Contacts of the helix formed by residues 28 - 39 (chain I) in PDB entry 6C6U
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 LEU 28 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I TYR* 3.1 24.3 + - + +
27I LEU* 1.3 82.1 - - - +
29I SER* 1.3 61.2 + - - +
30I ILE* 3.4 2.7 - - - -
31I GLN* 3.9 8.6 + - + +
32I LEU* 3.4 28.8 + - + +
133I ASN* 3.5 27.1 - - - +
134I GLY* 5.8 0.2 - - - -
524I ILE* 3.7 21.5 - - + +
527I LYS* 3.7 37.9 - - + +
528I ARG* 4.8 2.0 - - + -
711I ASP 3.5 23.3 - - - +
712I SER* 4.4 11.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 29 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I PRO* 5.5 1.5 - - - +
26I TYR* 2.7 38.4 + - - +
27I LEU 3.4 2.6 + - - -
28I LEU* 1.3 77.2 - - - +
30I ILE* 1.3 64.3 + - - +
32I LEU* 4.9 1.6 - - - -
33I ASP* 2.8 53.7 + - - +
528I ARG* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 30 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I LEU 4.8 1.1 - - - +
28I LEU 3.4 0.4 - - - -
29I SER* 1.3 80.4 - - - +
31I GLN* 1.3 65.6 + - + +
33I ASP* 4.4 0.4 - - - +
34I SER* 3.0 35.0 + - - -
147I SER* 3.7 23.8 - - - +
453I ILE* 5.6 4.0 - - + -
455I SER* 4.5 11.2 - - - -
527I LYS 5.5 3.4 - - - +
528I ARG* 4.0 33.7 - - + +
530I ILE* 6.1 1.1 - - + -
575I LEU* 4.0 28.9 - - + -
579I ALA 4.7 5.2 - - - +
580I GLN* 5.8 1.3 - - - -
581I THR* 4.3 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 31 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I LEU* 3.9 10.0 + - + +
29I SER 3.5 0.2 - - - -
30I ILE* 1.3 80.2 - - + +
32I LEU* 1.3 57.8 + - - +
34I SER* 3.9 2.8 - - - -
35I PHE* 3.0 32.1 + - - +
130I MET* 3.7 12.2 - - + +
134I GLY* 3.6 28.9 + - - +
136I PHE* 5.2 0.8 - - - -
144I VAL* 4.1 9.9 - - - +
145I ILE 3.2 29.6 + - - +
147I SER* 4.1 14.7 + - - -
455I SER* 5.7 0.6 - - - -
456I VAL* 3.5 20.0 + - - +
527I LYS* 3.7 34.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I TYR* 3.6 36.6 - - + +
28I LEU* 3.4 15.2 + - + +
29I SER* 4.7 2.0 - - - +
31I GLN* 1.3 78.8 - - - +
33I ASP* 1.3 61.2 + - - +
35I PHE* 4.4 0.4 - - - +
36I GLN* 2.9 32.1 + - - +
130I MET* 3.8 22.0 - - + -
131I THR 4.1 13.5 - - - +
132I ASP* 3.9 18.8 - - - +
134I GLY* 4.5 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 33 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I SER* 2.8 40.5 + - - +
30I ILE 4.4 0.2 - - - +
32I LEU* 1.3 78.8 - - - +
34I SER* 1.3 57.7 + - - +
36I GLN* 3.5 6.5 + - - +
37I LYS* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 34 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I ILE 3.0 20.6 + - - -
31I GLN* 3.9 2.9 - - - -
33I ASP* 1.3 77.9 - - - +
35I PHE* 1.3 57.8 + - - +
37I LYS* 3.1 18.5 + - - +
38I PHE* 2.9 25.1 + - - +
455I SER* 2.5 34.6 + - - -
456I VAL 4.4 2.0 - - - -
457I GLY* 3.0 20.0 + - - -
458I GLU 4.4 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 35 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I GLN 3.0 18.0 + - - +
32I LEU 4.4 0.7 - - - +
34I SER* 1.3 76.2 - - - +
36I GLN* 1.3 63.6 + - - +
38I PHE* 3.6 30.1 - + + -
39I ILE* 3.2 46.5 + - + +
127I ILE* 5.5 2.2 - - + -
128I PRO 3.5 21.3 - - - -
129I LEU* 4.1 8.7 - - + -
130I MET* 3.6 46.4 - - + -
136I PHE* 3.9 13.9 - + - -
456I VAL* 4.0 21.3 - - + -
457I GLY* 4.7 2.4 - - - +
460I ALA* 5.3 0.7 - - + -
506I PHE* 4.9 6.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 36 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I LEU 2.9 20.4 + - - +
33I ASP* 3.8 7.4 - - - +
35I PHE* 1.3 75.2 - - - +
37I LYS* 1.3 63.1 + - - +
39I ILE* 3.5 19.7 + - - +
40I GLU* 3.4 44.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 37 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I ASP 2.9 15.6 + - - +
34I SER* 3.1 21.1 + - - +
36I GLN* 1.3 78.4 - - - +
38I PHE* 1.3 61.9 + - - +
40I GLU* 4.8 5.4 + - - +
42I ASP* 5.7 2.1 - - - +
47I TYR* 4.5 37.8 - - + +
48I GLY* 3.8 11.6 + - - -
452I ARG* 6.0 1.6 - - - +
455I SER* 5.3 3.6 + - - -
457I GLY* 6.0 1.1 - - - -
458I GLU* 5.6 13.0 + - - +
583I GLU 5.1 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 38 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I SER 2.9 5.6 + - - +
35I PHE* 3.5 34.5 - + - +
36I GLN 3.2 0.6 - - - -
37I LYS* 1.3 81.3 - - - +
39I ILE* 1.3 70.3 + - + +
40I GLU 3.6 4.0 + - - +
48I GLY* 3.5 6.1 - - - -
49I LEU* 3.4 55.9 + - + +
127I ILE* 4.2 27.8 - - + -
457I GLY* 3.2 37.0 - - - -
460I ALA* 3.9 16.8 - - + -
461I GLU* 3.5 31.2 - - + -
464I PHE* 5.3 2.2 - - + -
506I PHE* 6.0 0.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 39 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I PHE* 3.2 43.5 + - + +
36I GLN* 3.5 14.1 + - - +
38I PHE* 1.3 82.3 - - + +
40I GLU* 1.3 64.1 + - - +
49I LEU* 5.0 3.6 - - + -
73I TYR* 4.5 5.2 - - + +
75I LEU* 3.6 44.9 - - + -
127I ILE* 4.0 7.6 - - + -
129I LEU* 3.8 18.6 - - + -
----------------------------------------------------------
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