Contacts of the strand formed by residues 38 - 43 (chain W) in PDB entry 5GAG
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 38 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8W VAL* 3.7 24.7 - - + -
29W ILE* 3.5 5.8 - - - -
30W ILE* 2.9 47.4 + - + +
36W ALA 3.6 1.1 + - - +
37W PRO* 1.3 73.4 - - - +
39W ALA* 1.3 61.4 + - - +
40W ILE* 3.7 25.7 + - + +
65W VAL* 4.2 9.0 - - + -
70W ILE* 3.9 26.7 - - + -
93W ARG* 4.2 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B G 4.9 2.9 - - - -
8W VAL* 3.5 9.2 - - - +
9W ARG* 3.0 41.5 + - + +
12W GLN* 3.9 26.0 - - - +
28W ALA 3.8 1.1 - - - +
29W ILE* 3.7 18.3 - - + +
37W PRO 4.1 1.8 + - - -
38W LEU* 1.3 72.4 - - - +
40W ILE* 1.3 61.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 40 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6W ALA* 3.9 8.5 - - + -
7W GLU 3.3 9.2 - - - +
8W VAL* 4.5 0.4 - - - -
9W ARG* 3.3 14.3 - - - -
27W PRO* 3.4 0.2 - - - +
28W ALA* 2.9 47.4 + - + +
29W ILE 4.4 0.2 - - - +
30W ILE* 3.7 27.8 - - + -
38W LEU* 3.7 30.7 - - + +
39W ALA* 1.3 77.3 - - - +
41W GLU* 1.3 59.4 + - - +
42W LEU* 3.6 25.8 - - + -
63W ILE* 4.1 10.3 - - + -
65W VAL* 4.0 17.7 - - + -
91W PHE* 4.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 41 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6W ALA* 3.1 16.5 - - - +
7W GLU* 2.8 51.4 + - - +
8W VAL 4.0 8.1 - - - +
9W ARG* 4.3 8.9 - - + +
20W LEU* 3.6 31.6 - - + +
25W LYS* 3.6 26.7 + - - +
26W PHE 3.5 5.2 - - - -
27W PRO* 4.3 0.4 - - + -
40W ILE* 1.3 75.2 - - - +
42W LEU* 1.3 77.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4W ILE* 3.7 20.0 - - + -
5W ASN 3.9 4.3 - - - +
6W ALA* 3.6 18.6 - - + -
25W LYS* 3.2 13.5 - - - +
26W PHE* 2.9 64.5 + - + +
28W ALA* 4.0 16.8 - - + -
40W ILE* 3.6 12.1 - - + -
41W GLU* 1.3 91.3 - - - +
43W ASP* 1.3 60.0 + - - +
44W HIS* 4.8 0.2 - - - -
47W VAL* 3.9 22.4 - - + -
63W ILE* 4.9 1.1 - - + -
89W ILE* 4.5 0.9 - - + -
91W PHE* 4.1 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 43 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4W ILE* 5.9 0.2 - - - +
5W ASN 4.6 5.4 + - - +
24W ASN* 4.2 7.4 - - - +
25W LYS* 4.2 21.4 - - - +
42W LEU* 1.3 71.7 - - - +
44W HIS* 1.3 68.1 + - - +
45W ASP* 3.2 19.0 + - - +
46W LYS* 3.1 54.0 + - + +
47W VAL* 3.3 13.1 + - - +
----------------------------------------------------------
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