Contacts of the helix formed by residues 58 - 72 (chain A) in PDB entry 2YXT
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 ASN 58 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL* 3.9 7.9 + - + +
57A LEU* 1.3 76.4 - - - +
59A SER* 1.3 59.6 - - - +
60A ASP* 2.9 18.3 + - - +
61A GLU* 2.9 50.6 + - - +
62A LEU* 2.9 26.3 + - - +
87A ASP* 5.9 1.6 - - - -
90A PHE* 4.1 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ASN* 1.3 72.9 - - - +
60A ASP* 1.3 65.3 + - - +
62A LEU* 3.3 8.7 + - - +
63A GLN* 2.9 29.8 + - - +
87A ASP* 5.1 1.8 + - - -
89A SER* 3.1 46.1 + - - -
90A PHE* 4.1 11.3 - - - +
93A MET* 3.8 14.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ASN* 2.9 16.3 + - - +
59A SER* 1.3 84.1 + - - +
61A GLU* 1.3 55.9 + - + +
63A GLN* 3.2 14.7 + - - +
64A GLU* 2.9 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL 4.1 4.3 - - - +
57A LEU* 3.4 21.7 - - + +
58A ASN* 2.9 45.7 + - - +
60A ASP* 1.3 73.7 - - + +
62A LEU* 1.3 66.0 + - - +
64A GLU* 3.3 7.9 + - - +
65A LEU* 3.0 27.2 + - - +
55B GLN* 3.4 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 4.5 11.0 - - + -
38A VAL* 3.8 29.2 - - + -
57A LEU* 3.8 9.1 - - + +
58A ASN 2.9 13.0 + - - +
59A SER 3.7 6.7 - - - +
61A GLU* 1.3 77.5 - - - +
63A GLN* 1.3 64.6 + - - +
65A LEU* 3.2 4.4 + - + +
66A TYR* 3.2 19.0 + - + +
90A PHE* 3.9 26.0 - - + +
93A MET* 3.6 25.8 - - + -
94A VAL* 3.9 23.6 - - + -
97A ILE* 3.7 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A SER 2.9 17.5 + - - +
60A ASP* 3.2 14.4 + - - +
62A LEU* 1.3 78.4 - - - +
64A GLU* 1.3 55.4 + - - +
66A TYR* 3.2 6.7 + - + +
67A GLU* 2.9 35.9 + - + +
93A MET* 3.7 27.0 - - + +
1319A PO4 3.1 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ASP 2.9 13.8 + - - +
61A GLU* 3.5 14.0 - - - +
63A GLN* 1.3 75.6 - - - +
65A LEU* 1.3 61.6 + - - +
67A GLU* 3.2 9.5 + - - +
68A GLY 3.1 17.3 + - - -
53B LYS* 3.4 49.8 + - + +
54B GLY 3.8 15.2 + - - +
55B GLN* 3.0 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A VAL* 4.1 12.3 - - + -
57A LEU* 3.9 24.7 - - + -
61A GLU 3.0 19.0 + - - +
62A LEU* 3.6 7.9 - - + +
64A GLU* 1.3 72.9 - - - +
66A TYR* 1.3 64.5 + - - +
68A GLY 3.2 9.4 + - - +
69A LEU* 3.2 19.2 + - + +
15B ILE* 4.3 11.4 - - + -
42B GLN* 3.5 42.0 - - + +
43B PHE 3.8 21.3 - - - -
44B SER* 3.5 9.1 - - - +
53B LYS* 4.9 1.3 - - - -
54B GLY* 3.9 9.6 - - - -
55B GLN* 3.9 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 5.7 2.5 - - + -
62A LEU* 3.2 10.7 + - + +
63A GLN* 3.6 8.7 - - - +
65A LEU* 1.3 79.0 - - - +
67A GLU* 1.3 52.8 + - + +
69A LEU* 3.0 18.6 + - + +
70A ARG* 2.7 54.9 + - + +
75A ASN* 2.6 40.4 + - + +
77A TYR* 6.1 0.2 - + - -
93A MET* 5.7 0.2 - - + -
97A ILE* 4.0 33.4 - - + -
100A GLU* 2.8 36.1 + - + +
101A LEU* 3.6 27.1 - - + +
1319A PO4 4.0 20.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLN* 2.9 22.9 + - + +
64A GLU* 3.2 13.0 + - - +
66A TYR* 1.3 78.7 - - + +
68A GLY* 1.3 52.7 + - - +
70A ARG* 3.2 36.6 + - - +
71A LEU* 2.7 63.8 + - + +
1319A PO4 5.4 4.7 - - - +
53B LYS* 4.8 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLU 3.1 10.9 + - - -
65A LEU 3.2 2.6 + - - -
67A GLU* 1.3 75.3 - - - +
69A LEU* 1.3 62.7 + - - +
71A LEU* 3.5 6.0 + - - +
72A ASN* 3.1 29.3 + - - -
44B SER* 3.5 23.8 - - - -
45B ASN* 4.0 0.7 - - - -
52B TRP* 4.9 2.7 - - - -
53B LYS* 4.0 16.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 4.7 7.9 - - + -
65A LEU 3.2 13.6 + - - +
66A TYR* 3.0 22.1 + - + +
68A GLY* 1.3 75.5 - - - +
70A ARG* 1.3 58.3 + - - +
72A ASN 3.2 2.6 + - - -
73A ASN 3.1 2.8 + - - -
74A MET* 2.6 58.6 + - + +
75A ASN* 4.2 1.8 - - + +
77A TYR* 3.5 29.4 - - + +
15B ILE* 3.9 22.7 - - + -
16B ARG* 4.1 6.3 - - + -
44B SER* 3.3 29.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TYR* 2.7 31.3 + - + +
67A GLU* 3.2 26.0 + - - +
69A LEU* 1.3 71.9 - - - +
71A LEU* 1.3 61.0 + - - +
73A ASN* 2.7 27.9 + - - +
75A ASN* 3.6 30.7 - - - +
100A GLU* 2.7 40.6 + - - -
1319A PO4 3.4 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLU* 2.7 52.7 + - + +
68A GLY* 3.9 3.6 - - - +
70A ARG* 1.3 75.3 - - - +
72A ASN* 1.3 57.3 + - - +
73A ASN* 3.3 0.9 + - - +
51B HIS* 3.2 54.9 + - + +
53B LYS* 5.0 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLY 3.1 13.2 + - - +
69A LEU 3.2 2.5 + - - +
70A ARG 3.0 1.2 - - - -
71A LEU* 1.3 75.0 - - - +
73A ASN* 1.3 72.0 + - - +
74A MET* 3.0 24.9 + - - +
45B ASN* 3.1 22.6 + - - +
49B TYR* 3.8 19.1 - - + +
50B ALA* 4.0 3.3 + - - +
51B HIS* 2.8 52.4 + - - +
287B MET* 5.5 1.9 - - - +
----------------------------------------------------------
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