Contacts of the helix formed by residues 3002 - 3022 (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 ILE3002 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3001D ALA* 1.3 87.0 - - + +
3003D ASP* 1.3 62.2 + - + +
3004D GLU 3.4 0.6 + - - -
3005D ASN* 3.9 13.6 + - - +
3006D LYS* 3.9 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP3003 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3001D ALA 4.2 3.6 + - - -
3002D ILE* 1.3 74.4 + - + +
3004D GLU* 1.3 89.2 + - - +
3005D ASN 3.3 1.3 - - - -
3006D LYS* 3.4 19.9 + - + +
3007D GLN* 3.4 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU3004 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3001D ALA* 3.2 36.9 + - - +
3002D ILE 3.4 0.8 - - - -
3003D ASP* 1.3 89.7 + - - +
3005D ASN* 1.3 63.7 + - - +
3006D LYS 3.2 0.2 - - - -
3007D GLN* 3.6 13.5 + - - +
3008D LYS* 3.3 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN3005 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3001D ALA 3.3 20.4 + - - -
3002D ILE* 3.9 10.7 + - - +
3003D ASP 3.3 0.2 - - - -
3004D GLU* 1.3 76.7 - - - +
3006D LYS* 1.3 62.1 + - + +
3008D LYS* 3.4 24.8 - - - +
3009D ALA* 3.2 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS3006 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2088D LYS* 5.9 0.2 - - - +
2089D THR* 4.7 5.3 + - - -
2136D GLY 4.0 18.8 - - - +
2137D ALA* 3.5 28.2 + - + +
2139D ASP* 3.6 28.7 + - - -
3002D ILE* 3.9 12.8 - - + +
3003D ASP* 3.4 24.1 + - + +
3004D GLU 3.2 0.6 - - - -
3005D ASN* 1.3 78.9 - - + +
3007D GLN* 1.3 52.5 + - + +
3009D ALA* 3.2 5.5 + - - +
3010D LEU* 2.7 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN3007 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3003D ASP* 3.4 14.6 + - - +
3004D GLU* 3.6 15.0 + - - +
3006D LYS* 1.3 73.8 - - + +
3008D LYS* 1.3 60.2 + - - +
3010D LEU* 3.5 18.6 - - + +
3011D ALA* 2.9 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS3008 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3004D GLU 3.3 12.0 + - - +
3005D ASN* 3.4 27.6 - - - +
3007D GLN* 1.3 79.3 - - - +
3009D ALA* 1.3 58.0 + - + +
3011D ALA* 4.4 3.0 - - - +
3012D ALA* 3.4 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3009 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2135D SER* 3.8 25.6 - - - +
2137D ALA* 4.6 2.5 - - + -
3005D ASN 3.2 8.9 + - - +
3006D LYS* 3.2 10.3 + - - +
3008D LYS* 1.3 76.7 - - - +
3010D LEU* 1.3 64.3 + - - +
3012D ALA* 3.5 8.3 - - - +
3013D ALA* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3010 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2089D THR* 4.7 12.8 - - + -
2115D LEU* 3.8 20.2 - - + -
2132D LEU* 5.4 0.9 - - + -
2135D SER* 5.1 0.9 - - - +
2137D ALA* 3.8 22.0 - - + +
2138D VAL* 4.4 9.9 - - + -
3006D LYS 2.7 20.2 + - - +
3007D GLN* 3.2 21.7 + - + +
3009D ALA* 1.3 70.5 - - - +
3011D ALA* 1.3 62.1 + - + +
3013D ALA* 2.9 8.4 + - - +
3014D LEU* 2.9 55.9 + - + +
3028D ARG* 6.3 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3011 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3007D GLN 2.9 15.7 + - - +
3008D LYS* 4.4 3.4 - - - +
3010D LEU* 1.3 78.3 - - + +
3012D ALA* 1.3 57.4 + - - +
3014D LEU* 3.8 9.0 - - - +
3015D GLY* 2.9 28.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3012 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3008D LYS 3.4 18.7 + - - +
3009D ALA* 3.5 10.1 - - - +
3010D LEU 3.1 0.2 - - - -
3011D ALA* 1.3 79.9 - - - +
3013D ALA* 1.3 54.6 + - - +
3015D GLY* 4.0 1.1 - - - -
3016D GLN* 3.1 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3013 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2131D ALA* 4.4 11.7 - - + +
2132D LEU* 4.9 6.3 - - + -
2135D SER* 3.9 21.3 - - - +
3009D ALA 3.1 12.5 + - - +
3010D LEU* 2.9 9.9 + - + +
3012D ALA* 1.3 75.0 - - - +
3014D LEU* 1.3 55.5 + - + +
3016D GLN* 3.2 10.3 + - - +
3017D ILE* 2.8 47.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3014 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2115D LEU* 3.8 31.0 - - + -
2132D LEU* 4.6 11.9 - - + -
3010D LEU* 2.9 52.3 + - + +
3011D ALA* 3.8 7.4 - - - +
3013D ALA* 1.3 76.4 - - + +
3015D GLY* 1.3 57.5 + - - +
3017D ILE* 3.4 7.5 + - - +
3018D GLU* 3.0 38.0 + - + +
3026D ILE* 4.4 17.3 - - + +
3027D MET* 5.9 1.3 - - - -
3028D ARG* 5.4 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY3015 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3011D ALA 2.9 16.6 + - - -
3012D ALA 4.0 0.9 - - - -
3014D LEU* 1.3 75.1 - - - +
3016D GLN* 1.3 57.5 + - - +
3018D GLU* 3.4 5.5 + - - +
3019D LYS* 3.0 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN3016 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2131D ALA* 5.2 8.3 - - + +
2134D ARG* 5.2 9.8 - - - +
3012D ALA 3.1 19.7 + - - +
3013D ALA* 3.4 9.0 - - - +
3015D GLY* 1.3 77.1 - - - +
3017D ILE* 1.3 66.5 + - + +
3019D LYS* 3.5 11.3 + - - +
3020D GLN* 3.1 50.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE3017 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2128D ILE* 3.8 38.6 - - + -
2131D ALA* 4.0 24.9 - - + -
2132D LEU* 4.0 26.7 - - + -
3013D ALA* 2.8 26.7 + - + +
3014D LEU* 3.7 8.5 - - + +
3016D GLN* 1.3 73.8 - - + +
3018D GLU* 1.3 54.6 + - - +
3020D GLN* 3.1 4.9 + - - -
3021D PHE* 2.7 42.4 + - + +
3025D SER* 4.0 8.3 - - - +
3026D ILE* 3.7 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU3018 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3014D LEU* 3.0 22.8 + - + +
3015D GLY* 4.0 4.4 - - - +
3017D ILE* 1.3 75.1 - - - +
3019D LYS* 1.3 58.7 + - - +
3022D GLY* 2.9 39.3 + - - +
3023D LYS 2.9 22.7 - - - +
3024D GLY* 3.6 8.3 - - - -
3025D SER* 3.7 4.2 + - - +
3026D ILE* 2.9 35.3 - - + +
3027D MET* 5.1 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS3019 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3015D GLY 3.0 18.2 + - - +
3016D GLN* 3.8 12.3 - - - +
3018D GLU* 1.3 77.3 - - - +
3020D GLN* 1.3 63.0 + - - +
3022D GLY 4.6 1.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN3020 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1158D GLU* 3.2 30.9 + - - +
2127D GLU* 4.4 5.0 - - - +
3016D GLN* 3.1 45.4 + - - +
3017D ILE* 3.5 4.1 - - - +
3019D LYS* 1.3 82.3 - - + +
3021D PHE* 1.3 91.8 + - + +
3022D GLY 3.6 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE3021 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1158D GLU* 4.4 4.5 - - - -
2120D ASP* 4.9 6.1 - - - +
2123D GLU 5.6 0.2 - - - -
2124D GLN* 3.3 50.0 + - + +
2127D GLU* 3.7 34.5 - - + -
2128D ILE* 4.2 12.6 - - + -
3017D ILE* 2.7 36.5 + - + +
3020D GLN* 1.3 105.3 - - + +
3022D GLY* 1.3 60.5 + - - +
3025D SER* 3.3 21.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY3022 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3018D GLU* 2.9 20.6 + - - +
3019D LYS 4.6 1.0 + - - -
3020D GLN 3.6 2.4 + - - -
3021D PHE* 1.3 79.3 - - - +
3023D LYS* 1.3 72.6 + - - +
3024D GLY 3.7 0.9 - - - -
3025D SER* 3.1 13.0 + - - -
----------------------------------------------------------
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