Contacts of the strand formed by residues 81 - 89 (chain 9) 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 9).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344 LYS* 4.0 23.4 - - - +
239 VAL* 4.3 4.0 - - - -
269 GLN* 3.5 9.6 - - - +
699 VAL* 3.4 2.7 - - - +
709 PHE* 2.8 46.3 + - - -
789 LYS* 5.6 1.9 - - - +
799 PRO* 3.0 15.2 + - - +
809 LEU* 1.3 72.0 + - - +
829 LEU* 1.3 70.8 + - - +
839 SER* 3.2 7.0 + - - +
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Residues in contact with LEU 82 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239 VAL* 4.1 12.2 - - + +
269 GLN* 2.8 29.4 + - + +
279 LEU* 3.7 40.8 - - + +
309 LYS* 5.4 6.2 - - + +
679 LEU* 3.9 26.7 - - + -
689 ARG 3.5 7.9 - - - +
699 VAL* 4.1 5.8 - - + +
819 THR* 1.3 76.0 - - - +
839 SER* 1.3 60.4 + - - +
849 ASN* 3.3 26.7 - - - +
859 TYR* 4.0 17.9 - - + -
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Residues in contact with SER 83 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529 ASN* 5.0 1.0 + - - -
689 ARG* 2.7 39.4 + - - -
699 VAL 4.5 0.3 - - - -
709 PHE* 3.6 26.5 + - - +
819 THR* 3.2 5.8 + - - +
829 LEU* 1.3 72.2 - - - +
849 ASN* 1.3 60.6 + - - +
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Residues in contact with ASN 84 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888 ASN* 3.0 21.4 + - - +
309 LYS* 6.3 0.4 - - - +
689 ARG* 2.9 33.5 + - + -
829 LEU* 3.3 8.4 - - - +
839 SER* 1.3 81.2 - - - +
859 TYR* 1.3 81.8 + - - +
989 PHE* 3.8 35.2 + - + -
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Residues in contact with TYR 85 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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878 THR 5.4 0.3 - - - +
888 ASN* 3.0 53.3 + - + +
279 LEU* 3.5 30.7 - - + -
309 LYS* 3.5 45.3 + - + +
319 GLU* 2.6 29.8 + - - -
659 VAL* 4.4 1.3 - - + -
669 HIS 3.1 13.2 - - - +
679 LEU* 4.3 9.6 - - + -
829 LEU* 4.0 11.0 - - + -
849 ASN* 1.3 87.3 + - - +
869 GLN* 1.3 70.5 + - - +
879 THR* 3.6 20.6 - - + -
989 PHE* 3.7 3.4 - - - -
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Residues in contact with GLN 86 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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868 GLN* 6.0 2.0 - - - +
878 THR 5.9 2.2 - - - -
888 ASN* 5.8 0.7 - - - -
659 VAL* 3.2 5.0 - - - +
669 HIS* 2.8 43.2 + - + +
859 TYR* 1.3 78.5 - - - +
879 THR* 1.3 64.3 + - - +
899 LYS* 3.2 36.0 + - - +
969 THR* 4.3 8.5 + - - -
989 PHE* 3.4 47.0 - - + +
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Residues in contact with THR 87 (chain 9).
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* 4.3 6.5 + - - -
858 TYR 5.3 0.3 - - - +
868 GLN* 5.9 1.6 - - - -
878 THR* 2.9 31.8 + - - +
888 ASN* 6.0 0.2 - - - +
319 GLU* 3.8 22.2 + - + +
359 PHE* 6.1 0.2 - - + -
649 PHE 4.1 0.2 - - - -
659 VAL* 3.8 22.0 - - + -
859 TYR* 3.6 30.9 - - + -
869 GLN* 1.3 77.7 - - - +
889 ASN* 1.3 78.1 + - - +
899 LYS* 3.3 12.2 + - - +
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Residues in contact with ASN 88 (chain 9).
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* 3.0 25.3 + - - +
318 GLU* 4.9 1.0 + - - +
848 ASN* 3.1 19.0 + - - +
858 TYR* 3.1 68.1 + - + +
868 GLN* 5.8 0.9 - - - -
878 THR 5.9 0.2 - - - +
639 ASP* 6.0 2.7 - - - -
649 PHE 3.7 3.8 + - - +
879 THR* 1.3 82.3 - - - +
899 LYS* 1.3 64.4 + - - +
939 ASP* 4.4 2.4 - - - +
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Residues in contact with LYS 89 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629 GLU 4.0 2.9 - - - +
639 ASP* 3.9 2.9 - - - +
649 PHE* 3.0 38.3 + - + +
669 HIS* 3.6 45.0 + - + +
869 GLN* 3.2 39.6 + - - +
879 THR 3.6 12.3 - - - +
889 ASN* 1.3 83.8 - - - +
909 ALA* 1.3 60.6 - - - +
939 ASP* 3.5 15.7 + - + +
949 GLU 5.0 4.4 + - - -
969 THR* 5.1 5.1 + - - +
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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