Contacts of the strand formed by residues 81 - 89 (chain 2) 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 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232 VAL* 4.2 3.6 - - - -
262 GLN* 3.6 7.0 - - - +
692 VAL* 3.4 2.9 - - - -
702 PHE* 2.8 54.7 + - + +
782 LYS* 5.2 13.9 - - - +
792 PRO* 3.5 16.8 - - + +
802 LEU* 1.3 79.7 - - - +
822 LEU* 1.3 64.0 + - - +
832 SER* 3.3 3.0 + - - -
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Residues in contact with LEU 82 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232 VAL* 4.0 18.7 - - + +
262 GLN* 2.8 30.0 + - + +
272 LEU* 3.8 38.4 - - + +
302 LYS* 5.5 5.7 - - + +
672 LEU* 4.2 24.7 - - + -
682 ARG 3.7 7.2 - - - +
692 VAL* 4.4 1.6 - - + +
812 THR* 1.3 72.1 - - - +
832 SER* 1.3 61.3 + - - +
842 ASN* 3.4 24.9 - - - +
852 TYR* 3.9 20.4 - - + -
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Residues in contact with SER 83 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522 ASN* 5.0 0.5 + - - -
682 ARG* 2.7 37.6 + - - +
702 PHE* 3.5 28.6 + - - +
812 THR* 3.3 3.6 + - - -
822 LEU* 1.3 73.5 - - - +
842 ASN* 1.3 62.8 + - - +
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Residues in contact with ASN 84 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881 ASN* 3.1 21.1 + - - +
302 LYS* 6.3 0.9 - - - +
682 ARG* 2.9 31.4 + - + -
822 LEU* 3.4 8.5 - - - +
832 SER* 1.3 82.4 - - - +
852 TYR* 1.3 81.8 + - - +
982 PHE* 3.8 34.1 + - + -
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Residues in contact with TYR 85 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881 ASN* 3.1 55.1 + - + +
272 LEU* 3.5 26.2 - - + -
302 LYS* 3.4 44.7 + - + +
312 GLU* 2.6 30.1 + - - -
652 VAL* 4.3 1.3 - - + -
662 HIS 3.1 13.5 - - - +
672 LEU* 4.1 15.5 - - + -
822 LEU* 3.9 13.7 - - + -
842 ASN* 1.3 85.1 + - - +
862 GLN* 1.3 68.9 + - - +
872 THR* 3.7 20.4 - - + -
982 PHE* 3.7 3.6 - - - -
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Residues in contact with GLN 86 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861 GLN* 6.1 0.8 - - - +
871 THR 6.0 1.1 - - - -
881 ASN* 5.8 0.7 - - - -
652 VAL* 3.3 5.0 - - - +
662 HIS* 2.8 46.0 + - + +
852 TYR* 1.3 80.7 - - - +
872 THR* 1.3 64.6 + - - +
892 LYS* 3.0 36.9 + - - +
962 THR* 4.5 7.6 + - - -
982 PHE* 3.3 47.1 - - + +
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Residues in contact with THR 87 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311 GLU* 4.3 6.6 + - - -
851 TYR 5.5 0.2 - - - +
861 GLN* 6.0 1.9 - - - -
871 THR* 2.9 31.4 + - - +
881 ASN* 6.0 0.4 - - - +
272 LEU* 5.3 0.2 - - + -
312 GLU* 3.9 21.3 + - + +
352 PHE* 6.0 0.7 - - + -
642 PHE 3.9 4.9 - - - -
652 VAL* 3.9 18.6 - - + -
852 TYR* 3.7 29.6 - - + -
862 GLN* 1.3 78.4 - - - +
882 ASN* 1.3 77.5 + - - +
892 LYS* 3.2 11.4 + - - +
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Residues in contact with ASN 88 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301 LYS* 3.2 26.1 + - - +
311 GLU* 4.9 1.1 + - - +
841 ASN* 3.1 27.6 + - - +
851 TYR* 3.1 56.0 + - + +
861 GLN* 5.9 0.9 - - - -
632 ASP* 6.0 3.4 - - - -
642 PHE 3.6 5.2 + - - +
872 THR* 1.3 81.9 - - - +
892 LYS* 1.3 65.5 + - - +
902 ALA 4.4 0.2 + - - -
932 ASP* 4.6 1.6 - - - +
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Residues in contact with LYS 89 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622 GLU 4.0 2.8 - - - +
632 ASP* 3.9 3.5 - - - +
642 PHE* 3.0 37.3 + - + +
662 HIS* 3.7 44.3 + - + +
862 GLN* 3.0 43.7 + - - +
872 THR 3.7 9.0 - - - +
882 ASN* 1.3 84.4 - - - +
902 ALA* 1.3 59.8 + - - +
932 ASP* 3.5 18.0 + - + +
942 GLU 5.2 2.2 + - - -
962 THR* 5.1 5.5 + - - +
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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
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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