Contacts of the helix formed by residues 3044 - 3051 (chain A) in PDB entry 3CMT
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 SER3044 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3042A THR* 3.0 19.0 + - - -
3043A GLY* 1.3 77.8 - - - +
3045A LEU* 1.3 62.1 + - - +
3047A LEU* 3.1 26.8 + - - +
3048A ASP* 3.1 16.1 + - - -
3260A PHE* 3.3 24.5 - - - -
3268A ILE* 4.0 12.3 - - - +
3270A PHE* 4.6 0.7 - - - -
3273A GLU* 2.5 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3045 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3044A SER* 1.3 71.4 - - - +
3046A SER* 1.3 59.1 + - - +
3048A ASP* 3.1 8.2 + - - +
3049A ILE* 3.0 36.1 + - + +
3270A PHE* 3.7 19.1 - - + -
3273A GLU* 2.9 16.6 + - + +
3274A LEU* 3.8 36.1 - - + -
3277A LEU* 4.0 24.2 - - + -
3320A GLU* 3.9 24.9 - - + +
3323A VAL* 4.2 10.1 - - + -
3324A ARG* 3.9 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER3046 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3044A SER* 3.4 1.4 + - - -
3045A LEU* 1.3 77.4 - - - +
3047A LEU* 1.3 57.6 + - - +
3049A ILE* 3.4 13.6 + - - +
3050A ALA* 2.9 27.5 + - - +
3257A GLN 4.7 1.1 - - - +
3258A ALA* 3.4 21.1 - - - +
3259A GLU 3.5 17.3 + - - -
3260A PHE* 4.1 0.9 - - - -
3273A GLU* 2.8 21.5 + - - +
3277A LEU* 4.2 18.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3047 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3042A THR* 3.5 31.2 - - + +
3044A SER* 3.1 20.4 + - - +
3046A SER* 1.3 74.6 + - - +
3048A ASP* 1.3 55.9 + - - +
3049A ILE 3.1 1.6 - - - -
3050A ALA* 3.0 3.5 + - + -
3051A LEU* 2.7 51.7 + - + +
3075A LEU* 4.0 24.9 - - + -
3223A LEU* 4.5 15.9 - - + -
3244A VAL* 4.3 22.7 - - + +
3246A VAL* 4.3 13.0 - - + -
3258A ALA* 3.6 13.0 - - + -
3260A PHE* 4.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP3048 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3041A SER* 3.0 20.3 + - - -
3042A THR* 2.9 31.2 + - - +
3044A SER 3.1 17.5 + - - +
3045A LEU* 3.1 9.7 + - - +
3047A LEU* 1.3 75.5 - - - +
3049A ILE* 1.3 62.2 + - + +
3051A LEU* 3.6 2.8 + - - +
3052A GLY 3.6 4.0 + - - -
3054A GLY* 3.1 48.4 + - - +
3055A GLY* 3.4 7.7 - - - +
3270A PHE* 5.6 0.3 - - - -
3324A ARG* 2.8 29.0 + - - +
3328A LEU* 3.4 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE3049 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3045A LEU* 3.0 40.6 + - + +
3046A SER* 3.6 8.5 - - - +
3048A ASP* 1.3 75.0 - - + +
3050A ALA* 1.3 62.3 + - - +
3052A GLY* 2.9 21.8 + - - -
3256A LYS* 4.2 8.7 + - + +
3277A LEU* 4.0 27.4 - - + -
3323A VAL* 4.1 12.6 - - + +
3324A ARG* 5.5 2.9 - - + -
3327A LEU* 3.8 37.5 - - + +
3328A LEU* 3.8 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3050 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3046A SER 2.9 18.0 + - - +
3047A LEU* 3.0 9.2 + - + +
3049A ILE* 1.3 76.8 - - - +
3051A LEU* 1.3 60.9 + - - +
3052A GLY* 3.2 1.2 + - - -
3246A VAL* 4.1 15.7 - - + +
3249A ASN* 4.8 0.2 + - - -
3253A ALA 4.3 5.9 - - - +
3256A LYS* 3.4 38.8 - - + +
3257A GLN 3.9 27.8 - - - +
3258A ALA* 4.2 1.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3051 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3042A THR* 3.6 31.9 - - + -
3047A LEU* 2.7 33.2 + - + +
3048A ASP* 3.7 7.2 - - - +
3049A ILE 3.1 0.2 - - - -
3050A ALA* 1.3 72.0 - - - +
3052A GLY* 1.3 56.0 + - - +
3053A ALA 2.9 9.9 + - - -
3055A GLY* 3.6 29.8 - - - +
3056A LEU* 4.0 7.6 - - + +
3221A VAL* 3.6 38.4 - - + -
3223A LEU* 4.3 8.7 - - + -
3246A VAL* 4.4 8.1 - - + -
3249A ASN* 3.2 23.3 + - - +
3251A ILE* 4.1 6.4 - - + +
3252A ALA* 3.3 3.5 - - - +
----------------------------------------------------------
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