Contacts of the strand formed by residues 55 - 60 (chain N) in PDB entry 1T6V
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 TYR 55 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38N ARG* 3.7 24.4 + - - -
49N ILE* 3.6 32.2 - - + +
50N SER 3.6 22.7 - - - +
51N LYS* 4.2 1.1 - - - -
52N GLY* 2.7 41.9 + - - +
53N GLY 3.2 0.2 - - - -
54N ARG* 1.3 112.2 + - + +
56N VAL* 1.3 61.8 + - - +
57N GLU 4.1 1.1 + - - -
68N LEU* 4.1 12.8 - - + -
69N ARG 3.3 2.2 - - - -
70N ILE* 3.8 42.6 - - + -
77N ASP* 4.4 1.4 + - - -
81N TYR* 5.1 2.4 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 56 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52N GLY* 5.8 0.2 - - - -
53N GLY 3.8 16.8 - - - +
55N TYR* 1.3 76.9 - - - +
57N GLU* 1.3 69.7 + - - +
58N THR* 4.1 7.2 + - - +
67N SER 3.8 0.7 - - - +
68N LEU* 3.4 4.7 - - - +
69N ARG* 2.7 53.3 + - + +
71N ASN* 4.3 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 57 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34N THR* 2.6 27.1 + - - -
36N TRP* 2.9 24.5 + - - +
51N LYS* 2.8 40.0 + - + +
55N TYR 4.1 1.6 + - - -
56N VAL* 1.3 79.5 - - - +
58N THR* 1.3 65.9 + - - +
59N VAL* 3.7 19.3 + - + +
66N PHE* 4.1 3.8 - - - +
67N SER 3.1 13.7 - - - +
68N LEU* 4.0 9.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 58 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56N VAL* 4.8 8.7 + - - +
57N GLU* 1.3 75.3 + - - +
59N VAL* 1.3 69.5 + - - +
60N ASN* 4.3 2.4 + - + +
65N SER 3.7 1.2 - - - +
66N PHE* 3.2 4.7 - - - -
67N SER* 2.8 47.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 59 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31N LEU* 4.1 18.8 - - + -
32N GLY 5.8 1.6 - - - +
34N THR* 4.3 6.3 - - + +
57N GLU* 3.7 30.3 + - + +
58N THR* 1.3 83.6 - - - +
60N ASN* 1.3 68.7 + - - +
61N SER* 4.2 5.5 + - - +
65N SER 3.3 8.3 - - - +
66N PHE* 4.2 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 60 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31N LEU* 4.4 0.3 - - - +
58N THR* 5.9 2.5 - - + -
59N VAL* 1.3 76.3 + - - +
61N SER* 1.3 60.1 + - - +
62N GLY* 3.1 8.1 + - - -
63N SER* 2.9 41.6 + - - +
64N LYS* 3.0 21.1 + - - -
65N SER* 2.9 20.8 + - - +
----------------------------------------------------------
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