Contacts of the strand formed by residues 80 - 85 (chain F) in PDB entry 5MQF
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 80 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F PHE* 3.7 2.6 - - - +
75F HIS* 2.8 36.9 + - - +
78F GLY 4.4 1.2 - - - -
79F SER* 1.3 80.7 + - - +
81F LEU* 1.3 62.5 + - - +
82F ALA 4.4 0.2 - - - -
92F LEU* 5.9 2.2 - - - -
93F TRP 2.9 15.9 - - - -
94F ASN* 5.3 0.7 - - - -
95F VAL* 4.9 1.6 - - - -
102F TYR* 5.2 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F LYS 3.3 15.3 - - - +
74F PHE* 3.9 11.0 - - + +
75F HIS 4.6 0.2 - - - +
80F THR* 1.3 76.2 - - - +
82F ALA* 1.3 60.1 + - - +
83F SER* 5.6 0.5 - - - -
91F LEU 3.4 1.6 - - - +
92F LEU* 4.7 0.4 - - - -
93F TRP* 2.9 39.0 + - + +
95F VAL* 4.0 19.5 - - + -
343F ILE* 5.9 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F CYS* 3.8 0.3 - - - +
73F LYS* 2.9 36.8 + - + +
74F PHE* 4.7 0.6 - - - +
75F HIS 5.5 0.2 - - - +
81F LEU* 1.3 71.2 - - - +
83F SER* 1.3 60.3 + - - +
90F ILE* 5.8 4.7 - - + -
91F LEU 2.7 16.8 - - - +
92F LEU* 4.5 3.8 - - + +
115F LEU* 5.3 7.8 - - + +
124F LEU* 6.0 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 83 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F VAL* 5.3 7.0 - - - -
71F CYS 3.3 13.9 - - - -
72F CYS* 4.2 10.8 - - - -
81F LEU 5.6 0.2 - - - -
82F ALA* 1.3 76.2 - - - +
84F ALA* 1.3 61.6 + - - +
89F LEU 4.2 1.6 - - - +
90F ILE* 3.8 4.1 - - - -
91F LEU* 2.9 42.7 + - - +
115F LEU* 5.0 2.9 - - - -
345F ALA* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F VAL* 3.3 4.8 - - - +
70F TYR* 2.4 29.9 + - + -
71F CYS 2.9 19.7 + - - +
83F SER* 1.3 74.4 - - - +
85F GLY* 1.3 52.6 + - - +
89F LEU 5.0 2.7 - - - -
90F ILE* 5.1 4.7 - - + +
112F VAL* 3.7 31.0 - - + +
114F GLU 4.6 2.9 - - - +
115F LEU* 3.7 24.3 - - + +
126F SER* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 85 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F GLY 5.2 1.3 - - - -
68F GLU 3.2 14.4 - - - -
69F VAL* 3.8 3.4 - - - -
70F TYR* 3.3 10.3 - - - +
83F SER 4.4 0.2 + - - -
84F ALA* 1.3 76.5 - - - +
86F PHE* 1.3 62.2 + - - -
87F ASP* 3.1 8.8 + - - -
88F ARG* 3.5 8.9 + - - -
89F LEU 4.7 7.8 + - - -
111F ALA* 4.8 0.2 - - - -
112F VAL* 3.6 19.0 + - - +
----------------------------------------------------------
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