Contacts of the strand formed by residues 75 - 79 (chain V) in PDB entry 3EXG
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 ARG 75 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20V ASP* 3.2 27.5 + - - -
22V LYS* 2.9 20.9 + - + +
23V VAL* 3.6 37.8 - - + +
24V PHE* 3.7 0.8 + - - -
73V GLY 4.2 4.7 + - - +
74V LEU* 1.3 81.4 + - - +
76V PRO* 1.3 66.5 - - - +
77V ILE* 4.1 1.9 - - - +
111V PRO* 3.5 23.7 - - - +
161V ILE* 3.4 15.7 + - + +
162V ARG* 3.3 15.8 + - - +
163V ASP 3.0 27.1 + - - -
164V ASN* 3.1 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 76 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24V PHE* 3.5 36.1 - - + +
26V LEU* 4.5 2.0 - - + -
66V ALA* 3.2 38.8 - - + +
70V ALA* 4.0 10.5 - - + +
74V LEU 3.4 8.3 - - - +
75V ARG* 1.3 94.8 - - - +
77V ILE* 1.3 61.2 + - - +
78V CYS 3.8 0.7 - - - -
111V PRO 3.9 7.1 - - - +
112V ILE* 4.0 10.8 - - + -
113V VAL* 3.2 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 77 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13V MET* 4.6 15.3 - - + -
17V LEU* 5.4 4.3 - - + -
23V VAL* 3.9 17.0 - - + -
24V PHE 2.8 16.7 + - - +
25V LEU* 3.4 25.4 - - + +
26V LEU* 3.0 26.2 + - - +
75V ARG 4.1 5.8 - - - +
76V PRO* 1.3 77.2 - - - +
78V CYS* 1.3 60.5 + - - +
113V VAL* 3.5 11.9 - - + +
115V ARG* 3.8 31.6 - - + -
157V ILE* 5.5 0.2 - - + -
161V ILE* 3.7 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 78 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26V LEU* 3.5 7.4 - - + -
62V PHE* 3.7 33.4 - - - -
63V ALA* 4.1 8.1 - - - -
66V ALA* 3.8 22.0 - - + -
76V PRO 3.8 0.6 - - - -
77V ILE* 1.3 73.4 - - - +
79V GLU* 1.3 58.7 + - - +
80V PHE* 3.9 11.7 + - - -
112V ILE* 4.7 1.8 - - + -
113V VAL 2.8 9.7 + - - +
114V PHE* 3.5 32.5 - - + +
115V ARG 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 79 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25V LEU* 4.6 3.5 - - + +
26V LEU 2.8 16.0 + - - +
27V GLY* 3.7 15.3 - - - -
28V GLU 4.4 9.0 + - - +
30V VAL* 3.7 28.9 - - + +
35V GLY* 5.3 4.3 - - - -
36V ALA* 4.9 7.6 + - - +
37V TYR* 5.4 2.6 - - - -
39V VAL* 5.0 6.5 - - - +
40V SER* 4.8 6.9 + - - -
62V PHE* 3.8 13.5 - - - -
77V ILE 3.6 1.2 + - - -
78V CYS* 1.3 74.5 - - - +
80V PHE* 1.3 80.8 + - - +
81V MET* 4.2 10.2 + - - +
115V ARG* 3.4 50.2 + - - +
116V GLY* 4.5 0.9 - - - -
117V PRO* 5.1 2.2 - - - +
----------------------------------------------------------
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