Contacts of the strand formed by residues 141 - 146 (chain H) in PDB entry 5IY8
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 VAL 141 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H LEU* 5.1 7.0 - - + -
60H ILE* 4.5 14.4 - - + -
61H ALA 3.8 5.2 - - - +
62H SER* 5.0 5.6 - - - -
92H MET 3.9 0.3 - - - +
93H TYR* 3.3 4.3 - - - -
94H GLY 2.8 57.9 + - - +
95H LYS* 3.8 5.4 - - - -
96H VAL* 3.8 19.1 - - + -
116H VAL* 3.8 23.6 - - + -
118H TYR* 4.0 10.6 - - + +
133H HIS 5.8 3.1 - - - +
135H PHE* 6.2 2.7 - - + -
138H ASP* 5.5 2.7 - - - +
139H SER 4.0 3.1 - - - +
140H ARG* 1.3 77.6 - - - +
142H TYR* 1.3 63.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 142 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A GLN* 3.5 34.4 + - - -
580A LEU* 4.2 11.0 - - + -
60H ILE* 3.1 23.6 - - - +
61H ALA* 2.9 26.6 + - + +
62H SER 3.8 22.7 - - - -
63H THR* 4.1 7.9 - - - +
64H LEU* 3.8 28.0 - - + -
70H LEU* 3.3 23.7 + - + +
71H ASP* 5.3 3.3 - - - -
91H VAL* 4.8 3.1 - - + -
92H MET 3.2 5.8 - - - +
93H TYR* 3.5 35.0 - + + -
118H TYR* 4.7 0.7 - - - -
140H ARG* 4.9 2.9 - - + +
141H VAL* 1.3 76.4 - - - +
143H LEU* 1.3 60.8 + - - +
144H LEU* 4.0 18.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H LEU* 3.5 27.6 - - + -
58H LEU* 3.7 38.6 - - + -
59H VAL 4.1 0.7 - - - -
60H ILE* 4.0 8.1 - - + -
90H TYR* 3.4 5.9 - - + +
91H VAL* 3.2 3.8 - - - -
92H MET* 2.7 68.6 + - + +
118H TYR* 3.7 29.8 - - + +
123H MET* 4.2 6.3 - - + -
141H VAL 4.3 0.2 - - - -
142H TYR* 1.3 73.4 - - - +
144H LEU* 1.3 67.7 + - - +
145H MET* 5.4 1.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H MET* 5.8 3.1 - - + -
4H ILE* 6.1 0.2 - - + -
58H LEU* 3.4 7.1 - - - +
59H VAL* 2.9 65.6 + - + +
61H ALA* 4.4 14.4 - - + +
64H LEU* 5.6 8.7 - - + -
88H PHE* 3.3 38.6 - - + -
90H TYR 3.4 3.1 - - - -
91H VAL* 3.6 28.0 - - + -
142H TYR* 4.0 21.5 - - + +
143H LEU* 1.3 80.5 - - - +
145H MET* 1.3 61.4 + - - +
146H LYS* 4.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 145 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H LEU* 4.6 15.9 - - + -
30H CYS* 6.3 2.0 - - - -
41H LEU* 5.0 13.0 - - + -
43H VAL* 5.0 7.4 - - - -
48H TYR* 3.8 28.9 - - + +
50H VAL* 4.6 0.7 - - + -
56H PHE* 3.4 43.3 - - + -
57H ARG 3.7 9.0 - - - +
58H LEU* 4.5 16.8 - - + +
88H PHE* 3.6 1.6 - - - +
89H GLU* 2.9 23.0 + - - -
90H TYR* 2.8 37.7 + - + +
143H LEU* 5.6 1.8 - - + -
144H LEU* 1.3 75.1 - - - +
146H LYS* 1.3 65.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 146 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H TYR* 4.6 1.3 + - - -
56H PHE* 4.9 0.2 - - - -
57H ARG* 3.0 78.7 + - + +
58H LEU* 5.4 0.7 - - - -
59H VAL* 5.2 4.5 - - + -
87H GLN* 4.8 5.8 + - - +
88H PHE* 3.4 53.2 - - + -
89H GLU* 3.7 10.3 - - - +
144H LEU 5.6 0.7 - - - +
145H MET* 1.3 79.5 - - - +
147H LYS* 1.3 76.8 + - - +
148H LEU* 2.3 24.1 + - - -
----------------------------------------------------------
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