Contacts of the strand formed by residues 36 - 41 (chain L) in PDB entry 1MWA
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 GLU 36 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34L HIS* 5.4 4.2 + - + +
35L ILE* 1.3 73.6 - - - +
37L ILE* 1.3 63.5 + - - +
38L GLN* 3.7 35.7 - - + +
45L LYS* 5.8 0.2 + - - -
81L ARG* 3.7 6.1 + - - +
82L VAL* 3.3 5.9 - - - +
83L LYS* 2.9 55.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 37 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25L CYS* 4.3 1.6 - - - -
27L VAL* 3.6 27.1 - - + -
35L ILE* 4.1 16.3 + - + -
36L GLU* 1.3 78.4 - - - +
38L GLN* 1.3 67.9 + - - +
39L MET* 4.8 1.1 - - + -
49L VAL* 5.4 5.0 - - - +
51L MET* 3.4 36.7 - - + +
64L ILE* 3.9 20.6 - - + +
66L ALA* 3.9 21.5 - - + -
80L CYS* 3.8 24.9 - - - -
81L ARG 3.7 2.9 - - - -
82L VAL* 4.4 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 38 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36L GLU* 3.7 35.2 + - + +
37L ILE* 1.3 79.7 - - - +
39L MET* 1.3 62.6 + - - +
40L LEU* 4.8 3.1 - - + -
45L LYS* 3.2 45.2 + - + +
49L VAL* 5.5 1.3 - - - -
80L CYS* 3.3 2.7 - - - -
81L ARG* 2.5 64.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 39 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9L VAL* 5.5 1.3 - - + -
23L LEU* 3.3 45.5 - - + +
24L ASN 4.2 1.6 - - - +
25L CYS* 4.0 15.0 - - + -
37L ILE* 4.8 0.7 - - + -
38L GLN* 1.3 76.3 - - - +
40L LEU* 1.3 61.3 + - - +
45L LYS* 3.6 4.9 - - - +
46L ILE* 2.9 33.7 + - + +
49L VAL* 3.4 46.1 - - + +
66L ALA* 3.9 19.1 - - + +
67L HIS* 3.9 2.5 - - - -
68L THR* 3.9 10.5 - - - +
79L ALA 3.3 7.9 - - - +
80L CYS* 4.0 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 40 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L GLN* 4.5 5.8 - - + +
39L MET* 1.3 77.5 - - - +
41L LYS* 1.3 59.5 + - - +
42L ASN 4.2 0.4 - - - -
43L GLY* 4.1 25.1 + - - +
44L LYS 3.7 2.2 - - - -
45L LYS* 3.3 28.5 - - + +
46L ILE* 4.4 2.7 - - - -
77L THR 3.6 0.3 - - - +
78L TYR* 3.1 10.7 - - - +
79L ALA* 2.6 54.9 + - + +
81L ARG* 3.1 54.1 - - + +
92L THR* 5.3 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 41 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40L LEU* 1.3 70.8 - - - +
42L ASN* 1.3 74.2 + - + +
43L GLY 2.9 0.4 - - - -
44L LYS* 2.6 42.6 + - - +
46L ILE* 4.1 14.7 - - + +
71L THR 5.3 3.2 + - - -
76L ASP* 4.1 21.4 + - - -
77L THR 3.4 3.4 - - - +
78L TYR* 3.2 40.5 + - + +
----------------------------------------------------------
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