Contacts of the helix formed by residues 31 - 40 (chain R) in PDB entry 2DFS
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 GLU 31 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19R PHE* 3.6 24.6 - - + -
21R LYS* 6.0 1.9 - - - -
27R ILE* 4.7 7.2 - - + -
28R THR* 3.0 31.2 + - + +
30R LYS* 1.3 78.3 - - - +
32R LEU* 1.4 61.0 + - - +
33R GLY 3.4 2.2 - - - -
34R THR* 2.6 52.2 + - - +
35R VAL* 3.0 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28R THR 3.8 2.4 + - - -
29R THR* 3.5 15.8 + - - +
30R LYS 3.3 3.0 - - - -
31R GLU* 1.4 76.4 - - - +
33R GLY* 1.3 62.9 + - - +
35R VAL* 3.3 19.7 - - + +
36R MET* 3.3 13.3 + - + +
48R LEU* 3.6 14.6 - - + -
51R MET* 4.1 16.4 - - + -
52R ILE* 3.5 30.5 - - + +
63R ILE* 3.7 31.0 - - + -
67R GLU* 5.6 2.0 - - - +
68R PHE* 3.7 27.4 - - + -
71R MET* 5.4 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 33 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30R LYS 4.6 2.2 + - - -
31R GLU* 3.4 1.0 - - - +
32R LEU* 1.3 78.2 - - - +
34R THR* 1.3 61.3 + - - +
36R MET* 3.5 4.0 + - - +
37R ARG* 3.1 44.0 + - - +
43R PRO* 5.6 0.2 - - - -
48R LEU* 3.4 34.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 34 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878M LEU* 3.8 34.1 - - + -
882M HIS* 3.7 9.0 - - - +
19R PHE* 3.4 13.8 - - - -
30R LYS 5.3 2.4 + - - +
31R GLU* 2.6 44.2 + - - +
33R GLY* 1.3 76.2 - - - +
35R VAL* 1.4 54.4 + - - -
37R ARG* 3.3 5.1 + - - +
38R SER* 3.0 28.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 35 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15R ALA* 5.0 2.0 - - + +
16R PHE* 4.5 9.9 - - + +
19R PHE* 3.8 27.3 - - + -
27R ILE* 4.1 21.1 - - + -
31R GLU 3.0 17.6 + - - +
32R LEU* 3.3 24.0 - - + +
34R THR* 1.4 73.2 + - - +
36R MET* 1.4 66.7 + - - +
38R SER* 3.2 11.3 + - - -
39R LEU* 3.2 18.2 + - + +
63R ILE* 5.0 0.2 - - + -
68R PHE* 3.6 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 36 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32R LEU* 3.3 14.1 + - + +
33R GLY* 3.8 8.3 - - - +
35R VAL* 1.4 76.3 - - - +
37R ARG* 1.3 56.7 + - - +
38R SER 3.2 0.2 - - - -
39R LEU* 3.2 18.4 + - - +
40R GLY 3.3 10.6 + - - -
41R GLN* 3.3 44.4 - - - +
43R PRO* 3.8 24.0 - - + -
48R LEU* 5.5 1.1 - - - -
51R MET* 3.6 42.0 - - + +
68R PHE* 3.9 20.6 - - + -
71R MET* 5.6 0.7 - - + -
72R MET* 3.9 26.5 - - + +
75R LYS* 5.9 0.2 - - + -
79R THR* 4.2 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 37 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872M LYS* 3.5 14.2 - - - +
875M ARG* 3.5 25.2 - - - +
876M GLY* 3.6 10.8 - - - +
878M LEU* 3.5 25.0 - - + +
879M ALA* 3.4 22.0 + - - +
33R GLY* 3.1 26.3 + - - +
34R THR* 3.3 5.9 + - - +
36R MET* 1.3 75.2 - - - +
38R SER* 1.3 55.9 + - - +
39R LEU 3.5 0.2 - - - -
40R GLY 4.2 6.6 - - - +
41R GLN 3.3 20.0 - - - +
43R PRO* 2.8 32.9 + - + +
44R THR 3.5 8.7 + - - -
45R GLU* 2.7 46.8 + - - +
48R LEU* 4.0 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 38 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879M ALA* 4.7 6.5 - - - +
882M HIS* 2.8 38.3 + - - +
883M TYR* 5.3 10.0 - - - -
12R PHE* 5.6 0.7 - - - -
15R ALA* 4.8 13.8 + - - +
19R PHE* 4.0 12.5 - - - -
34R THR 3.0 10.7 + - - -
35R VAL* 3.4 7.6 - - - -
37R ARG* 1.3 77.6 - - - +
39R LEU* 1.3 61.6 + - - +
40R GLY* 3.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10R ALA* 3.1 42.5 - - + +
12R PHE* 3.7 51.8 - - + +
15R ALA* 4.2 12.3 - - + -
16R PHE 5.7 0.2 - - - +
35R VAL* 3.4 12.8 - - + +
36R MET 3.3 9.4 - - - +
38R SER* 1.3 80.1 - - - +
40R GLY* 1.3 56.3 + - - +
41R GLN* 3.7 18.6 - - - +
68R PHE* 4.0 18.2 - - + -
72R MET* 3.9 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 40 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876M GLY* 5.3 3.3 - - - +
10R ALA* 5.5 1.8 - - - -
36R MET 3.3 1.2 + - - +
37R ARG* 4.2 8.0 - - - +
38R SER 3.7 0.9 - - - -
39R LEU* 1.3 81.5 - - - +
41R GLN* 1.3 70.7 + - - +
42R ASN* 4.4 8.2 + - - -
83R GLU* 3.9 13.7 - - - -
----------------------------------------------------------
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