Contacts of the strand formed by residues 27 - 33 (chain D) in PDB entry 1E8O
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 TYR 27 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C VAL* 5.6 10.8 - - + -
29C LEU 3.8 3.1 - - - -
30C LYS* 3.6 24.0 + - + +
25D SER* 3.8 28.0 - - - -
26D VAL* 1.3 72.9 - - - +
28D ILE* 1.3 74.7 + - - +
29D THR* 5.4 7.4 - - + -
60D ALA* 3.3 3.4 - - - +
61D THR* 2.8 46.1 + - - +
62D ASP 5.6 2.0 - - - -
63D GLY* 5.7 2.0 - - - -
122E C 3.7 21.1 + + - -
123E U 3.2 63.3 + + - -
124E G 5.3 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C VAL 3.8 0.7 - - - +
28C VAL* 3.4 1.0 - - - -
29C LEU* 2.8 53.1 + - + +
31C TYR* 6.4 0.9 - - + -
66C HIS* 4.4 9.1 - - + -
9D PHE* 5.9 1.3 - - + -
13D LEU* 4.5 7.9 - - + -
17D PHE* 4.1 17.9 - - + -
26D VAL* 4.5 5.6 - - + +
27D TYR* 1.3 87.1 - - - +
29D THR* 1.3 65.5 + - - +
30D LEU 4.3 0.2 - - - -
58D LEU* 4.2 13.7 - - + -
59D ARG 3.0 13.5 - - - +
60D ALA* 4.4 7.9 - - + -
83D TYR* 3.6 20.4 - - - +
87D LEU* 3.9 27.1 - - + -
91D MET* 5.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ARG* 5.2 9.0 - - - -
27C VAL 3.3 8.3 - - - -
28C VAL* 4.0 24.5 - - + -
27D TYR* 5.4 7.6 - - + -
28D ILE* 1.3 82.0 - - - +
30D LEU* 1.3 62.6 + - - +
31D LYS* 5.6 2.3 - - - +
57D LEU 3.6 4.3 + - - +
58D LEU* 3.8 4.7 - - - +
59D ARG* 3.0 55.5 + - + +
124E G 5.3 6.1 - - - +
125E U 5.6 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ARG* 3.8 2.9 - - - +
27C VAL* 2.9 43.3 + - + +
66C HIS* 3.4 32.0 - - + +
69C LEU* 4.8 0.4 - - + -
70C MET* 3.2 63.7 - - + +
73C MET* 3.9 12.7 - - + +
28D ILE 4.3 0.2 - - - -
29D THR* 1.3 73.0 - - - +
31D LYS* 1.3 74.9 + - - +
56D CYS* 4.1 15.5 - - + -
57D LEU 3.7 5.2 - - - +
58D LEU* 3.7 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C MET* 5.3 8.5 - - - -
24C LYS 5.5 3.4 - - - -
25C ALA 4.1 11.0 - - - +
26C ARG* 4.0 21.8 - - + +
73C MET* 3.3 10.3 - - - -
29D THR* 5.3 3.1 - - - +
30D LEU* 1.3 83.8 - - - +
32D LYS* 1.3 70.2 + - + +
33D TYR* 6.4 0.2 - - + -
56D CYS* 3.0 5.2 - - - -
57D LEU* 2.5 51.7 + - + +
59D ARG* 4.5 13.0 - - - +
125E U 3.2 22.9 + - - +
126E A 2.7 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C TYR* 3.8 14.7 + - - +
22C PRO* 3.2 33.9 - - + +
23C MET* 2.9 42.0 - - + +
25C ALA 5.2 1.9 + - - +
72C LEU 4.1 6.5 + - - -
73C MET* 3.2 45.2 + - + +
75C ALA 4.6 2.8 + - - -
31D LYS* 1.3 83.8 - - - +
33D TYR* 1.3 64.1 + - - +
34D ASP* 6.3 0.2 - - + -
54D ASN* 3.3 26.2 + - - +
55D LYS 4.1 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C MET* 4.6 1.8 - - - -
31D LYS* 3.4 0.6 + - + -
32D LYS* 1.3 79.7 - - - +
34D ASP* 1.3 84.8 + - - +
35D GLY 3.1 32.2 + - - -
54D ASN* 4.8 2.4 - - - +
55D LYS* 2.9 43.5 + - + +
57D LEU* 3.7 28.5 - - + +
70D VAL* 3.8 37.9 - - + -
126E A 3.9 41.5 + - - -
----------------------------------------------------------
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