Contacts of the helix formed by residues 3641 - 3658 (chain D) in PDB entry 6X34
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 PRO3641 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3639D ASN 4.5 2.0 - - - +
3640D LEU* 1.3 85.3 - - + +
3642D THR* 1.3 65.3 + - - +
3643D HIS* 3.1 6.3 - - + +
3644D ARG* 3.5 12.8 + - + +
3645D ALA* 3.1 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR3642 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1967D VAL* 5.4 5.7 - - - +
1968D ASP* 5.7 5.9 - - - +
1971D GLN* 4.4 16.4 + - - -
3640D LEU 3.1 6.4 + - - -
3641D PRO* 1.3 70.3 - - - +
3643D HIS* 1.3 66.9 + - + +
3645D ALA* 3.8 8.9 - - - +
3646D CYS* 3.3 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS3643 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2144D THR* 3.8 19.5 - - - +
2145D ILE 4.5 4.0 - - - -
2146D SER* 4.0 35.7 - - - +
2195D HIS* 4.7 11.2 - - + -
3641D PRO* 3.1 5.3 - - + +
3642D THR* 1.3 87.2 - - + +
3644D ARG* 1.3 61.4 + - - +
3646D CYS* 3.7 8.9 + - - +
3647D ASN 3.8 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG3644 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2143D TYR* 5.1 9.9 - - - +
2195D HIS* 5.1 8.3 - - + -
3641D PRO* 3.5 15.5 + - + +
3643D HIS* 1.3 77.1 - - - +
3645D ALA* 1.3 64.1 + - - +
3646D CYS 3.3 0.2 - - - -
3647D ASN* 3.5 8.8 + - - +
3648D MET* 3.3 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3645 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1967D VAL* 3.8 21.7 - - + +
1971D GLN* 5.3 5.6 - - - +
2007D ILE* 5.5 5.6 - - + +
3637D LEU* 5.0 14.1 - - + -
3640D LEU* 5.3 6.5 - - + -
3641D PRO 3.1 19.5 + - - +
3642D THR* 4.1 9.0 - - - +
3643D HIS 3.3 0.4 - - - -
3644D ARG* 1.3 76.3 - - - +
3646D CYS* 1.3 65.1 + - - +
3648D MET* 3.3 18.1 + - - +
3649D PHE 3.7 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS3646 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1963D ALA* 4.9 5.8 - - + +
1964D GLU* 4.4 15.0 - - + -
1967D VAL* 3.8 25.2 - - + +
2144D THR* 4.3 19.8 + - + +
3642D THR* 3.3 16.3 + - - +
3643D HIS 4.1 4.7 - - - +
3644D ARG 3.3 0.4 - - - -
3645D ALA* 1.3 78.5 - - - +
3647D ASN* 1.3 61.3 + - - +
3649D PHE* 3.3 17.2 + - - +
3650D LEU* 4.1 6.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN3647 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2143D TYR* 3.8 35.4 - - + +
2144D THR* 4.2 23.3 - - - +
3643D HIS 3.8 4.4 + - - +
3644D ARG* 3.5 9.3 + - - +
3645D ALA 3.3 0.4 - - - -
3646D CYS* 1.3 76.8 - - - +
3648D MET* 1.3 63.1 + - - +
3650D LEU* 3.3 23.1 + - + +
3651D GLU* 4.0 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET3648 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2004D GLN* 6.4 1.6 - - - -
2007D ILE* 4.6 21.9 - - + +
2008D ASN* 5.4 0.2 - - - +
3644D ARG 3.3 10.8 + - - +
3645D ALA* 3.3 13.6 + - - +
3646D CYS 3.2 1.0 - - - -
3647D ASN* 1.3 78.5 - - - +
3649D PHE* 1.3 60.2 + - - +
3650D LEU 3.4 0.3 + - - -
3651D GLU* 3.6 7.9 + - - +
3652D SER* 3.5 19.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE3649 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1962D PHE* 5.4 3.8 - + - -
1963D ALA* 3.6 32.5 - - + -
1966D TYR* 3.7 35.7 - + + -
1967D VAL* 4.9 14.8 - - + -
1970D LEU* 5.2 3.6 - - + -
2007D ILE* 4.9 10.0 - - + +
2010D LEU* 6.3 0.4 - - + -
2011D LEU* 3.9 30.5 - - + -
2032D LEU* 4.6 9.4 - - + -
3645D ALA 3.7 5.3 + - - +
3646D CYS 3.3 12.9 + - - +
3647D ASN 3.2 0.8 - - - -
3648D MET* 1.3 76.5 - - - +
3650D LEU* 1.3 60.5 + - + +
3651D GLU 3.4 0.2 - - - -
3652D SER* 3.9 4.3 - - - +
3653D TYR* 3.0 58.2 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3650 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1959D LEU* 3.6 29.8 - - + -
1960D ALA* 5.3 9.0 - - + -
1963D ALA* 4.5 16.4 - - + -
2139D LEU* 4.4 29.6 - - + +
2142D ALA* 3.9 39.0 - - + +
2143D TYR* 4.6 5.6 - - - +
2144D THR* 4.9 9.4 - - - +
3646D CYS 4.6 6.5 - - - +
3647D ASN* 3.3 14.1 + - + +
3648D MET 3.2 1.2 - - - -
3649D PHE* 1.3 80.9 - - + +
3651D GLU* 1.3 60.8 + - - +
3653D TYR* 3.5 12.3 + - + +
3654D LYS* 3.6 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU3651 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3647D ASN 4.0 3.6 + - - +
3648D MET* 3.6 10.8 + - - +
3649D PHE 3.4 0.4 - - - -
3650D LEU* 1.3 78.6 - - - +
3652D SER* 1.3 62.2 + - - +
3654D LYS* 3.4 17.7 + - - +
3655D ALA* 4.2 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER3652 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2007D ILE* 4.9 7.6 - - - -
2008D ASN* 3.3 32.3 + - - -
2011D LEU* 5.0 11.2 - - - -
3648D MET 3.5 13.1 + - - -
3649D PHE* 3.5 7.7 + - - -
3650D LEU 3.3 0.4 - - - -
3651D GLU* 1.3 77.0 - - - +
3653D TYR* 1.3 64.2 + - - +
3654D LYS 3.3 0.3 + - - -
3655D ALA* 3.6 5.5 + - - +
3656D ALA* 3.3 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR3653 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1959D LEU* 4.4 26.6 - - + +
1962D PHE* 5.9 3.1 - + - -
2032D LEU* 4.7 13.7 - - + -
2035D PHE* 5.5 5.0 - + - -
2036D HIS* 3.1 36.1 - + - +
2039D LEU* 5.1 8.7 - - + +
2135D LEU* 6.0 0.2 - - + -
2139D LEU* 5.6 7.2 - - + -
3649D PHE* 3.0 47.7 + + + +
3650D LEU* 3.9 8.5 - - + +
3651D GLU 3.3 0.6 - - - -
3652D SER* 1.3 75.3 - - - +
3654D LYS* 1.3 64.7 + - - +
3656D ALA* 3.4 10.9 + - + -
3657D TRP* 3.6 29.1 + + - -
3658D ILE* 3.4 32.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS3654 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2136D LEU* 6.1 3.8 - - + -
2139D LEU* 4.1 21.5 - - + +
3650D LEU 3.6 6.1 + - - +
3651D GLU* 3.4 14.3 + - - +
3652D SER 3.2 0.8 - - - -
3653D TYR* 1.3 78.7 - - - +
3655D ALA* 1.3 58.6 + - - +
3656D ALA 3.5 0.2 + - - -
3658D ILE* 3.2 15.8 - - + +
3659D LEU* 3.1 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3655 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3651D GLU 4.2 3.9 + - - +
3652D SER* 3.6 6.9 + - - +
3653D TYR 3.5 0.2 - - - -
3654D LYS* 1.3 77.4 - - + +
3656D ALA* 1.3 62.2 + - - +
3659D LEU* 3.8 27.0 - - + +
3660D THR* 5.2 3.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3656 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2011D LEU* 5.3 8.5 - - + +
2012D HIS* 6.0 7.2 - - - +
3652D SER 3.3 17.2 + - - +
3653D TYR* 3.8 10.5 - - + +
3654D LYS 3.2 1.8 - - - -
3655D ALA* 1.3 80.3 - - - +
3657D TRP* 1.3 88.4 + - + +
3660D THR* 3.3 16.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP3657 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2011D LEU 5.1 4.2 + - - -
2013D PHE* 3.2 59.8 - + + +
2014D LYS* 4.5 6.7 - - + -
2032D LEU* 4.4 19.7 - - + +
2033D LEU* 5.8 7.6 - - + -
2036D HIS* 3.3 47.3 + + + +
2040D LEU* 5.8 0.2 - - - +
3653D TYR* 3.6 28.4 + + + +
3656D ALA* 1.3 96.7 - - + +
3658D ILE* 1.3 63.7 + - - +
3659D LEU 3.8 0.7 - - - -
3660D THR* 3.9 14.1 - - + -
3661D GLU* 3.3 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE3658 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2036D HIS* 5.0 4.3 - - + +
2039D LEU* 5.5 6.3 - - + -
2040D LEU* 5.9 2.2 - - + -
2132D LEU* 4.8 12.6 - - + +
2135D LEU* 4.1 30.1 - - + -
2136D LEU* 4.0 28.3 - - + +
2139D LEU* 5.1 4.3 - - + -
3653D TYR* 3.4 45.8 - - + +
3654D LYS* 3.2 14.0 + - - +
3657D TRP* 1.3 83.7 - - + +
3659D LEU* 1.3 62.6 + - - +
3660D THR 3.2 5.1 + - - -
3661D GLU* 3.6 15.3 + - - +
3662D ASP* 4.2 3.1 + - - +
----------------------------------------------------------
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