Contacts of the helix formed by residues 62 - 76 (chain H) in PDB entry 3ECS
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 SER 62 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H SER* 3.4 16.5 + - - -
60H ASP* 2.8 24.6 + - - +
61H SER* 1.3 78.3 - - - +
63H VAL* 1.3 65.5 + - - +
64H ALA* 3.3 7.1 + - - +
65H VAL* 3.4 19.9 + - - +
66H SER* 3.8 7.6 + - - -
198H GLU* 3.4 26.2 - - - -
250H PHE* 4.3 4.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 63 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H SER 4.0 0.2 + - - -
62H SER* 1.3 71.2 - - - +
64H ALA* 1.3 65.3 + - - +
66H SER* 2.9 3.5 + - - -
67H SER* 2.8 23.0 + - - -
198H GLU* 4.1 12.8 + - + +
199H GLY* 4.7 2.9 - - - -
207H ILE* 3.9 31.6 - - + -
236H VAL* 3.6 38.1 - - + -
238H LEU* 4.5 3.1 - - + -
250H PHE* 3.6 50.0 - - + +
273H VAL* 5.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 64 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H SER* 4.7 3.1 - - - +
23H ALA* 3.8 22.5 - - + +
62H SER* 3.1 10.9 - - - +
63H VAL* 1.3 77.4 - - - +
65H VAL* 1.3 55.7 + - - +
67H SER* 3.4 6.6 + - - -
68H GLY* 2.7 35.5 + - - -
198H GLU* 3.3 25.5 + - + +
233H PHE* 4.5 0.7 - - - +
234H LYS* 4.4 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 65 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H PHE* 4.2 9.6 - - + -
22H SER* 3.3 40.2 - - - +
23H ALA* 4.3 6.7 - - - +
26H ALA* 3.7 21.7 - - + +
54H GLU* 4.8 8.4 - - - +
57H CYS* 3.5 30.7 - - + +
60H ASP* 4.5 7.6 - - + +
62H SER* 3.4 15.8 + - - +
63H VAL 3.3 0.6 - - - -
64H ALA* 1.3 78.5 - - - +
66H SER* 1.3 57.4 + - - +
69H GLY* 3.0 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 66 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H GLU* 5.2 8.0 - - - +
62H SER 3.8 1.5 + - - -
63H VAL* 2.9 14.0 + - - -
65H VAL* 1.3 77.2 - - - +
67H SER* 1.3 60.1 + - - -
68H GLY 3.2 1.3 - - - -
69H GLY* 3.3 0.6 + - - -
70H GLU* 2.8 30.8 + - - +
236H VAL* 5.0 4.3 - - - +
250H PHE* 4.0 27.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 67 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H VAL 2.8 12.4 + - - -
64H ALA* 3.4 6.8 + - - -
66H SER* 1.3 74.2 + - - +
68H GLY* 1.3 59.1 + - - +
70H GLU* 3.5 5.0 + - - +
71H LEU* 3.0 34.7 + - - +
233H PHE 2.7 22.7 + - - -
234H LYS* 3.4 11.3 + - - -
235H PHE 3.6 11.9 - - - -
236H VAL* 3.4 36.5 - - - +
237H ARG 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 68 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H ALA* 5.2 2.2 - - - -
27H ILE* 4.0 12.0 - - - +
64H ALA 2.7 16.9 + - - -
65H VAL 4.7 0.2 - - - -
67H SER* 1.3 76.3 + - - +
69H GLY* 1.3 64.0 + - - +
71H LEU* 3.0 7.3 + - - +
72H PHE* 2.9 23.6 + - - +
100H PHE* 4.5 2.4 - - - -
233H PHE* 3.5 23.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 69 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H ALA* 6.3 0.7 - - - -
27H ILE* 4.2 13.0 - - - +
30H LEU* 4.6 3.1 - - - +
54H GLU* 3.0 28.9 - - - +
65H VAL 3.0 21.9 + - - -
66H SER 3.3 1.1 + - - -
68H GLY* 1.3 75.7 - - - +
70H GLU* 1.3 61.7 + - - +
72H PHE* 3.2 4.8 + - - +
73H LEU* 3.1 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 70 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H GLU* 3.7 6.3 + - + +
66H SER* 2.8 20.6 + - - +
67H SER* 3.9 6.3 - - - +
69H GLY* 1.3 69.2 - - - +
71H LEU* 1.3 66.6 + - - +
73H LEU* 3.5 6.3 + - + +
74H ARG* 2.9 56.7 + - - +
237H ARG* 3.7 23.5 + - - +
304H TYR* 3.5 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67H SER* 3.0 21.6 + - - +
68H GLY* 3.3 11.7 - - - +
70H GLU* 1.3 77.6 - - + +
72H PHE* 1.3 52.5 + - - +
74H ARG* 3.0 7.0 + - + +
75H PHE* 2.8 39.0 + - + +
100H PHE* 3.9 23.1 - - + -
232H SER 5.3 0.2 - - - +
233H PHE* 4.8 14.6 - - + +
235H PHE* 4.3 13.7 - - + +
300H LEU* 6.1 0.2 - - + -
303H LEU* 5.2 23.3 - - + -
304H TYR* 3.6 42.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 72 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H ILE* 4.1 20.9 - - + -
30H LEU* 3.7 41.3 - - + -
31H LEU* 4.2 21.8 - - + -
34H LEU* 4.7 4.3 - - + -
50H THR* 5.8 2.0 - - - -
68H GLY 2.9 11.1 + - - +
69H GLY 3.4 7.6 - - - +
71H LEU* 1.3 75.3 - - - +
73H LEU* 1.3 66.4 + - - +
75H PHE* 3.0 2.9 + - - +
76H ILE* 2.9 54.6 + - + +
97H GLY* 3.4 36.6 - - - -
100H PHE* 3.5 30.2 - + + -
101H LEU* 5.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H LEU* 5.7 0.9 - - + -
47H ALA* 4.3 11.0 - - + +
50H THR* 3.9 26.0 - - + +
51H SER* 3.4 26.0 - - - +
54H GLU* 4.4 13.0 - - + +
69H GLY 3.1 12.9 + - - +
70H GLU* 4.0 6.1 - - + +
72H PHE* 1.3 84.0 - - + +
74H ARG* 1.3 56.0 + - - +
76H ILE* 4.0 15.3 - - + +
77H SER* 2.7 37.4 + - - +
93H MSE 5.0 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 74 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302G LYS* 6.3 1.8 - - - +
305G LEU* 6.3 0.8 - - - +
70H GLU* 2.9 51.9 + - - +
71H LEU* 3.2 8.3 - - + +
73H LEU* 1.3 76.7 - - - +
75H PHE* 1.3 63.8 + - - +
77H SER* 3.6 17.3 + - - +
237H ARG* 3.6 20.2 - - - +
304H TYR* 4.2 26.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 75 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71H LEU* 2.8 19.0 + - + +
72H PHE* 3.0 4.2 + - - +
74H ARG* 1.3 74.6 - - - +
76H ILE* 1.3 62.9 + - + +
77H SER 2.9 16.9 + - - +
96H ARG* 3.1 49.6 + - + -
99H LEU* 3.9 24.5 - - + -
100H PHE* 3.7 41.1 - + + -
103H ARG* 5.3 9.4 - - + -
306H ALA* 4.7 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 76 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H LEU* 3.7 30.3 - - + -
46H ARG* 6.0 0.2 - - - +
50H THR* 6.1 2.0 - - + +
72H PHE* 2.9 41.3 + - + +
73H LEU* 4.0 15.9 - - + +
75H PHE* 1.3 79.5 - - + +
77H SER* 1.3 54.8 + - - +
78H LEU* 4.3 0.7 + - - +
93H MSE 2.9 53.6 - - + +
96H ARG* 4.2 13.5 - - - -
97H GLY* 3.5 34.8 - - - +
----------------------------------------------------------
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