Contacts of the strand formed by residues 106 - 111 (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 LEU 106 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92P LYS* 4.0 36.6 - - + +
95P LEU* 4.0 38.3 + - + +
96P GLN* 4.2 14.3 - - + +
104P VAL 3.9 2.6 + - - -
105P LYS* 1.3 74.7 - - - +
107P GLU* 1.3 62.5 + - - +
108P PHE 3.3 25.1 - - - +
109P SER* 4.5 8.7 - - - +
118P MET* 3.7 26.5 - - + -
119P VAL 3.5 9.4 - - - +
120P MET* 4.2 6.7 - - + -
351P G98 5.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 107 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P THR* 4.3 3.1 + - - +
69P TYR* 3.6 33.8 - - + -
105P LYS* 4.0 16.7 - - - +
106P LEU* 1.3 77.2 - - - +
108P PHE* 1.3 89.7 + - + +
119P VAL 2.7 16.1 + - - +
120P MET* 4.0 2.9 - - - -
121P GLU* 3.6 23.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 108 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P THR* 3.2 34.3 - - - +
38P ALA* 3.9 17.7 - - + -
43P PHE* 3.8 24.7 - + - -
62P HIS* 4.2 22.0 - + - -
69P TYR* 4.3 15.7 - + - -
106P LEU* 3.3 12.8 - - - +
107P GLU* 1.3 98.7 - - + +
109P SER* 1.3 62.1 + - - +
110P PHE* 4.7 0.4 - - + -
119P VAL* 2.9 43.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 109 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34P ALA 3.8 7.8 + - - -
35P GLN 2.8 36.2 + - - +
37P THR* 2.9 17.6 + - - -
92P LYS* 3.8 34.5 + - - +
106P LEU* 4.5 9.2 - - - +
108P PHE* 1.3 75.4 - - - +
110P PHE* 1.3 66.4 + - - +
117P TYR 3.3 12.1 - - - -
118P MET* 4.6 2.9 - - - -
350P PHE* 4.4 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 110 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35P GLN 5.4 0.2 - - - -
36P ASN* 3.6 19.7 - - - +
38P ALA* 3.2 34.3 - - + +
39P HIS* 3.8 4.0 - + - -
40P LEU* 3.4 35.0 - - + -
43P PHE* 4.0 11.2 - + - -
71P MET* 4.0 12.3 - - + -
108P PHE* 4.9 0.2 - - + -
109P SER* 1.3 83.2 - - - +
111P LYS* 1.3 63.5 + - - +
112P ASP* 5.9 0.4 - - + -
117P TYR* 2.8 75.7 + + + +
119P VAL* 4.0 18.8 - - + -
350P PHE* 3.5 9.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 111 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194L ARG* 5.2 5.2 - - - +
35P GLN* 5.5 0.8 + - - -
36P ASN* 3.6 17.1 + - - +
76P LYS* 5.3 5.6 - - - +
110P PHE* 1.3 82.1 - - - +
112P ASP* 1.3 66.9 + - - +
115P ASN 3.3 14.4 - - - +
116P LEU* 4.0 15.0 - - + -
117P TYR* 4.1 4.9 - - - -
341P GLU* 5.9 3.1 - - - -
344P GLY 5.5 0.4 + - - -
347P PHE* 2.7 31.3 + - + +
348P SER* 3.2 15.8 + - - +
350P PHE* 2.8 32.0 + - + +
----------------------------------------------------------
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