Contacts of the helix formed by residues 39 - 50 (chain K) in PDB entry 6NIL
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 39 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K PHE* 4.0 0.7 - - - +
35K ARG* 3.2 42.1 + - + +
36K PRO* 3.5 25.4 + - + +
38K GLU* 1.3 79.4 - - - +
40K ARG* 1.3 79.4 + - - +
41K GLN 3.3 0.2 - - - -
42K ALA* 3.2 23.7 + - - +
43K ARG* 3.0 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 40 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28K LYS* 4.6 8.3 - - - +
29K TYR* 3.0 31.2 + - + -
30K THR* 4.7 1.0 - - - +
31K GLY 4.6 6.0 - - - +
32K PHE* 4.2 24.2 - - + +
33K ARG* 3.8 29.2 + - - +
35K ARG 4.8 1.3 + - - -
36K PRO 3.9 9.0 - - - +
37K HIS* 3.2 39.1 - - - +
39K GLU* 1.3 93.6 + - - +
41K GLN* 1.3 59.2 + - - +
43K ARG* 3.2 7.2 + - - +
44K PHE* 2.7 34.8 + - - +
118K ARG 5.4 0.6 + - - -
119K LEU* 3.4 27.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 41 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K HIS* 2.6 48.4 + - - +
38K GLU* 2.8 33.4 - - - +
39K GLU 3.3 0.6 - - - -
40K ARG* 1.3 80.7 - - - +
42K ALA* 1.3 61.6 + - - +
44K PHE* 3.8 7.7 - - - +
45K GLN* 3.0 30.4 + - - +
116K LEU* 3.3 32.8 - - + +
117K GLN* 3.4 17.2 + - - +
119K LEU* 4.0 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 42 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38K GLU 4.3 2.7 + - - +
39K GLU* 3.2 15.2 + - - +
41K GLN* 1.3 77.5 - - - +
43K ARG* 1.3 53.0 + - + +
45K GLN* 3.1 8.3 + - - +
46K ASN* 2.7 47.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 43 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292J ALA* 3.9 20.4 - - - +
324J GLU* 3.0 35.5 + - - -
32K PHE* 3.6 43.4 - - + -
35K ARG* 3.5 22.1 - - - +
39K GLU* 3.0 33.3 + - - +
40K ARG 3.2 6.8 + - - +
42K ALA* 1.3 79.7 - - + +
44K PHE* 1.3 60.6 + - - +
46K ASN* 4.0 8.5 - - - +
47K ALA* 3.1 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 44 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29K TYR* 3.5 56.1 - + + -
32K PHE* 5.1 0.6 - - - -
40K ARG 2.7 20.7 + - - +
41K GLN* 3.8 7.6 - - - +
43K ARG* 1.3 72.6 - - - +
45K GLN* 1.3 63.2 + - - +
47K ALA* 3.1 5.9 + - - +
48K CYS* 3.1 52.1 + - - -
55K ILE* 4.8 6.7 - - + -
57K PHE* 4.5 12.3 - + - -
95K VAL* 3.8 24.9 - - + -
97K LEU* 5.5 0.4 - - + -
114K ILE* 4.5 11.4 - - + -
116K LEU* 4.5 18.6 - - + -
119K LEU* 3.8 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 45 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41K GLN 3.0 18.6 + - - +
42K ALA* 3.6 6.7 - - - +
44K PHE* 1.3 80.6 - - - +
46K ASN* 1.3 62.5 + - - +
47K ALA 3.5 0.2 + - - -
48K CYS* 3.7 13.4 + - - +
49K ARG* 4.0 22.1 + - - +
88K LEU* 3.7 30.5 - - + +
116K LEU* 3.7 27.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 46 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42K ALA* 2.7 35.3 + - - +
43K ARG* 4.0 9.6 + - - +
45K GLN* 1.3 75.4 - - - +
47K ALA* 1.3 58.3 + - - +
48K CYS 3.6 0.2 + - - -
49K ARG* 4.5 4.8 + - - +
50K ASP* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29K TYR* 5.3 4.7 - - - +
32K PHE* 6.2 1.6 - - + -
43K ARG 3.1 18.7 + - - +
44K PHE* 3.1 6.2 + - - +
46K ASN* 1.3 75.0 - - - +
48K CYS* 1.3 61.7 + - - +
50K ASP* 2.9 25.3 - - - +
53K SER* 4.8 18.8 - - - +
54K GLU 4.9 2.5 - - - +
55K ILE* 4.6 19.7 - - + +
5L TRP* 4.8 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 48 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44K PHE* 3.1 59.0 + - - +
45K GLN* 3.7 5.1 + - - +
46K ASN 3.4 1.4 - - - -
47K ALA* 1.3 80.0 - - - +
49K ARG* 1.3 61.5 + - - +
55K ILE* 5.0 9.2 - - - -
86K VAL* 3.3 42.4 - - + +
88K LEU* 4.0 19.5 - - + -
95K VAL* 4.7 8.5 - - - -
97K LEU* 6.3 0.2 - - - -
116K LEU* 6.1 0.2 - - - -
5L TRP* 3.9 10.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 49 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45K GLN* 4.0 23.5 + - - +
46K ASN* 4.5 5.8 + - - +
48K CYS* 1.3 76.6 - - - +
50K ASP* 1.3 64.7 + - + +
86K VAL 4.9 6.3 - - - +
87K ASP* 5.8 0.2 - - - -
88K LEU* 4.2 35.5 - - + +
89K GLU* 5.3 3.1 - - - -
1L MET* 3.8 31.3 - - + +
2L GLU* 3.3 28.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 50 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46K ASN* 2.9 26.5 + - - +
47K ALA* 2.9 22.3 - - - +
49K ARG* 1.3 83.6 - - + +
51K GLY* 1.3 71.3 + - - +
52K ARG* 4.4 15.8 + - - +
53K SER* 5.0 3.8 + - - -
2L GLU* 4.9 2.0 - - - -
5L TRP* 3.5 18.7 - - - -
----------------------------------------------------------
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