Contacts of the strand formed by residues 52 - 58 (chain T) in PDB entry 5IYB
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 52 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45T ILE* 4.2 18.4 - - + -
46T ALA 3.8 2.9 - - - +
47T LYS* 3.3 38.4 - - + +
51T ARG* 1.3 80.9 + - - +
53T GLU* 1.3 66.5 + - - +
54T VAL* 4.2 9.6 + - + +
85T LEU* 5.4 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 53 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44T ARG 4.2 0.5 - - - +
45T ILE* 3.6 1.7 - - - +
46T ALA* 2.8 52.5 + - + +
48T THR* 5.9 3.3 - - + +
51T ARG* 2.8 41.9 + - + +
52T THR* 1.3 78.9 - - - +
54T VAL* 1.3 62.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19T TRP* 4.7 17.3 - - + -
43T LEU* 4.7 4.0 - - + -
44T ARG 3.7 2.9 - - - +
45T ILE* 4.0 31.6 - - + +
52T THR* 4.2 9.8 + - + +
53T GLU* 1.3 80.4 - - - +
55T SER* 1.3 70.5 + - - +
82T PRO* 4.0 3.1 - - - +
83T PHE* 3.1 55.2 + - + +
85T LEU* 4.8 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 55 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43T LEU* 3.1 12.2 - - - +
44T ARG* 2.8 67.8 + - - +
53T GLU 5.7 0.2 - - - -
54T VAL* 1.3 79.1 - - - +
56T PHE* 1.3 58.1 + - - +
57T THR* 4.9 0.2 + - - -
80T GLU* 3.7 22.1 + - - +
81T HIS 3.4 11.7 - - - -
82T PRO* 4.3 2.9 - - - -
83T PHE* 4.2 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 56 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16S VAL* 3.8 19.7 - - + -
127S PHE* 5.5 3.4 - + - -
27T LEU* 4.1 26.0 - - + -
31T TRP* 4.3 18.2 - + - -
40T VAL* 4.0 7.9 - - + -
41T GLY* 3.9 13.7 - - - -
42T LYS 3.2 34.3 - - - -
43T LEU* 3.6 11.7 - - + -
44T ARG* 4.7 0.4 - - - +
55T SER* 1.3 74.2 - - - +
57T THR* 1.3 81.7 + - - +
58T LEU* 3.8 10.1 - - + -
80T GLU* 3.5 1.4 - - - +
81T HIS* 2.6 55.1 + + + +
83T PHE* 3.6 24.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 57 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13S GLU* 5.5 4.7 - - - -
41T GLY* 3.6 1.0 - - - -
42T LYS* 2.8 39.8 + - - +
44T ARG* 3.4 26.4 + - - +
55T SER* 4.9 0.3 + - - -
56T PHE* 1.3 80.8 + - - +
58T LEU* 1.3 72.7 + - - +
80T GLU* 4.5 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26T TYR* 6.3 1.3 - - + -
27T LEU* 3.7 29.8 - - + -
30T GLN* 5.3 7.4 - - + -
40T VAL 4.3 0.9 - - - +
41T GLY* 4.4 0.2 - - - -
56T PHE* 3.8 12.9 + - + -
57T THR* 1.3 87.2 - - - +
59T ASN* 1.3 70.1 + - - +
60T GLU* 3.6 4.2 + - - +
62T LEU* 4.1 19.3 - - + +
63T ALA* 3.7 31.9 - - + +
80T GLU 5.7 1.2 - - - +
81T HIS* 4.9 16.9 + - + +
----------------------------------------------------------
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