Contacts of the strand formed by residues 23 - 27 (chain A) in PDB entry 3A4I
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 ALA 23 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 4.5 2.9 - - + -
22A LYS* 1.3 73.7 - - - +
24A ILE* 1.3 63.5 + - - +
44A ILE* 3.8 20.8 - - + +
47A ARG 3.0 7.8 + - - +
48A LEU* 4.1 3.4 - - + -
49A HIS* 2.8 29.2 + - - +
121A ALA* 3.9 2.4 - - - +
123A TYR* 3.2 18.2 - - + +
125A ILE* 3.8 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA* 1.3 76.7 - - - +
25A ILE* 1.3 64.0 + - - +
48A LEU* 4.5 2.0 - - - -
49A HIS* 3.3 13.2 - - + +
51A VAL* 3.7 16.2 - - + -
112A PHE* 3.7 15.3 - - + -
116A ALA* 3.6 26.7 - - + +
119A ILE* 3.6 29.4 - - + -
121A ALA* 4.1 11.7 - - + -
123A TYR 3.0 16.7 + - - +
124A LEU* 3.6 10.9 - - + +
125A ILE* 2.8 25.8 + - - +
155A LEU* 3.8 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 1.3 76.2 - - - +
26A ALA* 1.3 74.2 + - - +
27A LEU* 4.5 2.5 - - + -
33A SER* 3.6 28.3 - - - +
36A ALA* 4.0 12.6 - - + -
37A ALA* 3.6 26.5 - - + +
48A LEU* 3.9 15.9 - - + -
49A HIS 3.0 6.9 + - - -
50A ALA* 3.8 23.1 - - + -
51A VAL* 2.8 30.0 + - - +
112A PHE* 4.1 4.7 - - - -
124A LEU* 4.9 1.3 - - - -
125A ILE* 3.5 30.1 - - + +
126A GLN* 5.0 2.5 - - - -
----------------------------------------------------------
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 ILE* 1.3 79.3 - - - +
27A LEU* 1.3 60.3 + - - +
28A SER* 3.7 0.9 + - - -
33A SER* 3.5 18.9 - - - -
51A VAL 3.5 7.0 - - - +
108A PHE* 4.0 26.5 - - + -
112A PHE* 3.7 23.8 - - + -
124A LEU* 5.2 1.6 - - + +
125A ILE 4.6 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ILE* 3.6 3.6 + - + -
26A ALA* 1.3 72.9 - - - +
28A SER* 1.3 60.1 + - - +
29A GLY 4.7 3.4 - - - +
33A SER* 4.1 12.6 - - - +
34A SER* 4.6 2.2 - - - +
37A ALA* 3.5 32.1 - - + -
50A ALA* 3.8 20.2 - - + -
51A VAL 2.8 17.8 + - - +
52A PHE* 3.3 24.9 - - + -
53A VAL 4.5 1.7 + - - -
66A VAL* 4.6 4.0 - - + -
70A PHE* 3.8 37.5 - - + -
76A MET* 5.1 0.2 - - - -
78A LEU* 3.6 30.3 - - + -
108A PHE* 6.1 1.7 - - - -
----------------------------------------------------------
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