Contacts of the helix formed by residues 72 - 90 (chain A) in PDB entry 1YI8
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 ARG 72 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASP 4.4 3.0 + - - -
69A HIS* 2.7 65.9 + - + +
71A ASP* 1.3 106.9 + - - +
73A PRO* 1.3 66.9 - - - +
74A GLU 3.7 0.7 - - - -
75A GLN* 3.2 40.8 + - + +
76A VAL* 3.9 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 4.7 5.8 - - + -
69A HIS 3.8 2.4 - - - +
70A PHE 3.2 13.9 - - - +
71A ASP 3.2 9.2 - - - +
72A ARG* 1.3 86.7 - - - +
74A GLU* 1.3 54.5 + - + +
75A GLN 2.6 13.7 + - - -
76A VAL* 2.7 35.4 + - + +
77A ARG* 4.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG 3.6 0.6 + - - -
73A PRO* 1.3 77.8 - - - +
75A GLN* 1.3 59.7 + - - +
76A VAL 3.4 0.2 - - - -
77A ARG* 3.5 28.5 + - + +
78A GLU* 3.3 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A THR* 3.0 39.2 + - - +
69A HIS* 4.1 11.9 + - + -
72A ARG* 3.2 40.0 + - + +
73A PRO 2.6 6.1 + - - -
74A GLU* 1.3 73.2 - - - +
76A VAL* 1.3 61.4 + - - +
78A GLU* 3.8 2.1 + - - +
79A ASN* 2.6 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PRO* 3.6 24.5 - - + +
32A THR* 5.6 0.2 - - - +
62A ASP* 3.6 35.4 - - - +
65A ALA* 4.1 12.3 - - + -
66A LEU* 3.6 26.2 - - + -
69A HIS* 5.7 6.7 - - + +
72A ARG 3.9 2.4 + - - +
73A PRO* 2.7 26.1 + - + +
75A GLN* 1.3 76.7 - - - +
77A ARG* 1.3 78.4 + - + +
79A ASN* 3.1 3.7 + - - +
80A VAL* 3.1 18.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ASP* 5.5 0.9 - - - -
73A PRO 3.4 1.5 + - - +
74A GLU* 3.5 33.7 + - - +
76A VAL* 1.3 89.1 - - + +
78A GLU* 1.3 72.7 + - - +
80A VAL* 3.0 25.3 - - - +
81A LEU 4.1 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLU* 3.3 20.0 + - + +
75A GLN* 4.3 2.9 - - - +
77A ARG* 1.3 90.9 + - + +
79A ASN* 1.3 65.7 + - - +
80A VAL 3.0 1.3 + - - -
81A LEU* 3.4 9.4 + - - +
82A ALA* 3.2 18.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PRO* 3.5 14.8 - - - +
32A THR* 3.0 19.9 - - - +
33A GLY* 3.1 34.2 - - - +
34A ALA 4.3 1.0 - - - +
75A GLN* 2.6 28.9 + - - +
76A VAL 3.1 2.2 + - - +
78A GLU* 1.3 77.0 - - - +
80A VAL* 1.3 69.6 + - - +
82A ALA* 3.4 13.2 - - - +
83A VAL* 2.7 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PRO* 3.9 17.5 - - + -
60A LEU* 3.8 25.2 - - + +
62A ASP* 4.0 27.4 - - + +
76A VAL 3.1 12.0 + - - +
77A ARG* 3.0 21.3 + - - +
79A ASN* 1.3 82.1 - - - +
81A LEU* 1.3 74.8 + - + +
83A VAL* 3.2 2.9 + - - +
84A ALA 3.2 15.1 + - - -
101A VAL* 4.4 17.7 - - + -
324A VAL* 5.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ARG 4.1 0.6 + - - +
78A GLU* 3.4 9.2 + - - +
80A VAL* 1.3 85.3 - - + +
82A ALA* 1.3 61.3 + - - +
84A ALA* 3.5 4.4 - - - +
85A LEU* 3.2 21.7 + - - +
320A VAL* 3.8 37.5 - - + +
321A LEU* 4.6 15.7 - - + -
324A VAL* 4.2 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ALA* 4.7 13.2 - - + +
78A GLU 3.2 8.6 + - - +
79A ASN* 3.4 31.6 - - + +
80A VAL 3.1 0.2 - - - -
81A LEU* 1.3 77.7 - - - +
83A VAL* 1.3 62.3 + - - +
85A LEU* 3.2 23.9 - - - +
86A ASP* 3.2 13.4 + - - +
310A ARG* 4.9 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ASP* 4.7 8.3 - - + +
30A ARG 5.6 0.4 - - - -
31A PRO* 4.0 17.3 - - + -
32A THR 4.8 0.2 - - - +
33A GLY 3.4 26.2 - - - +
34A ALA* 4.8 0.7 - - - -
35A LEU* 3.9 14.1 - - + -
60A LEU* 3.7 20.4 - - + -
79A ASN 2.7 23.4 + - - +
80A VAL 3.8 2.5 - - - +
82A ALA* 1.3 69.4 - - - +
84A ALA* 1.3 71.4 + - - +
86A ASP* 2.9 16.0 + - - +
87A TYR* 3.0 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 4.7 3.5 - - + +
80A VAL 3.2 12.0 + - - +
81A LEU* 3.5 10.5 - - - +
83A VAL* 1.3 74.7 - - - +
85A LEU* 1.3 54.9 + - - +
87A TYR* 2.5 47.5 + - - +
88A LEU* 3.0 8.7 + - - +
99A CYS* 4.9 0.2 - - - -
320A VAL* 3.6 19.1 - - + -
323A PHE* 4.3 7.0 - - + -
324A VAL* 3.9 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU 3.2 10.6 + - - +
82A ALA* 3.2 14.6 - - - +
84A ALA* 1.3 77.9 - - - +
86A ASP* 1.3 58.2 + - - +
87A TYR 2.9 0.5 + - - -
88A LEU* 3.1 9.3 + - + +
89A ALA* 2.9 28.7 + - + +
310A ARG* 2.9 60.6 - - + +
313A TYR* 4.5 17.0 - - + -
314A GLU* 3.7 20.6 - - + +
320A VAL* 4.3 7.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ALA* 3.0 18.2 - - - +
35A LEU* 2.8 62.6 + - + +
44A LEU* 3.9 6.2 - - - +
82A ALA 3.2 8.9 + - - +
83A VAL* 2.9 10.0 + - - +
85A LEU* 1.3 78.2 - - - +
87A TYR* 1.3 58.1 + - - +
89A ALA* 4.0 7.3 - - - +
90A ALA* 3.5 22.0 + - - +
226A LEU* 3.9 12.0 + - - +
310A ARG* 2.7 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ASP* 2.7 37.4 + - - +
35A LEU* 4.2 6.3 - - + -
44A LEU* 3.8 18.6 - - + -
47A ARG* 3.8 9.2 - - - -
58A VAL* 3.1 43.7 - - + +
59A LEU 4.1 0.9 + - - -
60A LEU* 4.0 22.9 - - + +
83A VAL* 3.0 24.4 + - + +
84A ALA* 2.5 29.4 + - - +
86A ASP* 1.3 70.6 - - - +
88A LEU* 1.3 66.4 + - - +
89A ALA 3.2 0.9 - - - -
90A ALA* 3.3 9.0 + - - +
91A GLY 3.4 0.7 + - - -
92A LEU* 3.2 40.6 + - + +
99A CYS* 4.7 1.3 - - - -
323A PHE* 4.4 14.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ALA 3.0 8.0 + - - +
85A LEU* 3.7 8.5 - - + +
87A TYR* 1.3 79.0 - - - +
89A ALA* 1.3 63.3 + - - +
91A GLY* 3.2 13.0 + - - -
92A LEU 3.4 21.7 + - - +
94A PRO* 3.7 25.1 - - + -
309A ARG* 3.5 15.6 - - - -
313A TYR* 3.6 46.8 - - + +
320A VAL* 4.1 22.4 - - + -
323A PHE* 3.9 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 2.9 18.1 + - + +
86A ASP* 4.1 9.6 - - - +
88A LEU* 1.3 78.3 - - - +
90A ALA* 1.3 52.0 + - - +
226A LEU* 5.6 0.2 - - + -
306A ILE* 2.9 38.0 - - + +
309A ARG* 2.5 38.4 + - - -
310A ARG* 4.1 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 5.0 7.7 - - + +
44A LEU* 3.5 42.4 - - + +
48A VAL* 3.5 18.2 - - + +
86A ASP 3.5 7.7 + - - +
87A TYR 3.3 5.6 + - - +
88A LEU 3.3 0.4 - - - -
89A ALA* 1.3 77.6 - - - +
91A GLY* 1.3 56.7 + - - +
92A LEU* 3.8 1.6 - - + -
226A LEU* 4.4 7.2 - - + -
306A ILE* 4.4 6.7 - - + -
309A ARG* 3.8 5.5 + - - +
----------------------------------------------------------
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