Contacts of the strand formed by residues 104 - 109 (chain B) in PDB entry 2UYK
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 104 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE 2.9 20.5 + - - -
73B LYS* 3.1 19.2 - - - +
74B MET 2.9 23.7 + - - -
103B PRO* 1.3 77.6 - - - +
105B ARG* 1.3 61.4 + - - +
18C VAL* 3.7 10.9 - - + +
20C GLY* 3.6 12.3 - - - -
21C VAL* 3.6 23.3 - - + +
28C PHE* 3.5 28.2 - - - +
29C THR 4.0 2.0 - - - -
30C SER* 3.3 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LYS* 4.2 2.0 - - - +
74B MET 3.2 12.3 - - - +
76B VAL* 3.8 16.6 - - + +
84B PHE* 3.5 26.1 - - - -
87B ILE* 5.8 1.8 - - - +
88B ASN* 2.7 32.3 + - - +
91B TYR* 3.2 53.3 - - - +
103B PRO 3.8 0.2 + - - -
104B THR* 1.3 76.6 - - - +
106B SER* 1.3 71.8 + - - +
107B CYS* 4.6 7.4 - - - +
15C GLY* 4.9 0.2 - - - -
16C PRO* 3.8 7.6 - - - +
17C TYR* 4.0 39.3 - - + -
30C SER* 2.8 16.3 + - - +
31C GLY* 2.9 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LYS* 3.9 1.8 - - - +
74B MET 3.2 5.9 + - - -
75B THR* 3.5 15.8 - - - +
76B VAL 2.9 25.5 + - - -
105B ARG* 1.3 75.4 - - - +
107B CYS* 1.3 60.8 + - - +
108B VAL* 5.2 0.7 - - - -
31C GLY* 3.2 20.4 + - - -
77C PHE* 4.5 9.0 - - - -
120C GLU* 3.5 13.2 - - - -
122C GLU* 2.7 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B VAL* 3.3 21.3 - - + +
78B ILE* 4.3 17.5 - - - -
81B LEU* 5.0 3.4 - - - -
84B PHE* 3.2 46.2 - - + -
105B ARG* 4.6 10.3 - - - +
106B SER* 1.3 73.9 - - - +
108B VAL* 1.3 64.1 + - - +
114C PRO* 3.5 12.3 - - + +
120C GLU* 2.7 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B THR* 5.6 1.6 - - + -
76B VAL 3.3 4.0 + - - +
77B PHE* 3.6 31.7 - - + -
78B ILE* 3.0 29.5 + - - +
81B LEU* 5.4 1.3 - - - -
106B SER* 5.2 0.4 - - - -
107B CYS* 1.3 82.2 - - - +
109B GLN* 1.3 59.2 + - - +
110B VAL* 4.1 9.6 - - + -
77C PHE* 3.7 32.8 - - + -
110C VAL* 4.2 13.7 - - + -
112C ARG 4.3 2.7 - - - -
113C LEU* 3.6 22.9 - - + -
114C PRO* 4.9 2.0 - - - -
120C GLU* 3.7 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ILE* 3.2 5.4 - - + +
79B THR 3.4 35.0 + - - +
80B ASP* 3.6 5.4 + - - +
81B LEU* 2.8 40.6 + - + +
108B VAL* 1.3 70.1 - - - +
110B VAL* 1.3 62.6 + - - +
110C VAL* 3.4 5.9 - - - +
111C ALA* 2.9 41.9 + - - +
112C ARG* 2.9 41.5 + - + +
----------------------------------------------------------
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