Contacts of the helix formed by residues 28 - 39 (chain B) in PDB entry 1M1B
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 ASN 28 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B HIS* 1.3 102.4 + - - +
29B GLY* 1.3 66.5 + - - +
30B LEU* 3.2 12.7 + - - +
31B SER* 2.8 33.6 + - - -
32B ALA* 3.1 15.8 + - - +
53B GLN* 3.9 17.0 - - - +
70B VAL* 4.7 3.6 - - - -
74B MET* 3.2 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ASN* 1.3 73.5 - - - +
30B LEU* 1.3 62.2 + - - +
32B ALA* 3.2 4.7 + - - +
33B ARG* 3.1 18.6 + - - +
73B PHE* 3.9 18.4 - - - +
74B MET* 3.5 23.4 - - - +
77B ALA* 3.6 14.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ASN* 3.2 12.0 + - - +
29B GLY* 1.3 75.3 - - - +
31B SER* 1.3 63.0 + - - +
33B ARG* 3.2 7.6 + - + +
34B ILE* 3.1 33.3 + - + +
275B ILE* 5.5 13.7 - - + +
278B LEU* 3.9 41.5 - - + +
279B GLN* 5.8 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA* 3.5 6.4 - - - -
27B HIS* 2.9 46.7 + - - -
28B ASN* 2.8 19.5 + - - -
30B LEU* 1.3 74.6 - - - +
32B ALA* 1.3 58.3 + - - +
34B ILE* 3.2 14.3 + - - +
35B VAL* 2.8 33.1 + - - +
241B ASN* 5.1 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA* 3.6 15.3 - - + -
28B ASN 3.1 12.4 + - - +
29B GLY 3.4 9.4 - - - +
31B SER* 1.3 79.0 + - - +
33B ARG* 1.3 56.9 + - - +
35B VAL* 3.6 2.7 + - - +
36B GLN* 3.1 26.3 + - - +
43B ILE* 3.7 23.2 - - + +
74B MET* 4.0 28.5 - - + +
78B SER* 4.2 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLY 3.1 10.9 + - - +
30B LEU* 3.2 10.5 + - + +
32B ALA* 1.3 74.2 - - - +
34B ILE* 1.3 66.1 + - - +
36B GLN* 3.4 7.1 - - + +
37B GLU* 3.0 28.9 + - + +
76B ASP 4.6 2.8 + - - -
77B ALA* 3.2 47.7 + - - +
278B LEU* 3.2 32.4 + - + +
279B GLN* 4.3 10.1 + - - +
280B ARG* 3.2 58.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 3.1 27.6 + - + +
31B SER* 3.5 15.3 - - - +
33B ARG* 1.3 74.0 - - - +
35B VAL* 1.3 69.8 + - + +
37B GLU* 3.0 10.1 + - - +
38B ALA* 2.9 25.8 + - + +
241B ASN* 5.8 5.4 - - - +
278B LEU* 4.2 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B MET* 3.6 30.5 - - + +
25B GLU 3.8 7.2 - - - +
26B ALA* 4.3 6.1 - - + -
31B SER 2.8 22.9 + - - +
32B ALA 3.7 4.9 - - - +
34B ILE* 1.3 75.8 - - + +
36B GLN* 1.3 66.8 + - - +
38B ALA* 3.2 15.4 + - - +
39B GLY 3.4 6.8 + - - -
40B PHE* 3.5 33.9 + - + +
42B GLY 4.0 0.7 - - - +
43B ILE* 3.6 24.2 - - + -
80B VAL* 5.4 0.2 - - + -
241B ASN* 3.7 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ALA 3.1 12.9 + - - +
33B ARG* 3.4 13.7 - - - +
35B VAL* 1.3 82.9 - - - +
37B GLU* 1.3 69.5 + - - +
39B GLY* 3.2 15.9 + - - -
40B PHE 4.2 7.3 - - - +
77B ALA 4.9 1.3 + - - -
78B SER* 3.5 7.4 - - - +
79B ASP* 2.5 59.5 + - - +
80B VAL* 3.8 27.5 - - + +
280B ARG* 5.2 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ARG* 3.0 19.7 + - + +
34B ILE* 3.0 7.7 + - - +
36B GLN* 1.3 81.0 - - - +
38B ALA* 1.3 64.8 + - - +
39B GLY* 3.2 1.6 + - - -
277B ARG* 2.9 42.3 + - - +
278B LEU* 3.8 13.1 - - - +
280B ARG* 2.7 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE* 2.9 16.1 + - + +
35B VAL* 3.2 14.8 + - - +
37B GLU* 1.3 76.7 - - - +
39B GLY* 1.3 57.0 + - - +
40B PHE* 3.7 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLN 3.2 7.5 + - - -
37B GLU 3.1 5.5 - - - -
38B ALA* 1.3 81.1 - - - +
40B PHE* 1.3 68.9 + - - +
41B LYS* 3.4 9.4 + - - +
----------------------------------------------------------
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