Contacts of the strand formed by residues 140 - 146 (chain G) in PDB entry 5K0Y
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 140 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A U 3.5 37.0 - - - -
343A C 3.9 7.2 - - - -
71G ARG 4.3 4.9 - - - -
73G LEU* 3.8 30.7 - - + -
88G ILE* 6.4 0.2 - - + -
90G ARG* 6.3 0.4 - - - -
109G MET* 3.8 17.9 - - + +
111G VAL* 3.6 19.5 - - + -
112G HIS 3.5 5.0 + - - -
128G VAL* 3.9 17.5 - - + -
129G GLY* 3.5 22.4 - - - -
130G GLU* 3.6 22.2 - - + -
131G CYS* 4.7 1.3 - - - -
134G LEU* 3.7 6.0 - - - +
138G VAL* 3.0 23.2 - - - +
139G ARG* 1.4 96.6 - - + +
141G ASN* 1.4 62.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 141 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G LYS 3.2 23.3 + - - +
61G PRO* 3.3 22.8 - - - +
68G ILE* 4.5 16.8 - - + -
111G VAL* 4.2 3.4 - - - -
112G HIS* 3.2 36.0 + - - +
114G SER* 3.4 7.4 + - - -
128G VAL* 3.6 0.8 - - - -
129G GLY 3.1 27.7 + - - -
131G CYS* 5.0 3.1 - - + +
134G LEU* 4.2 8.7 - - + +
140G PHE* 1.4 76.5 - - - +
142G VAL* 1.4 82.4 + - - +
143G LEU* 3.2 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G PRO* 4.9 1.2 - - - +
86G ILE* 4.0 20.9 - - + -
111G VAL* 4.4 2.0 - - + -
112G HIS 3.3 18.4 + - - +
113G LEU* 4.2 10.3 - - + -
114G SER 5.0 0.2 - - - +
117G PHE* 3.1 30.5 - - + -
126G VAL* 3.5 31.6 - - + -
127G THR 4.1 3.6 - - - -
128G VAL* 3.9 11.9 - - + -
141G ASN* 1.4 84.6 - - - +
143G LEU* 1.4 59.8 + - - +
144G LYS 4.0 4.7 - - - +
145G VAL* 3.6 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G ILE* 3.7 34.3 - - + -
44G PHE* 4.1 30.3 - - + -
61G PRO* 3.9 16.8 - - + -
62G PHE* 3.9 15.6 - - + -
68G ILE* 3.9 27.6 - - + -
117G PHE* 3.3 16.5 - - - -
127G THR 3.1 11.3 + - - +
128G VAL 5.0 0.2 - - - -
129G GLY* 3.7 17.5 - - - +
141G ASN* 3.2 24.5 - - - +
142G VAL* 1.4 74.9 - - - +
144G LYS* 1.4 67.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 144 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G PHE* 3.7 31.6 - - + +
45G LYS* 3.4 26.7 + - - +
47G PRO* 4.3 20.4 - - - +
62G PHE* 5.6 0.6 - - - -
117G PHE* 3.9 9.9 - - + -
126G VAL* 3.6 1.4 - - - +
127G THR* 3.0 34.4 + - - +
142G VAL* 3.7 1.5 - - - -
143G LEU* 1.4 84.6 + - - +
145G VAL* 1.4 78.5 + - - +
146G THR* 3.8 7.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 145 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G VAL* 6.3 0.4 - - + -
113G LEU* 4.7 4.5 - - + -
117G PHE* 3.9 26.6 - - + -
120G VAL* 4.0 24.5 - - + -
124G ASP* 4.0 19.5 - - + +
125G ILE 3.8 12.8 - - - +
126G VAL* 4.0 9.2 - - + -
142G VAL* 3.6 24.0 - - + -
144G LYS* 1.4 81.2 - - - +
146G THR* 1.4 66.3 + - - +
147G LYS 4.1 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 146 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G ASP* 4.8 3.8 - - - +
125G ILE* 3.0 54.6 + - + +
126G VAL 4.5 0.9 - - - +
127G THR* 4.6 13.9 - - - +
144G LYS* 3.8 10.5 + - - -
145G VAL* 1.4 78.0 - - - +
147G LYS* 1.4 69.4 + - - +
148G ALA* 4.3 9.0 - - + +
----------------------------------------------------------
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