Contacts of the helix formed by residues 57 - 65 (chain H) in PDB entry 6B0B
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 ALA 57 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H PHE* 1.3 91.9 - - - +
58H TRP* 1.3 63.2 + - - +
59H ASP* 4.2 5.6 - - + +
60H ILE* 3.3 21.5 - - + +
135H VAL* 3.4 24.6 + - - +
138H LYS* 4.3 13.9 - - + +
140H THR* 4.0 23.8 - - + +
165H LEU* 6.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 58 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H ILE* 3.7 31.2 - - + -
46H LEU* 3.7 39.7 - - + -
48H VAL* 4.6 9.4 - - + -
54H LEU* 4.0 16.4 - - + -
56H PHE* 3.5 4.7 + - - +
57H ALA* 1.3 68.7 - - - +
59H ASP* 1.3 63.1 + - - +
60H ILE 3.1 2.9 - - - -
61H LEU* 2.9 44.0 + - + +
62H SER* 3.6 2.8 + - - -
65H PHE* 4.7 7.2 - + - -
201H ILE* 4.2 12.8 - - + -
208H TYR* 4.0 39.2 - + + +
209H THR 6.0 0.4 - - - -
211H VAL* 3.4 31.4 - - + +
213H GLN* 2.7 30.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 59 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57H ALA* 3.2 4.1 - - + -
58H TRP* 1.3 81.4 - - - +
60H ILE* 1.3 57.6 + - - +
61H LEU 3.1 0.2 - - - -
62H SER* 2.8 18.0 + - - -
63H PRO* 3.3 1.4 - - - +
140H THR* 3.0 28.1 + - - +
142H GLY* 3.5 26.1 + - - -
143H TRP* 2.7 36.6 + - + +
165H LEU* 4.5 8.1 - - + -
201H ILE* 4.2 20.3 - - - +
208H TYR* 5.6 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 60 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H VAL* 4.9 7.9 - - + -
56H PHE* 3.6 27.6 - - + -
57H ALA* 3.3 20.0 - - + +
59H ASP* 1.3 77.8 - - + +
61H LEU* 1.3 71.1 + - + +
62H SER 3.6 0.2 - - - -
63H PRO* 3.8 3.5 - - - +
64H GLN* 3.4 21.8 + - - +
97H MET* 4.5 5.0 - - + +
99H PHE* 4.1 28.0 - - + -
105H VAL* 4.7 21.2 - - + +
124H LEU* 5.3 0.8 - - + +
129H PHE* 4.7 10.1 - - + -
135H VAL* 4.3 22.7 - - + -
143H TRP* 4.6 9.0 - - + -
165H LEU* 5.2 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H MET* 4.7 9.8 - - + +
27H PHE* 4.6 2.5 - - + -
29H ILE* 3.8 22.7 - - + -
54H LEU* 4.3 2.0 - - + -
56H PHE* 4.1 24.0 - - + -
58H TRP* 2.9 42.3 + - + +
60H ILE* 1.3 95.1 - - + +
62H SER* 1.3 63.7 + - - +
63H PRO* 3.5 1.3 - - - -
64H GLN* 3.3 19.4 + - + +
65H PHE* 3.4 18.8 - - + -
124H LEU* 3.6 34.1 - - + -
213H GLN* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 62 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H TRP 3.6 4.4 + - - -
59H ASP* 2.8 27.4 + - - -
61H LEU* 1.3 73.5 - - - +
63H PRO* 1.3 61.9 - - - +
64H GLN 3.0 10.7 + - - -
65H PHE* 3.4 14.6 + - - +
143H TRP* 3.7 11.6 - - - -
199H LEU* 3.4 42.4 - - - +
201H ILE* 4.6 6.3 - - - -
213H GLN* 3.8 22.8 + - - +
215H GLU* 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 63 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H ASP 3.3 7.9 - - - +
60H ILE 3.8 8.5 - - - +
61H LEU 3.5 3.6 - - - -
62H SER* 1.3 96.9 - - - +
64H GLN* 1.3 59.8 + - - +
65H PHE 3.4 2.0 + - - -
70H LYS* 4.1 13.6 + - - +
95H ARG* 2.4 36.7 + - - +
97H MET* 4.8 4.9 - - + -
143H TRP* 3.8 13.9 - - + +
161H ILE* 6.5 0.7 - - + -
163H GLN* 3.8 31.2 - - - +
177H VAL* 6.5 0.4 - - + -
199H LEU* 4.8 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 64 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H MET* 4.8 11.9 - - + -
60H ILE 3.4 12.3 + - - +
61H LEU* 3.3 22.9 - - - +
62H SER 3.0 1.6 + - - -
63H PRO* 1.3 80.8 - - - +
65H PHE* 1.3 68.4 + - + +
93H TRP* 3.1 51.5 + - + -
95H ARG* 3.3 20.4 + - - +
97H MET* 3.2 31.3 - - - -
105H VAL* 5.1 0.8 - - - +
107H VAL* 3.8 21.8 - - + +
109H GLN* 5.4 2.1 + - - +
122H VAL* 5.5 1.7 - - + +
124H LEU* 4.8 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 65 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H PHE* 5.2 13.5 - + + -
16H VAL* 4.1 28.7 - - + -
18H MET* 4.5 19.1 - - + -
29H ILE* 5.6 4.0 - - + -
42H GLN* 4.8 11.9 - - - +
46H LEU* 4.1 30.1 - - + -
58H TRP* 4.7 7.0 - + - -
61H LEU* 3.4 25.1 - - + -
62H SER 3.4 8.0 + - - +
63H PRO 3.4 0.9 - - - +
64H GLN* 1.3 85.1 - - - +
70H LYS* 3.2 45.5 + - - +
120H TYR* 5.7 7.0 - + - -
122H VAL* 5.8 1.1 - - + -
213H GLN* 3.3 37.0 - - - +
215H GLU* 4.0 20.1 - - - +
----------------------------------------------------------
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