Contacts of the helix formed by residues 98 - 110 (chain A) in PDB entry 1M4U
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 ALA 98 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLY 3.2 6.8 - - - +
97A GLY* 1.3 77.3 - - - +
99A GLU* 1.3 69.6 + - + +
100A ASP 2.9 0.7 - - - -
101A LEU* 3.2 11.7 + - + +
102A ALA* 3.1 21.1 + - - +
179A PHE* 5.3 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLY* 3.8 21.9 + - - +
98A ALA* 1.3 79.6 - - + +
100A ASP* 1.3 64.6 + - - +
102A ALA* 3.3 9.2 + - - +
103A GLU* 3.2 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLY 3.6 10.2 - - - +
97A GLY* 3.5 22.4 - - - +
98A ALA 2.9 0.4 - - - +
99A GLU* 1.3 77.3 - - - +
101A LEU* 1.3 62.2 + - + +
103A GLU* 3.0 18.4 + - - +
104A LEU* 2.7 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLY 3.7 10.9 + - - +
98A ALA* 3.2 15.8 + - + +
100A ASP* 1.3 77.1 - - + +
102A ALA* 1.3 58.0 + - - +
104A LEU* 3.2 13.9 + - + +
105A ASP* 2.9 29.8 + - - +
158A LEU* 4.2 22.5 - - + +
179A PHE* 4.1 26.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ALA 3.1 12.3 + - - +
99A GLU* 3.6 11.7 - - - +
100A ASP 3.1 0.2 - - - -
101A LEU* 1.3 77.8 - - - +
103A GLU* 1.3 56.3 + - - +
105A ASP* 3.7 3.3 - - - +
106A GLN* 3.1 27.0 + - - +
109A ARG* 5.2 0.2 + - - -
179A PHE* 3.8 23.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLU 3.2 11.3 + - - +
100A ASP* 3.0 20.8 + - - +
102A ALA* 1.3 73.9 - - - +
104A LEU* 1.3 66.9 + - - +
106A GLN* 3.4 6.9 + - + +
107A LEU* 3.1 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ASP 2.7 16.6 + - - +
101A LEU* 3.6 13.0 - - + +
103A GLU* 1.3 77.4 - - - +
105A ASP* 1.3 57.3 + - - +
107A LEU* 3.0 14.6 + - + +
108A LEU* 2.8 58.9 + - + +
158A LEU* 4.3 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU 2.9 17.1 + - - +
102A ALA 3.7 5.4 - - - +
103A GLU 3.2 0.2 - - - -
104A LEU* 1.3 77.7 - - - +
106A GLN* 1.3 57.2 + - - +
108A LEU* 3.3 10.7 + - - +
109A ARG* 2.6 65.7 + - - +
156A PRO* 3.4 22.3 - - - +
158A LEU* 5.0 6.0 - - + +
179A PHE* 3.3 45.1 - - + +
182A ARG* 3.6 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ALA 3.1 15.5 + - - +
103A GLU* 3.9 7.1 - - - +
104A LEU 3.3 0.2 - - - -
105A ASP* 1.3 78.2 + - - +
107A LEU* 1.3 68.4 + - + +
109A ARG* 3.3 29.5 + - - +
110A GLN* 3.2 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLU* 3.1 41.3 + - + +
104A LEU* 3.0 16.8 + - + +
106A GLN* 1.3 78.8 - - + +
108A LEU* 1.3 66.4 + - + +
110A GLN* 2.9 25.9 + - + +
111A ARG* 4.0 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 2.8 42.0 + - + +
105A ASP 3.7 3.1 - - - +
107A LEU* 1.3 78.6 - - + +
109A ARG* 1.3 62.9 + - - +
110A GLN 3.1 1.0 + - - -
111A ARG* 3.3 22.2 + - - +
112A PRO* 4.0 2.4 - - - +
154A PHE* 4.3 4.2 - - + -
156A PRO* 4.0 19.7 - - + -
157A VAL 4.9 2.7 - - - +
158A LEU* 3.1 35.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ALA 5.2 0.4 + - - -
105A ASP* 2.6 45.3 + - - +
106A GLN* 3.6 29.0 + - - +
107A LEU 3.1 0.6 - - - -
108A LEU* 1.3 73.2 - - - +
110A GLN* 1.3 62.5 + - - +
111A ARG 3.3 0.7 + - - -
112A PRO* 3.6 7.7 - - - +
151A SER* 2.5 59.4 + - - +
152A GLN* 4.3 1.6 - - - +
154A PHE* 3.2 34.5 - - - +
156A PRO* 3.7 12.6 - - + -
182A ARG* 3.4 43.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLN* 3.2 38.4 + - + +
107A LEU* 2.9 18.1 + - + +
109A ARG* 1.3 88.9 + - - +
111A ARG* 1.3 82.2 + - + +
112A PRO* 3.5 5.8 - - - +
151A SER* 3.7 21.1 + - - -
----------------------------------------------------------
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