N ILE* 4.6 4.0 - - + -
762N GLY 3.7 9.3 + - - +
763N VAL* 3.5 31.6 - - + -
766N PHE* 3.8 35.2 - - + +
777N HIS 2.8 2.4 + - - -
778N PHE* 1.3 76.3 - - - +
780N SER* 1.3 57.1 + - - +
781N LEU 3.3 1.7 + - - -
782N ALA* 4.4 2.4 - - + +
783N TYR* 2.9 43.4 + - + +
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Residues in contact with SER 780 (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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375N PHE* 4.3 0.6 - - - -
378N CYS* 3.9 10.0 - - - -
410N VAL* 3.5 36.2 - - - +
413N LYS* 4.3 21.0 - - - +
448N LEU* 4.5 5.2 + - - +
777N HIS 3.0 13.1 + - - -
779N LEU* 1.3 77.3 - - - +
781N LEU* 1.3 73.8 + - - +
782N ALA 3.6 0.4 - - - -
783N TYR* 3.7 24.1 - - - +
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Residues in contact with LEU 781 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413N LYS* 4.5 12.1 - - - +
448N LEU* 4.9 8.3 - - + +
451N ALA* 4.2 21.3 - - + -
452N ASN* 5.0 3.6 - - - +
483N LEU* 3.9 27.4 - - + -
486N MET* 4.8 12.8 - - + -
756N HIS* 5.1 2.6 + - - -
758N PRO* 3.2 42.1 - - + +
759N SER* 3.5 2.4 + - - -
761N VAL* 5.4 2.7 - - + -
762N GLY* 4.2 2.5 - - - +
778N PHE* 3.5 27.1 + - + +
779N LEU 3.3 0.4 - - - -
780N SER* 1.3 95.5 - - - +
782N ALA* 1.3 59.4 + - - +
783N TYR 3.4 3.6 - - - +
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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