Contacts of the strand formed by residues 18 - 23 (chain B) in PDB entry 1AXS
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 18 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ALA* 3.6 38.6 - - + +
10B GLU 5.7 0.4 - - - +
12B MET* 4.3 11.7 - - + -
17B SER* 1.3 76.1 - - - +
19B LYS* 1.3 69.9 + - - +
20B ILE* 5.2 3.1 - - + -
80B MET 3.7 0.9 - - - +
81B GLN* 3.1 8.5 - - - +
82B LEU* 2.9 59.9 + - + -
109B VAL* 4.1 17.9 - - + -
823B LEU* 3.8 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B SER 4.1 0.2 - - - +
8B GLY* 3.7 18.9 - - - -
9B ALA 4.6 0.7 + - - -
18B VAL* 1.3 81.4 - - - +
20B ILE* 1.3 65.1 + - - +
21B SER* 5.2 1.2 + - - +
70B THR* 4.5 6.8 + - - +
79B TYR* 3.8 44.4 - - + +
80B MET 3.3 4.0 - - - +
81B GLN* 4.2 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLU* 4.5 5.2 - - + +
7B SER 3.4 17.0 - - - +
8B GLY* 5.3 1.1 - - - -
9B ALA 5.7 0.4 - - - +
18B VAL* 5.2 2.5 - - + -
19B LYS* 1.3 77.2 - - - +
21B SER* 1.3 71.3 + - - +
36B TRP* 3.8 17.9 - - + -
79B TYR* 3.2 9.4 - - - +
80B MET* 2.9 58.5 + - + +
82B LEU* 4.2 11.4 - - + -
90B TYR* 3.7 28.5 - - + -
107B THR* 4.1 22.9 - - + -
109B VAL* 4.2 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU 3.9 3.1 - - - -
6B GLU* 3.0 23.4 - - - +
7B SER* 2.8 25.3 + - - -
8B GLY* 4.9 0.9 - - - -
19B LYS* 4.1 1.6 + - - +
20B ILE* 1.3 79.1 - - - +
22B CYS* 1.3 61.7 - - - +
23B LYS* 5.2 0.7 - - - -
77B THR* 4.0 6.5 - - - -
78B ALA 3.4 5.4 - - - -
79B TYR* 3.6 23.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 3.7 20.9 - - - -
5B LEU 3.1 5.2 - - - -
6B GLU* 4.7 0.2 - - - -
21B SER* 1.3 76.5 - - - +
23B LYS* 1.3 63.7 + - - +
24B ALA 3.4 3.0 + - - -
29B PHE* 4.8 1.2 - - - -
34B ILE* 4.6 12.3 - - - +
36B TRP* 3.6 18.2 - - + -
77B THR* 3.9 1.8 - - - +
78B ALA* 2.9 35.4 + - + +
92B CYS* 2.0 47.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLN* 3.1 8.7 - - - +
4B LEU* 3.4 2.1 - - - -
5B LEU* 2.7 52.7 + - + +
21B SER* 5.2 0.8 - - - -
22B CYS* 1.3 69.4 - - - +
24B ALA* 1.3 76.4 + - - +
25B THR* 4.6 5.6 - - - +
75B SER* 3.7 23.1 + - - +
76B ASN* 3.8 1.6 - - + -
77B THR* 3.3 23.7 + - + +
----------------------------------------------------------
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