Contacts of the strand formed by residues 73 - 78 (chain 3) in PDB entry 5NER
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 ILE 73 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673 LYS* 2.4 31.5 + - - +
713 ASP* 2.9 15.4 + - - +
723 ARG* 1.3 76.6 - - - +
743 LEU* 1.3 59.3 + - - +
753 ALA 4.2 7.4 - - - +
763 GLN* 3.4 40.2 - - + +
1343 LYS* 3.0 38.4 - - + +
1853 CYS* 6.2 0.2 - - + -
1863 LEU 3.8 4.3 - - - +
1873 PHE* 3.4 21.8 - - + -
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Residues in contact with LEU 74 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573 PHE* 5.3 1.4 - - - -
643 VAL* 3.7 46.9 - - + +
653 THR 4.4 9.9 - - - +
663 THR* 5.5 0.7 - - + -
673 LYS* 4.3 12.0 + - + +
723 ARG 4.1 3.4 - - - +
733 ILE* 1.3 80.1 - - - +
753 ALA* 1.3 60.0 + - - +
1213 TYR* 3.9 31.6 - - + -
1863 LEU* 2.9 29.0 + - + +
1873 PHE 4.7 0.2 - - - +
1883 GLN* 3.4 42.8 - - + +
1993 LEU* 4.7 0.9 - - + -
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Residues in contact with ALA 75 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573 PHE* 3.4 35.0 - - + -
643 VAL* 5.3 0.4 - - + -
733 ILE* 4.2 3.3 - - - +
743 LEU* 1.3 80.6 - - - +
763 GLN* 1.3 62.8 + - - +
773 PHE* 4.3 13.5 - - + -
853 HIS* 4.9 3.4 - - - +
1843 VAL 4.5 1.3 - - - -
1853 CYS* 3.7 0.3 - - - -
1863 LEU* 2.7 45.2 + - + +
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Residues in contact with GLN 76 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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733 ILE* 3.4 35.4 - - + +
753 ALA* 1.3 78.5 - - - +
773 PHE* 1.3 62.6 + - - +
853 HIS* 4.9 6.1 + - - -
1323 PRO* 3.1 35.0 + - + +
1333 PRO 3.0 23.4 + - - -
1343 LYS* 5.5 2.3 - - - +
1833 TRP* 5.1 5.9 - - + -
1843 VAL 3.6 5.4 - - - -
1853 CYS* 3.4 20.7 - - - -
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Residues in contact with PHE 77 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553 LEU* 4.0 26.7 - - + -
573 PHE* 5.2 0.9 - + - -
753 ALA* 4.3 11.0 - - + -
763 GLN* 1.3 83.8 - - - +
783 ASP* 1.3 78.6 + - - +
793 LEU* 5.3 2.5 - - + -
833 ALA* 4.5 7.2 - - + -
853 HIS* 3.3 42.2 - + + +
863 MET* 4.4 20.6 - - + -
1073 LEU* 4.5 12.3 - - + -
1833 TRP* 3.5 6.4 - - - -
1843 VAL* 3.1 57.4 + - + +
1863 LEU* 6.4 0.7 - - + -
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Residues in contact with ASP 78 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1991 ALA* 5.0 4.5 - - - +
2001 ARG* 3.2 47.2 + - - +
773 PHE* 1.3 88.6 - - - +
793 LEU* 1.3 60.7 + - - +
803 SER* 2.8 18.2 + - - +
833 ALA* 3.7 11.8 - - + +
1803 VAL* 4.9 3.9 - - + +
1823 GLY 3.7 7.1 - - - +
1833 TRP* 2.8 29.5 + - - -
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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
------------------------------------------------------------
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