Contacts of the strand formed by residues 52 - 58 (chain A) in PDB entry 2YB6
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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 4.7 8.5 - - - -
40A ILE 4.0 2.7 - - - -
41A PHE* 3.6 34.8 - - + +
50A ASP 3.7 8.5 + - - +
51A GLY* 1.3 74.4 - - - +
53A PHE* 1.3 61.4 + - - +
54A LYS* 3.9 5.5 + - - +
74A SER* 4.0 1.6 + - - -
148A SER* 2.8 44.7 + - - +
149A TRP* 3.5 12.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 3.2 6.6 - - - +
40A ILE* 2.9 49.2 + - + +
42A GLY 4.2 4.9 - - - -
48A PHE* 4.0 27.6 - + - -
51A GLY* 3.7 25.8 - - - -
52A THR* 1.3 72.7 - - - +
54A LYS* 1.3 61.6 + - - +
55A LEU* 3.4 2.3 - - - +
72A PHE* 3.7 21.5 - + + -
74A SER* 3.5 10.3 - - - +
75A LYS 4.4 0.9 - - - -
76A MET* 3.6 15.0 - - + -
113A LEU* 4.2 16.4 - - + -
144A ILE* 3.6 35.0 - - + -
145A VAL* 4.2 5.6 - - + -
148A SER* 3.8 22.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA 3.4 7.6 - - - +
39A VAL* 5.0 10.1 - - + -
52A THR 4.6 4.0 - - - +
53A PHE* 1.3 75.2 - - - +
55A LEU* 1.3 55.8 + - - +
72A PHE* 3.6 5.9 - - - -
73A LEU* 2.8 50.0 + - + -
74A SER* 2.8 19.6 + - - +
148A SER 4.8 9.0 - - - -
150A ASN 4.4 2.0 + - - -
151A ASP 3.4 27.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASN* 3.6 4.3 + - - +
38A ALA* 2.9 46.5 + - + +
40A ILE* 3.7 39.5 - - + +
53A PHE 3.4 20.0 - - - +
54A LYS* 1.3 75.0 - - - +
56A VAL* 1.3 69.4 + - - +
57A ILE* 5.3 0.2 - - + -
70A VAL* 3.8 14.8 - - + -
71A ARG 3.2 8.3 - - - +
72A PHE* 3.7 20.6 - - + -
73A LEU* 4.1 2.1 - - - +
87A ILE* 3.7 30.5 - - + -
106A LEU* 4.6 2.2 - - + -
109A ILE* 4.2 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLN* 3.7 27.8 - - + +
36A TRP 3.3 9.0 - - - +
37A ASN* 4.1 15.5 - - - +
55A LEU* 1.3 78.4 - - - +
57A ILE* 1.3 65.7 + - - +
58A GLU* 3.8 9.6 - - + +
69A THR 4.0 0.3 - - - +
70A VAL* 3.5 3.7 - - - +
71A ARG* 2.9 75.6 + - + +
73A LEU* 4.5 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A MET 3.7 0.9 - - - +
35A GLN* 3.4 5.9 - - - +
36A TRP* 2.9 48.0 + - + +
38A ALA* 4.2 14.4 - - + -
55A LEU* 5.3 0.2 - - + -
56A VAL* 1.3 76.9 - - - +
58A GLU* 1.3 65.0 + - - +
59A PHE* 3.5 31.1 - - + -
68A PRO* 3.6 18.6 - - + -
69A THR 3.5 5.2 - - - +
70A VAL* 4.1 17.5 - - + -
102A VAL* 3.8 28.7 - - + -
105A ILE* 5.7 4.5 - - + -
106A LEU* 4.1 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASN* 5.5 1.2 + - - -
34A MET* 3.6 4.2 - - - +
35A GLN* 2.7 46.2 - - - +
56A VAL* 3.8 11.3 - - + +
57A ILE* 1.3 73.2 - - - +
59A PHE* 1.3 64.8 + - - +
68A PRO* 3.2 5.1 - - - +
69A THR* 2.9 47.7 + - - +
71A ARG* 4.1 15.2 + - + +
----------------------------------------------------------
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