Contacts of the strand formed by residues 36 - 43 (chain A) in PDB entry 4M7A
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 36 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 3.9 15.5 - - + -
15A ILE* 3.9 26.0 - - + -
27A LEU* 4.0 13.5 - - + -
29A GLY 3.4 1.3 - - - +
30A PHE* 3.5 26.0 - - + -
34A THR* 3.1 16.4 + - + +
35A ASN* 1.3 72.3 - - - +
37A PHE* 1.3 59.4 - - - +
38A LEU* 4.0 13.9 + - + +
55A LEU* 3.8 3.6 - - - +
56A LEU* 2.9 40.3 + - + +
61A ILE* 4.1 19.1 - - + -
64A VAL* 4.1 18.8 - - + -
3G PRO* 4.4 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ASN* 2.8 56.8 + - + -
29A GLY* 2.6 26.4 + - - +
35A ASN 4.0 0.4 + - - -
36A LEU* 1.3 71.4 - - - +
38A LEU* 1.3 85.2 + - - +
39A THR* 4.3 8.1 - - + -
53A ALA* 4.4 4.7 - - + -
54A GLN 3.9 7.9 - - - -
55A LEU* 4.9 3.6 - - + +
1G MET 3.6 20.6 - - - +
3G PRO* 4.2 10.0 - - + +
6G LEU* 3.3 37.7 - - + -
81G LEU* 4.3 12.1 - - + -
85G ILE* 5.3 0.4 - - + -
86G ILE* 3.6 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 5.0 0.7 - - + -
15A ILE* 3.6 34.1 - - + -
23A LEU* 4.6 8.1 - - + -
25A ALA* 4.2 12.1 - - + -
26A SER 3.5 10.5 - - - +
27A LEU* 4.0 20.0 - - + -
28A ASN* 4.7 0.4 - - - -
36A LEU* 4.2 9.0 - - + +
37A PHE* 1.3 88.4 - - - +
39A THR* 1.3 65.3 + - - +
41A VAL* 3.8 17.7 - - + -
53A ALA* 3.3 4.9 - - - -
54A GLN* 2.8 44.5 + - + +
56A LEU* 4.1 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA* 3.5 1.9 - - - +
26A SER* 2.8 41.0 + - - -
28A ASN* 2.1 39.1 + - - +
37A PHE* 4.3 16.2 - - + -
38A LEU* 1.3 80.0 - - - +
40A ASN* 1.3 70.8 + - - +
41A VAL* 3.5 2.9 - - - -
52A LYS 3.1 13.7 - - - +
53A ALA* 4.5 4.7 - - + -
86G ILE* 4.7 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 2.8 36.8 + - - +
24A ILE 3.6 0.9 - - - +
26A SER* 5.0 2.0 - - - +
39A THR* 1.3 75.3 - - - +
41A VAL* 1.3 61.4 + - - +
42A PHE* 5.0 0.3 - - - +
49A PHE* 3.4 24.6 - - - -
51A SER 3.6 6.1 - - - -
52A LYS* 2.8 46.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.0 33.9 - - + -
24A ILE 3.5 8.5 - - - +
25A ALA* 3.8 8.7 - - + -
38A LEU* 3.8 30.7 - - + +
39A THR* 3.9 6.7 - - - +
40A ASN* 1.3 74.7 - - - +
42A PHE* 1.3 66.7 + - - +
49A PHE* 3.4 12.5 - - - -
50A ILE* 3.0 25.7 + - + -
51A SER 2.8 18.7 + - - +
54A GLN* 4.3 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 5.2 4.5 - - - +
23A LEU* 3.3 13.4 - - - +
24A ILE* 2.9 42.2 + - + +
40A ASN 5.0 1.6 - - - +
41A VAL* 1.3 79.6 - - - +
43A ASN* 1.3 64.0 + - - +
47A LYS* 4.9 4.5 - - - -
48A GLU 3.1 17.7 - - - +
49A PHE* 4.5 5.4 - - + -
50A ILE* 4.3 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU* 5.4 9.0 - - - +
22A SER* 3.3 17.1 + - - +
23A LEU* 4.5 4.5 - - - +
42A PHE* 1.3 71.7 - - - +
44A ARG* 1.3 59.9 + - - +
45A ILE* 4.0 7.6 + - - +
46A SER* 2.9 34.9 + - - -
47A LYS* 2.4 34.8 + - - -
48A GLU* 2.8 16.3 + - + +
50A ILE* 4.2 11.9 - - + +
----------------------------------------------------------
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