Contacts of the strand formed by residues 81 - 89 (chain 8) 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 8).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238 VAL* 4.2 3.8 - - - -
268 GLN* 3.7 7.2 - - - +
698 VAL* 3.4 3.3 - - - -
708 PHE* 2.8 56.0 + - + +
788 LYS* 6.1 0.9 - - + -
798 PRO* 3.4 18.4 - - + +
808 LEU* 1.3 80.7 - - - +
828 LEU* 1.3 61.7 - - - +
838 SER* 3.3 4.7 + - - -
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Residues in contact with LEU 82 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238 VAL* 3.9 18.3 - - + +
268 GLN* 2.8 31.4 + - + +
278 LEU* 3.8 38.8 - - + +
308 LYS* 5.4 6.3 - - + +
678 LEU* 4.1 24.7 - - + -
688 ARG 3.6 8.7 - - - +
698 VAL* 4.4 0.7 - - + +
818 THR* 1.3 71.7 - - - +
838 SER* 1.3 60.1 + - - +
848 ASN* 3.4 25.4 - - - +
858 TYR* 3.9 19.7 - - + -
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Residues in contact with SER 83 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528 ASN* 5.0 0.9 + - - -
688 ARG* 2.8 38.8 + - - +
698 VAL 4.4 0.3 - - - -
708 PHE* 3.5 28.4 + - - +
818 THR* 3.3 3.5 + - - -
828 LEU* 1.3 73.6 - - - +
848 ASN* 1.3 61.7 + - - +
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Residues in contact with ASN 84 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308 LYS* 6.2 0.9 - - - +
688 ARG* 2.9 34.9 + - + +
828 LEU* 3.4 6.2 - - - +
838 SER* 1.3 82.1 - - - +
858 TYR* 1.3 88.0 + - - +
988 PHE* 3.8 33.3 + - + -
889 ASN* 3.1 20.0 + - - +
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Residues in contact with TYR 85 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278 LEU* 3.5 24.7 - - + -
308 LYS* 3.5 43.9 + - + +
318 GLU* 2.6 30.3 + - - -
658 VAL* 4.3 1.1 - - + -
668 HIS 3.2 13.5 - - - +
678 LEU* 4.1 16.2 - - + -
828 LEU* 3.9 12.1 - - + -
848 ASN* 1.3 88.4 + - - +
868 GLN* 1.3 70.3 + - - +
878 THR* 3.7 20.9 - - + -
988 PHE* 3.7 2.9 - - - -
879 THR 5.3 0.5 - - - +
889 ASN* 3.1 54.1 + - + +
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Residues in contact with GLN 86 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658 VAL* 3.2 5.1 - - - +
668 HIS* 2.9 42.2 + - + +
858 TYR* 1.3 79.4 - - - +
878 THR* 1.3 64.4 + - - +
898 LYS* 3.0 36.9 + - - +
968 THR* 4.6 7.0 + - - -
988 PHE* 3.3 46.8 - - + +
869 GLN* 6.0 2.0 - - - +
879 THR 5.9 1.6 - - - -
889 ASN* 5.8 0.9 - - - -
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Residues in contact with THR 87 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318 GLU* 3.8 21.4 + - + +
358 PHE* 5.9 1.1 - - + -
648 PHE 3.9 4.7 - - - -
658 VAL* 4.2 17.3 - - + -
858 TYR* 3.7 29.6 - - + -
868 GLN* 1.3 78.0 - - - +
888 ASN* 1.3 75.7 + - - +
898 LYS* 3.3 12.3 + - - +
319 GLU* 4.4 7.4 + - - -
859 TYR 5.4 0.5 - - - +
869 GLN* 5.9 1.4 - - - -
879 THR* 2.9 31.0 + - - +
889 ASN* 5.9 0.6 - - - +
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Residues in contact with ASN 88 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638 ASP* 5.7 5.1 - - - +
648 PHE 3.5 5.2 + - - -
878 THR* 1.3 81.3 - - - +
898 LYS* 1.3 64.7 + - - +
908 ALA 4.4 0.2 + - - -
938 ASP* 4.6 1.6 - - - +
309 LYS* 3.1 24.5 + - - +
319 GLU* 5.0 0.8 + - - +
849 ASN* 3.0 28.3 + - - +
859 TYR* 3.0 57.8 + - + +
869 GLN* 5.8 0.7 - - - -
879 THR 6.0 0.2 - - - +
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Residues in contact with LYS 89 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628 GLU 3.9 2.8 - - - +
638 ASP* 3.9 3.1 - - - +
648 PHE* 3.0 36.7 + - + +
668 HIS* 3.7 43.4 + - + +
868 GLN* 3.0 46.0 + - - +
878 THR 3.7 9.0 - - - +
888 ASN* 1.3 84.6 - - - +
908 ALA* 1.3 61.7 + - - +
938 ASP* 3.5 16.7 + - + +
948 GLU 5.1 2.4 + - - -
968 THR* 5.1 5.7 + - - +
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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