Contacts of the helix formed by residues 76 - 82 (chain P) in PDB entry 3E8E
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 LYS 76 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74P LEU 3.2 2.2 + - - -
75P ASP* 1.3 69.9 - - - +
77P GLN* 1.3 62.7 + - - +
79P VAL* 3.3 5.0 + - - +
80P VAL* 3.1 27.7 + - - +
111P LYS* 5.3 6.9 - - + +
112P ASP 3.0 28.4 + - - -
113P ASN 3.3 12.7 + - - -
114P SER 3.0 20.0 + - - +
115P ASN 3.9 4.3 - - - +
116P LEU* 3.8 28.9 - - + -
341P GLU* 4.1 12.7 + - - +
342P LYS* 2.7 30.4 + - + +
343P CYS* 4.2 6.4 - - + -
344P GLY* 4.7 2.6 - - - +
347P PHE* 3.5 39.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 77 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75P ASP* 2.9 13.3 + - - +
76P LYS* 1.3 77.1 - - - +
78P LYS* 1.3 59.1 + - + +
80P VAL* 3.5 2.9 + - - +
81P LYS* 2.9 36.2 + - - +
114P SER 5.7 0.4 - - - +
342P LYS* 3.3 47.6 - - + +
343P CYS* 4.1 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 78 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53P SER 3.8 19.4 + - - +
54P PHE* 3.5 21.7 - - + -
55P GLY 5.9 0.2 - - - +
75P ASP* 3.0 33.8 + - + +
77P GLN* 1.3 75.8 - - + +
79P VAL* 1.3 60.6 + - - +
81P LYS* 3.7 21.1 - - - +
82P LEU* 2.9 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54P PHE* 3.7 26.5 - - + -
74P LEU* 4.0 14.4 - - + -
75P ASP 3.0 23.5 + - - +
76P LYS* 3.3 8.9 + - - +
78P LYS* 1.3 78.5 - - - +
80P VAL* 1.3 60.9 + - - +
82P LEU 3.7 0.5 - - - -
83P LYS 3.2 4.2 + - - -
84P GLN* 2.8 48.5 + - + -
85P ILE* 3.6 3.1 - - - +
88P THR* 3.4 27.6 - - + -
116P LEU* 4.8 1.8 - - + -
347P PHE* 3.7 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 80 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76P LYS 3.1 20.4 + - - +
77P GLN 3.7 4.5 - - - +
79P VAL* 1.3 74.2 - - - +
81P LYS* 1.3 65.8 + - - +
83P LYS* 3.3 15.1 + - - +
85P ILE* 3.6 27.2 - - + +
343P CYS* 3.7 18.2 - - + -
346P GLU* 4.2 12.8 - - + +
347P PHE* 3.5 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 81 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77P GLN* 2.9 26.0 + - - +
78P LYS* 3.7 26.9 - - - +
80P VAL* 1.3 78.1 - - - +
82P LEU* 1.3 69.6 + - + +
83P LYS* 3.2 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53P SER* 3.5 40.4 - - - +
54P PHE* 3.7 14.6 - - + -
78P LYS* 2.9 24.2 + - + +
81P LYS* 1.3 90.0 - - + +
83P LYS* 1.3 73.6 + - - +
84P GLN* 3.4 22.8 + - + +
23Q HIS* 5.7 7.0 - - + -
24Q ASP* 4.3 7.4 + - - +
----------------------------------------------------------
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