Contacts of the helix formed by residues 104 - 113 (chain A) in PDB entry 1MBU
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 THR 104 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASN* 3.6 24.0 - - - +
6A LEU* 3.8 5.8 - - - -
39A SER* 3.2 15.2 + - - +
102A GLU* 4.2 17.5 - - - +
103A VAL* 1.3 76.7 - - - +
105A GLY* 1.3 63.7 + - - +
106A ALA* 3.1 14.2 + - - +
107A ASN* 2.9 34.0 + - - +
108A VAL* 3.1 15.6 + - - +
138A ILE* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASN* 5.1 0.6 + - - -
6A LEU* 4.1 13.6 - - - +
34A LEU* 4.0 12.9 - - - +
37A ASN* 3.3 28.2 + - - +
39A SER* 3.6 3.2 + - - -
40A ALA* 3.7 9.2 - - - +
104A THR* 1.3 73.5 - - - +
106A ALA* 1.3 56.3 + - - +
108A VAL* 3.1 5.0 + - - +
109A LEU* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A SER* 2.9 31.3 + - - +
40A ALA* 3.8 8.9 - - - +
43A ALA* 4.8 7.9 - - + -
104A THR* 3.1 4.2 - - - +
105A GLY* 1.3 74.6 - - - +
107A ASN* 1.3 65.6 + - - +
109A LEU* 3.2 7.7 + - - +
110A VAL* 3.0 25.5 + - - +
134A VAL* 4.0 1.3 - - + +
137A PHE* 5.9 0.9 - - + -
138A ILE* 3.6 26.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ALA* 4.0 8.9 - - + +
94A HIS* 5.3 4.6 + - + +
95A VAL* 3.4 31.7 - - + +
102A GLU 3.7 5.7 - - - +
103A VAL* 4.3 6.3 - - + -
104A THR* 2.9 39.0 + - - +
106A ALA* 1.3 75.1 - - - +
108A VAL* 1.3 61.4 + - - +
110A VAL* 3.2 10.3 + - - +
111A ALA* 3.1 21.1 + - - +
138A ILE* 3.9 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 6.0 0.7 - - + -
6A LEU* 3.5 27.4 - - + -
30A LEU* 3.7 34.8 - - + -
34A LEU* 3.8 14.1 - - + -
87A VAL* 3.8 7.4 - - + -
88A LEU* 4.3 11.4 - - + -
91A ALA* 3.9 19.7 - - + -
103A VAL* 4.3 1.3 - - + -
104A THR 3.1 14.0 + - - +
105A GLY* 3.1 8.2 + - - +
107A ASN* 1.3 73.4 - - - +
109A LEU* 1.3 65.1 + - - +
111A ALA* 3.0 12.5 + - - +
112A ILE* 3.1 13.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 3.8 27.4 - - + -
34A LEU* 4.4 6.1 - - + -
40A ALA* 3.9 28.0 - - + +
43A ALA* 4.1 7.4 - - + -
44A LEU* 4.0 16.8 - - + -
105A GLY 2.9 12.4 + - - +
106A ALA* 3.4 8.3 - - - +
108A VAL* 1.3 77.6 - - - +
110A VAL* 1.3 63.3 + - - +
112A ILE* 3.1 21.3 + - + +
113A PHE* 3.3 15.4 - - + -
124A LEU* 3.9 24.9 - - + -
134A VAL* 4.0 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A HIS* 4.0 12.2 - - + +
106A ALA 3.0 19.1 + - - +
107A ASN* 3.3 10.5 - - - +
109A LEU* 1.3 79.3 - - - +
111A ALA* 1.3 61.0 + - - +
112A ILE 3.3 0.3 + - - -
113A PHE* 3.3 26.0 + - - +
114A SER* 4.4 1.6 + - - -
131A ARG* 3.6 39.9 - - + +
134A VAL* 3.5 24.0 - - + -
135A VAL* 4.0 15.9 - - + -
138A ILE* 3.9 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A VAL* 3.4 29.1 - - + +
90A ARG* 3.0 42.4 + - + +
91A ALA* 3.8 15.5 - - + +
94A HIS* 4.6 2.9 - - - +
107A ASN 3.1 9.6 + - - +
108A VAL 3.0 9.9 + - - +
110A VAL* 1.3 78.2 - - - +
112A ILE* 1.3 63.6 + - - +
114A SER* 3.1 6.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 4.0 17.0 - - + -
30A LEU* 4.5 5.4 - - + -
31A LEU* 4.1 35.9 - - + -
34A LEU* 4.2 16.4 - - + -
87A VAL* 3.8 20.0 - - + -
108A VAL 3.1 12.1 + - - +
109A LEU* 3.1 12.3 + - + +
111A ALA* 1.3 76.4 - - - +
113A PHE* 1.3 57.5 + - - +
115A GLU* 2.9 25.5 + - - +
120A ALA* 4.0 18.8 - - + -
121A ALA* 3.8 11.1 - - - +
124A LEU* 3.9 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 3.3 29.2 - - + -
110A VAL* 3.4 12.6 - - - +
111A ALA 3.2 0.8 - - - -
112A ILE* 1.3 77.6 - - - +
114A SER* 1.3 61.1 + - - +
115A GLU 3.4 1.1 + - - -
116A GLN* 4.1 5.7 + - - +
121A ALA* 4.4 5.8 - - - +
124A LEU* 3.7 33.4 - - + -
125A ARG* 2.8 47.0 + - + +
129A VAL* 3.2 36.8 - - + -
130A SER* 3.7 10.8 - - - -
131A ARG* 3.7 42.0 - - + -
134A VAL* 3.9 14.4 - - + -
----------------------------------------------------------
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