Contacts of the strand formed by residues 11 - 16 (chain H) in PDB entry 4XLR
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 11 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224G TYR 4.3 2.7 - - - +
225G PHE* 4.0 28.7 - + + -
226G ALA* 2.9 49.4 - - + +
227G ASN 3.8 4.2 - - - +
228G PRO* 3.5 26.8 - - + +
229G GLU* 3.4 13.3 - - - +
9H PRO 3.4 1.7 + - - +
10H VAL* 1.3 75.0 - - - +
12H THR* 1.3 65.7 + - - +
13H ALA* 4.1 13.7 - - + -
23H PHE* 3.8 24.7 - + + -
24H VAL 3.8 8.1 - - - -
25H LEU* 3.6 20.4 - - + -
208H LEU* 4.9 5.6 - - + -
211H LEU* 4.3 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 12 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228G PRO* 4.1 0.4 - - - -
229G GLU* 3.7 32.3 + - + +
10H VAL* 3.9 14.4 + - - +
11H PHE* 1.3 79.8 + - - +
13H ALA* 1.3 64.7 + - - +
14H THR* 4.2 11.7 - - + -
22H GLU 4.2 0.2 - - - +
23H PHE* 3.3 3.6 - - - +
24H VAL* 2.8 42.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 13 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228G PRO* 3.3 29.1 - - + +
229G GLU 2.8 19.2 + - - +
230G ALA* 3.1 12.5 - - - +
11H PHE* 4.1 5.2 - - + -
12H THR* 1.3 76.8 - - - +
14H THR* 1.3 60.9 + - - +
15H THR* 3.9 6.2 + - + +
22H GLU 3.6 3.6 - - - -
23H PHE* 3.4 29.4 - - + +
208H LEU* 4.7 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 14 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229G GLU 3.9 9.2 - - - +
231G SER* 3.3 32.1 - - - +
12H THR* 4.5 10.5 - - + -
13H ALA* 1.3 72.5 - - - +
15H THR* 1.3 62.0 + - - +
21H GLY* 3.7 0.7 - - - -
22H GLU* 2.9 42.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 15 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230G ALA* 4.3 11.7 - - + +
231G SER 2.9 21.2 + - - +
232G LEU* 3.1 13.3 - - - +
13H ALA* 3.9 9.0 + - + +
14H THR* 1.3 78.7 - - - +
16H GLN* 1.3 61.8 + - - +
17H GLY 5.1 4.4 + - - -
20H TYR 3.6 9.4 - - - -
21H GLY* 3.7 14.6 - - - -
23H PHE* 3.9 19.1 - - + -
206H THR* 5.4 4.4 + - - +
207H PRO* 4.8 6.3 - - + -
208H LEU* 4.9 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 16 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232G LEU* 3.7 20.8 - - + +
233G LEU* 3.9 39.2 + - - +
15H THR* 1.3 75.2 - - - +
17H GLY* 1.3 65.5 + - - +
19H HIS* 3.3 12.7 - - + -
20H TYR* 2.9 44.5 + - + +
----------------------------------------------------------
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