Contacts of the helix formed by residues 64 - 77 (chain Y) in PDB entry 6CP3
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 64 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D HIS* 4.5 26.5 - - + +
56D GLU* 5.6 8.5 - - + +
57D ASN* 4.8 10.4 - - - +
63Y SER* 1.3 77.5 + - - +
65Y LYS* 1.3 65.7 + - + +
66Y ASP 3.4 0.2 - - - -
67Y ARG* 3.5 5.5 + - - +
68Y ASN* 3.3 21.7 + - + +
93Y SER* 3.8 9.5 + - - +
94Y GLU* 3.7 38.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 65 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D GLN* 5.2 20.0 - - + -
63Y SER* 2.5 16.5 + - - +
64Y LEU* 1.3 75.4 - - + +
66Y ASP* 1.3 76.4 + - - +
68Y ASN* 3.1 10.3 + - + +
69Y SER* 2.9 30.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 66 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ARG 5.7 0.3 - - - +
18A ILE* 4.5 19.8 - - + +
21A VAL* 5.0 8.0 - - - +
62Y LEU* 4.3 27.2 - - + +
63Y SER* 3.3 20.3 + - - -
65Y LYS* 1.3 93.9 + - - +
67Y ARG* 1.3 60.0 + - - +
69Y SER* 3.2 7.3 + - - +
70Y VAL* 2.9 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 67 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62Y LEU* 5.0 6.0 - - + +
63Y SER 4.1 13.7 + - - +
64Y LEU 3.5 9.7 + - - +
65Y LYS 3.3 0.2 - - - -
66Y ASP* 1.3 77.3 - - - +
68Y ASN* 1.3 60.8 + - - +
70Y VAL* 3.3 9.0 + - - +
71Y ILE* 3.0 29.0 + - - +
93Y SER* 4.3 22.0 - - - +
96Y ASN* 5.4 4.7 - - - +
98Y LEU* 4.8 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 68 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64Y LEU* 3.3 14.2 + - + +
65Y LYS* 3.1 13.4 + - + +
67Y ARG* 1.3 78.0 - - - +
69Y SER* 1.3 59.2 + - - +
71Y ILE* 3.2 13.4 - - - +
72Y ASP* 2.9 37.8 + - - +
90Y LYS* 5.2 8.2 - - - +
93Y SER* 4.3 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 69 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 5.7 0.2 - - - -
17A ARG* 5.7 4.9 - - - +
65Y LYS* 2.9 20.3 + - - -
66Y ASP* 3.2 10.0 + - - -
68Y ASN* 1.3 75.1 - - - +
70Y VAL* 1.3 56.0 + - - +
71Y ILE 3.2 0.2 - - - -
72Y ASP* 3.2 12.7 + - - +
73Y ALA* 2.7 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 70 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 3.7 30.3 - - + -
18A ILE* 5.5 4.3 - - + -
53Y LEU 5.7 0.2 - - - +
57Y LEU* 3.7 33.0 - - + +
58Y LEU* 5.8 2.5 - - + -
62Y LEU* 6.3 0.9 - - + -
66Y ASP* 2.9 23.0 + - + +
67Y ARG* 3.3 8.7 + - - +
69Y SER* 1.3 73.4 - - - +
71Y ILE* 1.3 57.9 + - + +
73Y ALA* 3.1 6.5 + - - +
74Y ILE* 2.6 51.7 + - + +
98Y LEU* 5.4 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 71 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67Y ARG 3.0 18.4 + - - +
68Y ASN* 3.2 15.9 - - - +
70Y VAL* 1.3 78.3 - - + +
72Y ASP* 1.3 62.9 + - - +
74Y ILE* 3.1 13.2 + - + +
75Y VAL* 2.9 41.9 + - + +
86Y VAL* 4.8 7.4 - - + +
89Y LEU* 3.5 53.6 - - + -
90Y LYS* 4.8 4.9 - - + +
93Y SER* 4.1 19.1 - - - -
98Y LEU* 4.3 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 72 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68Y ASN* 2.9 36.1 + - - +
69Y SER* 3.6 12.9 - - - +
70Y VAL 3.2 0.2 - - - -
71Y ILE* 1.3 78.8 - - - +
73Y ALA* 1.3 59.5 + - - +
75Y VAL* 3.4 12.7 - - + +
76Y GLU* 2.9 39.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 3.7 25.4 - - + +
13A ILE* 4.9 12.1 - - + -
14A LEU* 4.2 20.0 - - + -
69Y SER* 2.7 21.5 + - - +
70Y VAL* 3.1 10.1 + - - +
72Y ASP* 1.3 73.8 - - - +
74Y ILE* 1.3 62.7 + - - +
76Y GLU* 3.4 26.7 + - - +
77Y THR 3.8 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 74 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 5.4 2.9 - - - -
14A LEU* 6.1 2.7 - - + -
43Y VAL* 4.1 29.2 - - + -
46Y THR* 5.6 7.2 - - + +
47Y VAL* 4.8 15.5 - - + -
58Y LEU* 6.2 4.7 - - + -
70Y VAL* 2.6 35.7 + - + +
71Y ILE* 3.3 18.8 - - + +
73Y ALA* 1.3 76.3 - - + +
75Y VAL* 1.3 66.2 + - + +
76Y GLU 3.6 0.3 + - - -
77Y THR* 3.8 11.7 + - - +
78Y HIS* 3.4 18.2 + - - +
89Y LEU* 4.7 11.2 - - + -
98Y LEU* 6.5 0.9 - - + -
101Y PHE* 5.9 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 75 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71Y ILE* 2.9 27.3 + - + +
72Y ASP* 3.4 24.2 - - + +
74Y ILE* 1.3 81.0 - - + +
76Y GLU* 1.3 64.2 + - + +
77Y THR 3.2 2.5 - - - -
78Y HIS* 2.8 38.8 - - + +
79Y LYS* 4.1 2.3 + - - -
81Y LEU* 4.7 6.7 - - + +
86Y VAL* 3.9 30.1 - - + -
89Y LEU* 5.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 76 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLN* 4.1 8.5 - - - +
10A VAL* 4.7 8.0 - - + +
13A ILE* 3.7 28.9 - - - +
72Y ASP* 2.9 24.7 + - - +
73Y ALA* 3.5 17.2 - - - +
74Y ILE 3.3 0.4 - - - -
75Y VAL* 1.3 79.5 - - + +
77Y THR* 1.3 63.0 + - - +
78Y HIS* 3.3 2.3 + - - -
79Y LYS 4.9 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 77 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLN* 3.9 25.1 + - - +
7A PRO* 4.6 7.1 - - - +
10A VAL* 3.2 29.8 - - - +
46Y THR* 4.8 19.2 + - + +
73Y ALA 3.8 2.5 + - - -
74Y ILE* 3.8 14.9 + - - +
75Y VAL 3.2 0.2 - - - -
76Y GLU* 1.3 80.4 - - - +
78Y HIS* 1.3 70.7 + - + +
----------------------------------------------------------
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