Contacts of the strand formed by residues 22 - 26 (chain A) in PDB entry 3SOQ
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 22 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PRO* 1.3 76.3 - - - +
23A LEU* 1.3 59.6 + - - +
24A LEU 4.1 0.2 - - - -
33A LEU* 4.3 26.5 - - + -
34A VAL 3.5 6.1 - - - +
35A ASP* 3.7 34.8 - - + +
273A ALA* 3.6 5.0 - - - -
274A PHE* 2.9 50.8 + - + +
400A NAG 5.3 3.8 - - - +
401A FUC 5.3 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PRO* 4.4 5.2 - - + -
22A LEU* 1.3 80.3 - - - +
24A LEU* 1.3 60.4 + - - +
25A TYR* 3.8 2.4 + - - -
32A ARG 3.6 1.0 - - - +
33A LEU* 3.4 6.3 - - - -
34A VAL* 2.8 51.5 + - + +
36A ALA* 3.9 20.6 - - + -
231A THR* 4.2 8.3 - - + -
238A TYR* 3.8 44.6 - - + -
247A ILE* 4.2 19.3 - - + -
261A ILE* 4.8 3.6 - - + -
271A ILE* 4.1 12.6 - - + -
272A HIS 3.5 2.5 - - - +
273A ALA* 4.0 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 1.3 70.9 - - - +
25A TYR* 1.3 60.4 + - - +
31A LEU* 4.7 4.5 - - + -
32A ARG 3.4 15.3 - - - +
33A LEU* 3.5 17.6 - - + +
46A VAL* 4.3 14.1 - - + -
56A VAL* 3.9 32.4 - - + +
57A ASP* 4.3 7.9 - - - +
58A PHE* 4.4 8.3 - - + -
65A ILE* 4.0 29.8 - - + -
271A ILE* 3.2 2.6 - - - +
272A HIS* 2.8 45.9 + - + +
274A PHE* 4.0 25.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU 3.9 10.5 - - - -
24A LEU* 1.3 76.1 - - - +
26A ALA* 1.3 73.3 + - - +
27A ASN* 4.3 3.6 - - + -
31A LEU* 3.5 3.4 - - - +
32A ARG* 2.9 67.6 + - + -
34A VAL* 3.8 23.1 - - + -
43A ALA* 3.4 9.7 - - - +
56A VAL* 4.4 3.6 - - - -
240A THR* 4.7 3.8 - - + -
247A ILE* 3.7 15.0 - - + -
262A HIS* 2.9 31.1 + + - -
265A ILE* 3.7 32.0 - - + +
268A PRO* 4.8 4.3 - - + -
270A ASP 3.2 12.3 - - - +
271A ILE* 4.0 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 1.3 79.8 - - - +
27A ASN* 1.3 60.6 + - - +
28A ARG 3.8 0.2 - - - -
31A LEU* 3.6 23.3 - - + -
53A ALA 3.8 12.6 - - - +
54A ALA 3.3 29.2 - - - +
55A ALA 4.6 0.4 - - - +
56A VAL* 4.0 9.4 - - + +
268A PRO 3.7 0.2 - - - -
269A MET* 2.8 26.9 + - + -
270A ASP 2.9 8.9 + - - +
----------------------------------------------------------
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