Contacts of the strand formed by residues 16 - 21 (chain A) in PDB entry 1P9B
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 VAL 16 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASN* 1.3 81.5 - - + +
17A VAL* 1.3 59.6 + - - +
220A LEU* 3.6 29.2 - - + -
224A LYS 5.1 0.9 - - - +
226A VAL* 3.4 15.7 - - + +
228A ILE* 4.8 11.2 - - + -
256A VAL* 6.5 0.2 - - + -
262A ILE* 5.9 4.3 - - + -
266A LYS* 3.1 30.7 - - + +
267A LEU* 3.5 15.2 - - + +
268A ASN* 2.6 40.9 + - - +
269A LEU 3.3 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLY* 3.7 20.9 - - - +
15A ASN 4.8 0.7 - - - -
16A VAL* 1.3 74.8 - - - +
18A ALA* 1.3 59.7 + - - +
19A ILE* 4.8 2.5 - - + -
36A LEU* 5.0 5.8 - - + -
226A VAL 3.0 7.4 + - - +
227A LEU* 3.5 22.4 - - + +
228A ILE* 2.7 34.7 + - - +
267A LEU* 4.5 1.3 - - - -
269A LEU* 3.0 43.3 - - + -
271A VAL* 3.8 16.6 - - + -
423A TRP* 6.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 1.3 72.8 - - - +
19A ILE* 1.3 61.6 + - - +
20A LEU* 3.8 6.9 + - + -
228A ILE* 3.5 16.8 - - + -
256A VAL* 4.3 18.8 - - + -
267A LEU* 3.9 19.7 - - + +
269A LEU 3.1 8.7 + - - +
270A VAL* 3.6 11.4 - - + +
271A VAL* 2.8 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 4.8 2.0 - - + -
18A ALA* 1.3 74.7 - - - +
20A LEU* 1.3 62.1 + - - +
21A GLY 4.3 0.3 + - - -
29A LYS* 4.4 13.6 - - + +
32A ILE* 3.4 28.0 - - + -
33A ILE* 3.2 33.9 - - + +
36A LEU* 3.9 21.5 - - + -
227A LEU* 4.0 10.1 - - + -
228A ILE 2.8 13.4 + - - +
230A GLY* 2.9 31.3 + - - +
271A VAL* 3.7 14.6 - - + +
273A VAL* 3.3 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA* 4.4 5.8 - - + -
19A ILE* 1.3 86.6 - - - +
21A GLY* 1.3 63.6 + - - +
22A ALA* 4.4 0.7 - - - +
29A LYS* 4.9 0.2 - - - -
46A PHE* 4.0 28.0 - - + -
230A GLY* 4.2 5.6 - - - -
251A THR 4.3 10.1 - - - +
252A THR* 4.4 0.9 - - - -
253A VAL* 3.9 24.7 - - + +
256A VAL* 4.2 9.4 - - + -
270A VAL* 3.8 25.1 - - + -
271A VAL 3.0 10.4 + - - +
272A GLY* 3.4 7.2 - - - -
273A VAL* 3.0 24.3 + - - -
330A ASN* 3.8 32.4 + - - +
332A ILE* 5.7 1.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 1.3 74.3 - - - +
22A ALA* 1.3 59.9 + - - -
23A GLN 3.5 2.5 - - - -
27A GLU* 3.6 25.8 - - - -
29A LYS* 3.7 17.1 - - - +
230A GLY* 5.6 0.6 - - - -
232A ASN 4.7 2.4 + - - -
233A ALA* 3.6 5.4 - - - +
234A ALA* 3.1 24.6 + - - +
251A THR 5.3 1.1 + - - +
273A VAL* 3.7 6.7 - - - -
330A ASN* 4.3 3.8 + - - -
----------------------------------------------------------
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