Contacts of the helix formed by residues 3030 - 3036 (chain D) 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 GLY3030 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2101D PRO* 5.9 0.4 - - - -
2111D ILE* 3.1 27.2 + - - +
2112D ASP* 3.6 21.7 - - - +
3028D ARG 3.2 1.0 + - - -
3029D LEU* 1.3 79.0 - - - +
3031D GLU* 1.3 57.2 + - - +
3033D ARG* 2.8 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU3031 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3027D MET* 4.7 12.4 - - + +
3028D ARG* 3.2 57.4 + - + +
3030D GLY* 1.3 77.0 - - - +
3032D ASP* 1.3 63.5 + - - +
3033D ARG* 3.2 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP3032 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2101D PRO* 5.5 0.3 - - - +
2116D CYS* 5.3 0.7 - - + +
2118D GLN* 5.1 1.9 - - - +
3027D MET* 3.4 40.9 - - + +
3028D ARG 3.4 6.4 + - - +
3029D LEU* 3.1 14.5 + - - +
3031D GLU* 1.3 76.6 - - - +
3033D ARG* 1.3 69.6 + - - +
3034D SER* 2.6 29.5 + - - -
3035D MET* 3.1 46.4 + - + +
3036D ASP* 4.2 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG3033 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3029D LEU 4.9 0.2 + - - -
3030D GLY 2.8 32.3 + - - -
3031D GLU* 3.2 12.6 + - - +
3032D ASP* 1.3 78.1 + - - +
3034D SER* 1.3 57.5 + - - +
3035D MET 2.8 11.2 + - - -
3036D ASP* 2.8 58.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER3034 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2118D GLN* 4.8 6.9 + - - +
3027D MET* 5.2 1.9 - - - +
3032D ASP* 2.6 22.2 + - - -
3033D ARG* 1.3 77.6 - - - +
3035D MET* 1.3 58.6 - - - +
3036D ASP 3.5 3.5 - - - +
3183D LYS* 3.6 29.1 - - - +
3184D GLN* 6.4 2.0 - - - -
3186D ASN* 5.6 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET3035 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2094D ASP* 4.8 1.6 - - - +
2099D LEU* 3.9 14.2 - - + +
2101D PRO* 3.3 39.1 - - + +
2116D CYS* 3.6 32.1 - - + +
2118D GLN* 3.4 39.7 - - + +
3029D LEU* 3.7 15.5 - - + -
3032D ASP* 3.1 46.0 - - + +
3033D ARG 2.8 0.4 + - - -
3034D SER* 1.3 79.9 + - - +
3036D ASP* 1.3 64.4 + - - +
3037D VAL* 3.6 5.9 + - - +
3060D ARG* 5.3 0.2 + - - -
3183D LYS* 4.9 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP3036 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2101D PRO* 4.4 6.7 - - - +
2102D ILE* 4.3 17.6 - - + +
3032D ASP 4.2 2.3 - - - +
3033D ARG* 2.8 60.4 + - - +
3034D SER 4.6 3.5 - - - +
3035D MET* 1.3 80.5 - - - +
3037D VAL* 1.3 64.8 + - - +
3038D GLU* 3.6 5.2 + - - +
3058D MET 5.8 0.2 - - - +
3183D LYS* 6.2 0.5 - - - -
3186D ASN* 5.4 3.6 - - - +
----------------------------------------------------------
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