Contacts of the helix formed by residues 272 - 294 (chain 4) in PDB entry 4C2M
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 ILE 272 (chain 4).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2704 LEU 3.4 4.4 + - - +
2714 PRO* 1.3 70.5 - - - +
2734 VAL* 1.3 66.3 + - - +
2744 SER* 4.5 6.7 - - - +
2754 ASN* 3.1 49.4 + - + +
2764 LYS* 3.4 12.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 273 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2714 PRO* 3.4 13.4 + - + +
2724 ILE* 1.3 71.3 - - - +
2744 SER* 1.3 61.8 + - - +
2764 LYS* 3.1 8.8 + - + +
2774 LYS* 2.8 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 274 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2724 ILE* 3.4 8.4 - - - +
2734 VAL* 1.3 79.8 - - - +
2754 ASN* 1.3 73.6 + - - +
2774 LYS* 3.3 14.7 + - - +
2784 ILE* 3.3 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 275 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2724 ILE* 3.1 39.3 + - + +
2744 SER* 1.3 88.2 + - - +
2764 LYS* 1.3 66.7 + - + +
2784 ILE* 3.5 21.8 + - - +
2794 VAL* 3.9 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 276 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2714 PRO* 4.1 28.3 - - + -
2724 ILE* 3.4 10.4 + - + +
2734 VAL* 3.1 10.8 + - + +
2754 ASN* 1.3 76.8 - - + +
2774 LYS* 1.3 66.5 + - - +
2784 ILE 3.3 0.5 + - - -
2794 VAL* 3.3 9.4 + - - +
2804 PHE* 3.1 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 277 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2734 VAL* 2.8 19.7 + - + +
2744 SER* 3.4 17.5 - - - +
2754 ASN 3.3 0.2 - - - -
2764 LYS* 1.3 75.7 - - - +
2784 ILE* 1.3 57.8 + - + +
2804 PHE* 4.3 7.9 - - + -
2814 ASP* 2.8 59.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 278 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2744 SER 3.3 13.4 + - - +
2754 ASN* 3.6 15.3 - - - +
2764 LYS 3.2 0.2 - - - -
2774 LYS* 1.3 79.4 - - + +
2794 VAL* 1.3 65.9 + - + +
2814 ASP* 4.0 3.1 - - - +
2824 ASP* 3.0 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 279 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2754 ASN 3.9 9.8 + - - +
2764 LYS* 3.3 9.2 + - - +
2784 ILE* 1.3 81.2 - - + +
2804 PHE* 1.3 59.9 + - - +
2824 ASP* 3.3 6.5 + - - +
2834 GLU* 3.1 42.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 280 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2764 LYS 3.1 13.9 + - - +
2774 LYS* 3.8 7.2 - - + +
2794 VAL* 1.3 78.7 - - + +
2814 ASP* 1.3 66.5 + - - +
2834 GLU* 3.7 19.4 + - + +
2844 VAL* 3.1 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 281 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2774 LYS* 2.8 60.5 + - - +
2784 ILE* 4.0 5.1 - - - +
2804 PHE* 1.3 72.9 - - - +
2824 ASP* 1.3 64.1 + - - +
2844 VAL* 4.0 5.3 - - - +
2854 SER* 2.8 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 282 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2784 ILE* 3.0 31.5 + - - +
2794 VAL* 3.6 7.6 - - - +
2804 PHE 3.3 0.4 - - - -
2814 ASP* 1.3 81.7 - - - +
2834 GLU* 1.3 57.1 + - - +
2854 SER* 3.3 4.6 + - - -
2864 ILE* 3.0 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 283 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2794 VAL* 3.1 28.4 + - - +
2804 PHE* 3.7 25.2 - - + +
2824 ASP* 1.3 79.2 - - - +
2844 VAL* 1.3 61.9 + - + +
2864 ILE* 4.0 8.2 - - - +
2874 GLU* 3.0 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 284 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2804 PHE* 3.1 44.6 + - + +
2814 ASP* 4.0 5.6 - - - +
2834 GLU* 1.3 78.1 - - + +
2854 SER* 1.3 61.8 + - - +
2874 GLU* 4.3 10.1 - - - +
2884 ASN* 2.8 52.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 285 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2814 ASP* 2.8 25.1 + - - +
2824 ASP* 3.7 5.4 - - - -
2844 VAL* 1.3 72.8 - - - +
2864 ILE* 1.3 64.7 + - - +
2884 ASN* 3.9 4.2 - - - +
2894 LYS* 3.0 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 286 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2824 ASP* 3.0 27.2 + - + +
2834 GLU* 4.0 5.8 - - - +
2854 SER* 1.3 78.4 - - - +
2874 GLU* 1.3 64.5 + - - +
2894 LYS* 3.3 4.8 + - - +
2904 GLU* 3.1 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 287 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2834 GLU* 3.0 24.0 + - - +
2844 VAL* 3.6 10.8 - - + +
2864 ILE* 1.3 78.2 - - - +
2884 ASN* 1.3 60.1 + - - +
2904 GLU* 3.2 4.8 + - - +
2914 SER* 2.7 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 288 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2844 VAL* 2.8 42.3 + - - +
2854 SER* 4.1 4.2 - - - +
2874 GLU* 1.3 77.7 - - - +
2894 LYS* 1.3 61.8 + - - +
2914 SER* 3.6 10.0 + - - -
2924 HIS* 3.2 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 289 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2854 SER 3.0 18.4 + - - +
2864 ILE* 3.9 4.7 - - - +
2874 GLU 3.2 0.2 - - - -
2884 ASN* 1.3 77.6 - - - +
2904 GLU* 1.3 65.7 + - - +
2924 HIS* 3.5 7.0 + - - +
2934 LYS* 3.3 24.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 290 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2864 ILE* 3.1 26.3 + - + +
2874 GLU* 3.2 4.9 + - - +
2894 LYS* 1.3 80.2 - - - +
2914 SER* 1.3 64.8 + - - +
2934 LYS* 3.1 47.9 + - + +
2944 GLU* 4.0 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 291 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2874 GLU* 2.7 30.4 + - - +
2884 ASN* 3.6 13.0 + - - -
2904 GLU* 1.3 76.6 - - - +
2924 HIS* 1.3 68.8 + - - +
2934 LYS 3.2 1.0 + - - -
2944 GLU* 3.6 8.5 + - - +
2954 LEU* 4.0 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 292 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2884 ASN* 3.2 27.9 + - + +
2894 LYS* 3.9 6.8 - - + +
2904 GLU 3.2 0.4 - - - -
2914 SER* 1.3 81.8 - - - +
2934 LYS* 1.3 64.5 + - - +
2944 GLU 3.2 1.5 + - - -
2954 LEU* 3.3 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 293 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2894 LYS* 3.3 15.1 + - + +
2904 GLU* 3.1 43.1 + - + +
2924 HIS* 1.3 79.1 - - - +
2944 GLU* 1.3 65.1 + - + +
2954 LEU 3.6 1.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 294 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2904 GLU 4.0 1.6 + - - +
2914 SER 3.6 8.4 + - - +
2924 HIS 3.2 0.2 - - - -
2934 LYS* 1.3 84.8 - - + +
2954 LEU* 1.3 64.2 + - - +
2964 ASP* 4.0 1.7 + - - +
----------------------------------------------------------
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