Contacts of the helix formed by residues 100 - 105 (chain A) in PDB entry 2M8N
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 ARG 100 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TRP* 3.7 4.0 - - - +
81A ASP* 3.1 47.0 + - - +
84A HIS 6.0 2.7 - - - -
86A VAL* 3.5 38.8 - - - +
98A GLU 3.8 1.0 + - - -
99A PRO* 1.3 76.4 - - - +
101A GLY* 1.3 77.5 + - - +
102A SER* 3.2 17.3 - - - +
103A ASP* 3.0 26.5 + - - +
104A ILE* 3.1 14.4 + - - +
108A THR* 6.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ALA* 3.9 24.2 - - - -
80A TRP* 3.4 11.1 - - - -
81A ASP* 2.8 22.1 + - - -
100A ARG* 1.3 73.0 - - - +
102A SER* 1.3 58.0 + - - +
104A ILE* 3.2 5.7 + - - +
105A ALA* 3.1 23.9 + - - +
133A TRP* 3.7 12.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ALA* 4.7 3.6 - - - +
81A ASP* 5.1 0.6 + - - -
100A ARG* 3.2 13.4 - - - +
101A GLY* 1.3 72.6 - - - +
103A ASP* 1.3 63.5 + - - +
104A ILE 3.3 0.2 - - - -
105A ALA* 3.5 7.5 + - - +
106A GLY 3.2 2.4 + - - -
107A THR* 2.8 40.4 + - - +
108A THR* 3.1 25.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PRO* 4.6 2.4 - - - +
98A GLU 4.4 1.7 - - - +
99A PRO* 3.6 3.2 - - + +
100A ARG* 3.0 35.5 + - - +
102A SER* 1.3 79.1 - - - +
104A ILE* 1.3 57.6 + - - +
106A GLY* 3.1 13.9 + - - -
108A THR* 3.3 26.0 - - - +
109A SER* 2.6 39.4 + - - +
113A GLU* 5.3 1.1 - - - +
114A GLN* 4.3 5.4 + - - +
117A TRP* 3.4 23.9 - - + -
126A VAL* 5.4 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PRO* 3.3 19.2 - - - +
80A TRP* 3.5 46.4 - - + +
99A PRO* 4.0 14.6 - - + -
100A ARG 3.1 7.7 + - - +
101A GLY 3.4 6.5 - - - +
103A ASP* 1.3 72.2 - - - +
105A ALA* 1.3 59.2 + - - +
106A GLY 3.0 5.4 + - - -
126A VAL* 3.8 19.5 - - + +
129A ILE* 4.0 12.6 - - + -
130A TYR* 3.3 32.6 - - + +
133A TRP* 3.6 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PRO* 4.4 2.0 - - - +
53A ASN* 5.2 5.7 - - - +
73A ILE* 4.1 16.6 - - + -
77A ALA* 5.8 1.1 - - + -
101A GLY 3.1 15.0 + - - +
102A SER* 4.1 7.0 - - - +
103A ASP 3.4 0.4 - - - -
104A ILE* 1.3 75.3 - - - +
106A GLY* 1.3 59.5 + - - +
107A THR* 3.2 15.9 + - - +
130A TYR* 3.5 42.3 + - + +
133A TRP* 4.4 2.0 - - + -
----------------------------------------------------------
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