Contacts of the strand formed by residues 103 - 109 (chain B) in PDB entry 1UKC
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 PHE 103 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLY* 3.2 38.1 - - - -
51B MET 3.1 9.2 - - - +
52B ARG* 3.7 44.9 - - + -
53B TYR* 3.6 3.8 - - - -
82B GLY* 3.9 12.6 - - - +
83B PRO* 3.6 29.2 - - + -
100B ASP* 3.4 25.4 - - - -
101B CYS* 2.8 29.0 + - - +
102B LEU* 1.3 74.2 - - - +
104B ILE* 1.3 59.8 + - - +
105B ASN* 4.8 5.7 - - - +
155B PHE* 3.2 5.0 - - - +
156B ASN* 3.0 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLY 3.7 0.3 + - - -
51B MET* 2.8 46.2 + - + +
53B TYR* 3.9 14.6 - - + -
103B PHE* 1.3 74.2 - - - +
105B ASN* 1.3 69.4 + - - +
153B VAL* 3.6 22.2 - - + -
154B THR 3.4 12.6 - - - +
155B PHE* 3.9 12.8 - - + +
186B ALA* 4.2 17.0 - - + +
189B TRP* 3.6 55.0 - - + -
190B VAL* 3.9 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PHE 3.3 9.0 - - - +
49B LEU* 3.6 5.4 - - + +
50B GLY* 2.8 34.2 - - - +
51B MET* 4.4 0.2 - - - -
81B TYR* 3.5 34.1 - - + +
82B GLY 5.2 0.2 - - - +
103B PHE* 4.8 4.6 - - - +
104B ILE* 1.3 79.7 + - - +
106B VAL* 1.3 63.3 + - - +
107B PHE* 4.8 4.9 - - + -
136B ASN* 4.5 5.2 + - - +
152B PHE 3.8 0.6 - - - +
153B VAL* 3.2 8.5 - - - +
154B THR* 2.8 57.7 + - - +
155B PHE* 4.3 4.3 + - - -
156B ASN* 5.4 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ASP 3.9 1.2 - - - +
47B GLU* 3.6 1.9 - - - +
48B PHE* 2.8 39.1 + - - +
49B LEU* 4.9 0.2 - - - +
51B MET* 3.6 19.7 - - + -
105B ASN* 1.3 78.9 - - - +
107B PHE* 1.3 76.6 + - - +
108B LYS* 4.3 1.8 - - + -
151B VAL* 3.9 13.2 - - + -
152B PHE 3.4 3.1 - - - +
153B VAL* 4.1 6.3 - - + -
189B TRP* 4.1 13.7 - - + -
194B ILE* 4.0 18.6 - - + -
197B PHE* 3.6 38.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B VAL* 4.1 3.1 - - + -
46B ASP 3.5 3.8 - - - -
47B GLU* 3.5 34.5 - - + -
49B LEU* 4.2 12.6 - - + -
81B TYR* 3.4 24.2 - - - -
105B ASN* 4.8 9.2 - - + -
106B VAL* 1.3 76.9 - - - +
108B LYS* 1.3 61.3 + - - +
137B TYR 3.6 17.0 - - - -
138B ASN* 3.3 23.3 - - - -
139B GLY 3.8 15.7 - - - -
140B THR* 4.0 8.7 - - - -
143B ILE* 3.5 19.2 - - + +
151B VAL* 3.5 6.4 - - - +
152B PHE* 2.8 54.9 + + + +
154B THR* 4.9 3.1 - - - -
1D NAG 4.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ILE* 4.4 15.2 - - - +
45B VAL* 3.3 7.9 - - - -
46B ASP* 2.8 44.2 + - + +
48B PHE* 3.8 23.8 - - + -
106B VAL* 4.3 10.8 - - + -
107B PHE* 1.3 76.9 - - - +
109B PRO* 1.3 88.8 + - + +
110B SER 3.6 8.1 + - - -
112B ALA* 2.8 28.9 + - - -
143B ILE* 4.0 2.9 - - - +
151B VAL* 3.8 5.8 - - + -
197B PHE* 3.2 42.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B GLY 3.5 7.4 - - - +
45B VAL* 4.4 0.9 - - - -
108B LYS* 1.3 106.2 + - + +
110B SER* 1.3 64.9 + - - +
111B THR* 3.2 6.1 - - - +
112B ALA* 3.1 16.2 + - + +
118B LEU* 3.7 19.1 - - + -
143B ILE* 4.0 5.8 - - + -
148B ASP* 3.3 43.7 - - + +
150B ILE 3.4 22.4 - - - +
151B VAL* 4.1 0.9 - - + -
----------------------------------------------------------
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