Contacts of the strand formed by residues 68 - 76 (chain F) in PDB entry 5MWF
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 ASP 68 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F ASP* 3.4 0.5 - - - +
66F GLU* 3.1 5.9 - - - +
67F CYS* 1.3 66.5 - - - +
69F THR* 1.3 60.3 + - - +
97F VAL* 3.6 21.1 - - + -
99F GLY 4.0 3.1 - - - -
100F GLY* 5.1 0.4 - - - -
150F ASP* 2.5 9.1 + - - +
151F TRP* 2.3 53.8 + - + +
152F ASP* 3.5 2.3 - - - +
404F CA 2.3 27.1 - - - -
405F CA 2.4 21.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 69 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F LEU* 4.2 16.6 - - + +
39F ASN* 5.7 2.5 - - + -
67F CYS* 3.1 20.3 + - + +
68F ASP* 1.3 73.2 - - - +
70F TYR* 1.3 60.5 + - - +
97F VAL* 3.3 20.5 - - - +
98F LEU* 3.3 8.8 + - - +
99F GLY 3.2 9.3 + - - -
100F GLY 3.2 21.5 + - - +
101F ASN* 4.5 4.0 - - - -
103F PHE* 4.1 15.9 - - - -
148F ALA* 5.9 0.9 - - - -
149F TRP 3.1 9.0 - - - -
163F ILE* 3.6 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 70 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F THR* 1.3 73.6 - - - +
71F VAL* 1.3 69.3 + - - +
72F ARG* 5.0 5.2 - - + -
94F ALA* 5.1 5.8 - - + -
95F THR 3.3 24.2 - - - +
96F PRO 3.3 18.2 - - - +
97F VAL* 4.1 1.1 - - - +
98F LEU* 4.3 2.5 - - - -
147F GLU 4.0 0.3 - - - +
148F ALA* 3.9 1.4 - - - -
149F TRP* 2.7 73.2 + + + +
150F ASP 3.8 1.6 - - - -
151F TRP* 3.5 59.2 - + + -
161F LEU* 5.0 4.2 - - - +
3L FUC 4.6 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F LEU* 4.5 9.4 - - + -
34F LEU* 3.6 36.6 - - + -
37F LEU* 4.9 11.0 - - + -
70F TYR* 1.3 74.9 - - - +
72F ARG* 1.3 65.7 + - - +
73F VAL* 4.1 19.1 - - + -
94F ALA* 3.3 5.1 - - - +
95F THR* 2.9 43.9 + - + +
98F LEU* 4.3 5.8 - - + +
103F PHE* 5.5 0.2 - - + -
130F VAL* 4.8 5.2 - - + -
146F VAL* 4.1 16.2 - - + -
147F GLU 3.5 7.9 - - - +
148F ALA* 5.2 2.2 - - - -
190F LEU* 5.1 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 72 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135E GLN* 2.9 35.6 + - - +
70F TYR* 5.0 5.8 - - + -
71F VAL* 1.3 79.2 - - - +
73F VAL* 1.3 70.2 + - - +
74F CYS* 4.7 3.9 - - + +
88F CYS* 4.3 19.0 - - - -
92F HIS* 3.5 35.4 + - - +
93F GLY 3.7 11.9 + - - +
94F ALA* 4.1 9.6 - - + +
145F ILE 3.9 0.9 - - - +
146F VAL* 3.7 2.9 - - - +
147F GLU* 2.9 54.8 + - - +
149F TRP* 3.9 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 73 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F PHE* 5.3 1.6 - - + -
32F LEU* 3.9 26.0 - - + -
71F VAL* 4.1 7.4 - - + -
72F ARG* 1.3 82.1 + - - +
74F CYS* 1.3 63.4 + - - +
92F HIS* 3.2 7.7 - - - +
93F GLY 2.8 33.6 + - - +
130F VAL* 3.8 37.7 - - + -
132F ILE* 4.0 18.6 - - + -
144F LEU* 3.7 26.7 - - + -
145F ILE 3.7 2.9 - - - +
146F VAL* 4.8 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 74 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F ARG* 4.7 7.6 - - + +
73F VAL* 1.3 76.2 - - - +
75F LEU* 1.3 61.9 + - - +
76F LYS* 4.8 9.4 - - - -
85F THR 5.7 0.4 - - - -
86F GLY 5.3 0.9 - - - -
87F PRO 5.1 0.2 - - - -
88F CYS* 2.0 53.2 - - - -
91F GLY 4.1 2.2 - - - -
143F THR 4.1 0.3 - - - +
144F LEU* 3.6 7.1 - - - +
145F ILE* 2.9 59.3 + - + +
147F GLU* 6.4 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F PHE* 3.8 39.7 - - + -
74F CYS* 1.3 75.7 - - - +
76F LYS* 1.3 63.0 + - - +
88F CYS* 3.0 13.1 - - - -
90F TYR* 2.9 45.1 + - + +
91F GLY 3.1 16.6 + - - +
132F ILE* 4.2 13.0 - - + -
134F PHE* 6.3 0.9 - - + -
138F TRP* 4.2 9.6 - - + -
142F PHE* 3.8 27.1 - - + -
143F THR 3.4 16.8 - - - +
144F LEU* 4.3 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 76 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F CYS* 4.8 5.5 - - - -
75F LEU* 1.3 78.0 - - - +
77F GLU* 1.3 74.5 + - - +
79F GLN* 3.2 25.4 - - - +
83F THR* 3.2 24.8 + - - +
85F THR 2.6 30.3 + - - +
86F GLY* 4.5 2.7 - - - -
87F PRO 3.6 16.2 - - - +
88F CYS* 4.1 2.0 - - - -
89F SER* 3.4 21.3 - - - +
90F TYR* 3.4 19.8 - - - -
142F PHE* 3.7 0.3 - - - +
143F THR* 2.8 35.6 + - - +
145F ILE* 3.9 17.4 - - + +
----------------------------------------------------------
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