Contacts of the strand formed by residues 81 - 89 (chain 6) 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 6).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236 VAL* 4.0 4.0 - - - -
266 GLN* 3.6 7.0 - - - +
696 VAL* 3.3 2.3 - - - -
706 PHE* 2.9 57.1 + - + +
786 LYS* 6.3 2.5 - - - -
796 PRO* 3.3 20.2 - - + +
806 LEU* 1.3 75.6 - - - +
826 LEU* 1.3 61.7 + - - +
836 SER* 3.2 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236 VAL* 3.9 12.4 - - + +
266 GLN* 2.9 28.8 + - + +
276 LEU* 3.8 36.3 - - + +
306 LYS* 5.3 3.1 - - + -
676 LEU* 4.0 25.6 - - + -
686 ARG 3.6 7.9 - - - +
696 VAL* 4.2 6.5 - - + +
816 THR* 1.3 71.2 - - - +
836 SER* 1.3 62.6 + - - +
846 ASN 3.4 23.8 - - - +
856 TYR* 3.8 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 83 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155 GLU* 5.5 3.1 - - - +
526 ASN* 5.0 0.7 + - - -
686 ARG* 2.8 37.2 + - - +
706 PHE* 3.7 26.0 + - - +
816 THR* 3.2 3.5 + - - -
826 LEU* 1.3 73.3 - - - +
846 ASN* 1.3 64.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 84 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135 THR* 3.1 24.9 + - - +
145 ALA* 3.1 11.2 + - - +
155 GLU* 3.0 45.7 + - + +
686 ARG* 2.9 33.6 + - + +
826 LEU* 3.4 6.3 - - - +
836 SER* 1.3 79.9 - - - +
856 TYR* 1.3 79.3 + - - +
986 PHE* 3.7 29.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 85 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135 THR* 3.6 4.5 - - - -
145 ALA* 3.1 50.6 + - + +
276 LEU* 3.6 27.8 - - + -
306 LYS* 3.4 34.8 + - + +
316 GLU* 2.7 29.5 + - - -
656 VAL* 4.2 2.2 - - + -
666 HIS 3.1 13.9 - - - +
676 LEU* 4.1 15.0 - - + -
826 LEU* 3.8 14.1 - - + -
846 ASN* 1.3 84.3 + - - +
866 GLN* 1.3 63.7 + - - +
876 THR* 3.6 23.8 - - + -
986 PHE* 3.7 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 86 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115 PRO* 5.4 4.4 + - - +
125 ALA 5.1 4.7 - - - +
135 THR* 4.0 23.2 - - + +
656 VAL* 3.2 6.5 - - - +
666 HIS* 2.8 46.4 + - + +
856 TYR* 1.3 78.8 - - - +
876 THR* 1.3 64.4 + - - +
896 LYS* 3.3 36.7 + - - +
966 THR* 4.7 7.8 + - - -
986 PHE* 3.5 42.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 87 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125 ALA 5.8 0.6 + - - -
276 LEU* 5.5 0.2 - - + -
316 GLU* 4.0 20.2 - - + +
356 PHE* 6.2 0.7 - - + -
646 PHE 4.0 4.5 - - - -
656 VAL* 4.5 13.7 - - + -
856 TYR* 3.6 31.6 - - + -
866 GLN* 1.3 76.7 - - - +
886 ASN* 1.3 87.4 + - - +
896 LYS* 3.3 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 88 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395 LYS* 4.7 12.3 + - - -
636 ASP* 5.8 9.9 + - - +
646 PHE 3.5 6.1 + - - +
656 VAL* 5.3 0.4 - - - +
876 THR* 1.3 90.4 + - - +
896 LYS* 1.3 63.4 + - - +
906 ALA 4.2 0.2 + - - -
936 ASP* 4.5 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 89 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115 PRO* 5.8 7.5 - - - +
566 LYS* 4.5 0.2 - - - +
626 GLU 4.1 0.3 - - - +
636 ASP* 3.8 4.7 - - - +
646 PHE* 3.0 38.7 + - + +
666 HIS* 3.7 41.2 - - + +
866 GLN* 3.3 42.3 + - - +
876 THR 3.7 12.1 - - - +
886 ASN* 1.3 83.4 - - - +
906 ALA* 1.3 59.3 + - - +
936 ASP* 3.5 16.4 + - + +
946 GLU 5.1 4.4 + - - -
966 THR* 5.3 4.8 + - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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