Contacts of the strand formed by residues 38 - 45 (chain A) in PDB entry 3E7O
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 GLY 38 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A 35F 5.3 2.0 + - - -
34A SER 3.5 13.3 - - - +
35A GLY 3.0 15.1 - - - +
36A ALA 3.2 3.9 + - - +
37A GLN* 1.3 80.9 - - - +
39A ILE* 1.3 64.9 + - - -
40A VAL* 4.4 4.5 + - - +
55A LYS* 3.8 18.2 - - - -
56A LYS 3.3 11.0 - - - -
58A SER* 3.5 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 5.6 2.7 - - + +
16A ALA* 5.8 5.8 - - + +
18A SER* 3.9 28.5 - - - +
20A PHE* 3.4 25.4 - - + -
31A PRO* 5.8 4.9 - - + -
33A GLY 3.8 11.2 - - - +
34A SER* 4.9 7.9 - - - +
35A GLY 4.3 9.2 - - - +
38A GLY* 1.3 77.7 - - - +
40A VAL* 1.3 65.7 + - - +
41A CYS* 5.5 1.8 - - - -
55A LYS* 3.5 0.7 - - - -
56A LYS* 3.1 36.3 + - + +
58A SER* 4.7 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A 35F 3.6 49.8 - - + +
31A PRO* 3.5 5.2 - - - +
32A ILE* 2.9 46.5 + - + -
33A GLY* 2.9 20.1 + - - +
38A GLY 4.6 2.0 - - - +
39A ILE* 1.3 81.5 - - - +
41A CYS* 1.3 68.2 + - - +
53A ALA* 4.1 9.9 - - + -
54A VAL 3.3 9.9 - - - +
55A LYS* 4.0 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 3.4 37.2 - - - -
20A PHE* 3.9 22.2 - - + -
29A LEU* 4.2 16.2 - - + -
30A LYS 3.3 8.1 - - - +
31A PRO* 3.9 11.2 - - - -
32A ILE* 4.0 5.8 - - - -
39A ILE* 5.5 1.8 - - - -
40A VAL* 1.3 75.9 - - - +
42A ALA* 1.3 64.8 + - - +
53A ALA* 3.3 3.5 - - - -
54A VAL* 2.6 43.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A 35F 6.1 1.3 - - + -
28A GLN 3.5 3.0 - - - +
29A LEU* 3.2 5.7 - - - -
30A LYS* 2.8 45.4 + - + +
32A ILE* 3.9 14.8 - - + +
41A CYS* 1.3 73.2 - - - +
43A ALA* 1.3 59.7 + - - +
51A ASN* 5.6 1.8 - - + -
52A VAL 3.2 9.9 - - - +
110A LEU* 4.0 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR* 4.2 11.7 - - + -
27A GLN 3.5 7.0 - - - +
28A GLN 4.3 0.9 - - - -
29A LEU* 3.7 25.6 - - + -
42A ALA* 1.3 76.0 - - - +
44A PHE* 1.3 60.0 + - - +
51A ASN* 3.2 5.0 - - - -
52A VAL* 2.6 41.5 + - + +
54A VAL* 3.8 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG 3.1 4.2 - - - +
26A TYR* 3.6 1.0 - - - -
27A GLN* 2.8 47.3 + - + +
28A GLN* 4.7 8.4 + - + +
43A ALA* 1.3 72.5 - - - +
45A ASP* 1.3 65.4 + - - +
46A THR* 3.7 23.2 + - + -
49A GLY* 3.7 36.3 - - - -
50A ILE* 3.8 13.2 - - - -
51A ASN* 4.0 16.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG* 3.0 39.8 + - - +
26A TYR* 3.4 26.8 + - + -
43A ALA 3.6 0.4 + - - -
44A PHE* 1.3 72.4 - - - +
46A THR* 1.3 54.7 + - - +
47A VAL 3.0 14.2 + - - -
48A LEU* 3.3 24.0 - - + +
49A GLY* 2.7 36.2 + - - -
50A ILE 2.8 18.6 + - - +
52A VAL* 4.0 12.7 - - + +
107A VAL* 5.5 0.5 - - - +
----------------------------------------------------------
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