Contacts of the strand formed by residues 81 - 89 (chain 3) in PDB entry 4N6V
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 THR 81 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233 VAL* 4.3 0.7 - - - -
263 GLN* 3.8 5.2 - - - +
693 VAL* 3.3 6.2 - - - +
703 PHE* 2.9 58.8 + - + +
723 SER* 5.9 0.7 - - - +
783 LYS* 5.4 7.2 - - + -
793 PRO* 3.1 25.4 - - + +
803 LEU* 1.3 74.9 - - - +
823 LEU* 1.3 61.2 + - - +
833 SER* 3.2 6.9 + - - -
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Residues in contact with LEU 82 (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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233 VAL* 4.1 16.2 - - + +
263 GLN* 2.9 27.2 + - + +
273 LEU* 3.8 38.4 - - + +
303 LYS* 4.6 15.0 + - + +
673 LEU* 4.1 26.0 - - + -
683 ARG 3.6 7.4 - - - +
693 VAL* 4.3 6.1 - - + +
813 THR* 1.3 70.8 - - - +
833 SER* 1.3 61.0 + - - +
843 ASN 3.4 23.6 - - - +
853 TYR* 3.9 21.5 - - + -
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Residues in contact with SER 83 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523 ASN* 5.2 0.3 + - - -
683 ARG* 2.8 38.7 + - - -
703 PHE* 3.6 25.6 - - - +
813 THR* 3.2 5.4 + - - -
823 LEU* 1.3 73.0 - - - +
843 ASN* 1.3 62.7 + - - +
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Residues in contact with ASN 84 (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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683 ARG* 2.8 34.7 + - + +
823 LEU* 3.4 7.6 - - - +
833 SER* 1.3 82.8 - - - +
853 TYR* 1.3 86.4 + - - +
983 PHE* 3.6 37.8 + - + -
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Residues in contact with TYR 85 (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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273 LEU* 3.6 29.8 - - + -
303 LYS* 3.5 32.9 + - + +
313 GLU* 2.6 34.3 + - - -
653 VAL* 5.6 0.7 - - + -
663 HIS 3.1 15.0 - - - +
673 LEU* 4.2 14.1 - - + -
823 LEU* 3.9 16.8 - - + -
843 ASN* 1.3 90.5 + - - +
863 GLN* 1.3 69.7 + - - +
873 THR* 3.8 17.5 - - + -
983 PHE* 3.6 4.3 - - - -
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Residues in contact with GLN 86 (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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653 VAL* 3.3 6.1 - - - +
663 HIS* 2.9 49.7 + - + +
853 TYR* 1.3 80.5 - - - +
873 THR* 1.3 64.5 + - - +
893 LYS* 3.5 35.1 + - - +
963 THR* 4.9 8.3 + - - -
983 PHE* 3.6 43.0 - - + +
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Residues in contact with THR 87 (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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313 GLU* 4.0 18.6 - - + +
353 PHE* 6.1 0.7 - - + -
643 PHE 4.1 4.0 - - - -
653 VAL* 4.2 15.5 - - + -
853 TYR* 3.8 26.5 - - + -
863 GLN* 1.3 80.7 - - - +
883 ASN* 1.3 86.0 + - - +
893 LYS* 3.3 9.6 + - - +
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Residues in contact with ASN 88 (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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633 ASP* 5.6 11.8 - - - +
643 PHE 3.4 7.3 + - - +
653 VAL* 5.2 0.2 - - - +
873 THR* 1.3 90.8 + - - +
893 LYS* 1.3 63.0 + - - +
903 ALA* 4.2 0.3 + - - +
933 ASP* 4.6 1.7 - - - +
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Residues in contact with LYS 89 (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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623 GLU 3.9 0.5 - - - +
633 ASP* 3.9 5.7 - - - +
643 PHE* 3.0 38.0 + - + +
663 HIS* 3.7 41.9 + - + +
863 GLN* 3.5 39.2 + - - +
873 THR 4.1 9.0 - - - +
883 ASN* 1.3 82.9 - - - +
903 ALA* 1.3 59.7 + - - +
933 ASP* 3.5 20.5 + - + +
943 GLU 4.9 3.8 + - - -
963 THR* 5.4 4.0 + - - -
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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