Contacts of the helix formed by residues 84 - 93 (chain C) in PDB entry 3DEG
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 84 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ILE* 5.0 9.6 - - + -
79C PRO* 4.6 18.2 - - + -
81C HIS* 3.8 22.4 + - + +
82C VAL 3.2 0.4 - - - -
83C ASP* 1.3 76.9 - - - +
85C SER* 1.3 63.0 + - - +
86C TYR 3.3 3.4 - - - -
87C GLU* 3.3 31.1 + - + +
88C VAL* 2.9 26.7 + - + +
343C LEU* 4.1 13.0 - - + -
346C LEU* 3.3 27.1 - - + -
347C HIS* 3.6 29.6 - + + -
350C ILE* 2.9 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C HIS 4.3 1.6 - - - -
82C VAL* 3.1 36.2 + - - +
83C ASP 3.2 3.4 + - - -
84C PHE* 1.3 77.1 - - - +
86C TYR* 1.3 61.8 + - - +
88C VAL* 3.4 5.3 + - - +
89C SER* 3.1 23.2 + - - -
115C ASN* 6.1 0.4 - - - -
118C THR* 6.0 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ASP 5.2 0.2 + - - -
84C PHE 3.3 0.8 - - - -
85C SER* 1.3 76.6 - - - +
87C GLU* 1.3 72.8 + - + +
89C SER* 2.8 24.9 + - - -
90C ARG* 3.0 38.6 + - + +
270C VAL* 5.4 6.2 + - + -
271C GLY* 5.4 1.8 - - - -
287C GLY 2.4 25.6 + - - -
288C PHE* 3.7 0.9 - - - -
289C LYS* 2.8 67.6 + - + +
290C LYS 4.9 1.1 - - - -
291C VAL* 4.1 31.9 - - + -
343C LEU* 6.3 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C LYS* 3.7 26.1 + - - +
79C PRO* 5.3 2.1 - - + +
84C PHE* 3.3 32.4 + - + +
86C TYR* 1.3 88.3 - - + +
88C VAL* 1.3 63.0 + - + +
90C ARG* 3.3 8.5 + - - +
91C SER* 3.2 23.6 + - - -
270C VAL* 6.2 4.0 - - + -
291C VAL* 6.4 0.7 - - + -
320C ASN 5.3 4.5 - - - +
321C ASP* 5.4 5.0 - - - +
322C ALA* 5.6 5.4 + - - +
323C SER* 5.1 7.8 + - - +
343C LEU* 5.9 2.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C THR* 3.8 9.2 - - + -
79C PRO* 3.3 38.6 - - + +
81C HIS 3.8 13.7 - - - +
84C PHE* 2.9 20.5 + - + +
85C SER* 3.6 6.7 - - - +
87C GLU* 1.3 75.9 - - - +
89C SER* 1.3 64.3 + - - +
91C SER* 3.1 9.4 + - - -
92C LEU* 3.1 38.2 + - + +
115C ASN* 3.6 28.3 - - + +
118C THR* 5.1 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C SER 3.1 11.5 + - - -
86C TYR* 2.8 22.1 + - - -
88C VAL* 1.3 77.7 - - - +
90C ARG* 1.3 79.1 + - - +
92C LEU* 3.4 11.2 + - - +
93C ALA* 2.8 30.7 + - - +
118C THR* 5.9 6.5 - - - -
122C MET* 3.9 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C TYR* 3.0 39.9 + - + +
87C GLU* 3.6 9.0 - - - +
88C VAL 3.2 0.2 - - - -
89C SER* 1.3 111.2 + - - +
91C SER* 1.3 62.6 + - - +
93C ALA* 3.5 32.8 + - - +
94C ALA* 3.6 8.8 + - - +
122C MET* 4.1 10.5 - - - +
194C LEU* 4.3 13.8 - - + +
270C VAL* 5.9 7.6 - - + -
271C GLY* 5.8 9.4 - - - -
286C PRO 3.8 20.2 + - - -
287C GLY* 3.6 27.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C SER* 5.1 0.9 - - - -
55C LYS* 4.3 14.5 + - - -
76C ILE* 3.4 29.5 - - - +
77C ASP 5.2 2.0 - - - -
78C THR* 5.2 8.7 - - - -
79C PRO* 5.9 0.4 - - - -
87C GLU 3.2 11.0 + - - -
88C VAL* 3.1 11.0 + - - -
90C ARG* 1.3 73.7 - - - +
92C LEU* 1.3 63.8 + - - +
94C ALA* 3.0 25.6 + - - +
95C CYS* 3.3 12.8 - - - -
196C ILE* 4.8 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C SER* 3.3 23.1 - - - +
10C ILE* 4.9 6.7 - - + -
78C THR* 4.6 9.2 - - + +
88C VAL* 3.1 37.1 + - + +
89C SER* 3.7 9.2 - - - +
91C SER* 1.3 72.8 - - - +
93C ALA* 1.3 56.9 + - - +
94C ALA 3.0 4.9 - - - -
95C CYS* 3.0 27.8 + - - +
98C ALA* 4.7 5.2 - - + -
115C ASN 4.0 16.8 - - - +
118C THR* 4.2 11.0 - - - +
119C ALA* 4.3 16.2 - - + +
122C MET* 4.1 13.2 - - - -
124C LEU* 3.6 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C SER 2.8 18.6 + - - +
90C ARG* 3.5 33.2 - - - +
91C SER 3.2 0.2 - - - -
92C LEU* 1.3 75.0 - - - +
94C ALA* 1.3 56.3 + - - +
95C CYS 3.3 4.5 + - - +
122C MET* 3.7 19.7 - - + +
124C LEU* 5.8 0.4 - - - -
194C LEU* 5.0 4.7 - - + +
213C LYS* 2.8 24.8 + - - -
----------------------------------------------------------
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