Contacts of the strand formed by residues 50 - 57 (chain D) in PDB entry 1YXU
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 GLY 50 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D SER* 3.0 6.8 - - - -
47D GLY 2.9 32.8 + - - -
48D GLY 3.3 1.0 - - - -
49D PHE* 1.3 82.5 - - - +
51D SER* 1.3 62.5 + - - -
68D HIS 3.5 8.7 - - - -
69D VAL* 4.9 3.6 - - - -
70D GLU 5.7 0.7 - - - -
73D ARG* 4.3 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D LEU* 4.1 9.3 - - - +
45D GLY 3.5 4.9 - - - -
46D SER* 3.8 11.0 - - - -
50D GLY* 1.3 73.7 - - - -
52D VAL* 1.3 61.2 + - - +
53D TYR* 4.0 22.3 + - - -
66D ILE 3.6 1.7 - - - +
67D LYS* 3.4 1.4 - - - +
68D HIS* 2.9 45.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D LEU* 3.6 2.3 - - - +
44D LEU* 2.8 29.1 + - + +
45D GLY 2.8 14.2 + - - +
49D PHE* 3.7 9.0 - - + -
51D SER* 1.3 76.3 - - - +
53D TYR* 1.3 63.7 + - - +
65D ALA* 4.0 16.4 - - + -
66D ILE 3.3 7.6 - - - +
67D LYS* 3.7 24.9 - - + -
850D AMP 3.7 63.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D VAL* 4.1 17.0 - - + -
41D GLY 3.4 19.7 - - - +
42D PRO* 3.2 4.3 - - + -
43D LEU* 3.7 31.6 - - + +
44D LEU* 4.1 4.7 - - - -
51D SER* 4.0 19.9 - - - -
52D VAL* 1.3 76.9 - - - +
54D SER* 1.3 64.6 + - - +
65D ALA* 3.4 5.5 - - - -
66D ILE* 2.8 37.0 + - + +
68D HIS* 3.7 33.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D VAL* 4.0 1.2 - - - +
41D GLY* 2.5 31.1 + - - +
42D PRO* 2.7 36.3 + - - -
44D LEU* 3.8 20.5 - - - +
53D TYR* 1.3 76.9 - - - +
55D GLY* 1.3 52.6 + - - +
64D VAL 3.9 3.6 - - - -
66D ILE* 4.6 0.6 - - - +
122D ARG* 3.2 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D GLN 3.3 11.7 - - - -
41D GLY* 4.1 1.6 - - - -
53D TYR 3.7 0.2 + - - -
54D SER* 1.3 75.7 - - - +
56D ILE* 1.3 64.0 + - - +
64D VAL* 2.9 40.1 + - - -
66D ILE* 4.1 9.9 - - - -
122D ARG* 3.0 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D TYR* 4.5 1.1 - - - +
39D GLN* 3.0 58.5 + - + +
55D GLY* 1.3 82.6 - - - +
57D ARG* 1.3 74.9 + - - +
58D VAL* 3.2 2.5 + - + -
61D ASN* 4.0 27.1 - - + +
62D LEU 3.3 7.6 - - - +
63D PRO* 4.6 4.3 - - + -
64D VAL* 3.4 3.8 - - - +
122D ARG* 4.2 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D GLN* 3.6 14.1 - - + +
38D TYR* 3.5 35.6 + - + -
56D ILE* 1.3 71.0 - - - +
58D VAL* 1.3 58.9 + - - +
59D SER* 2.8 26.2 + - - +
60D ASP* 2.8 35.7 + - - +
61D ASN* 3.1 29.8 + - - -
62D LEU* 2.8 57.4 + - + +
64D VAL* 4.1 6.1 - - + +
107D LEU* 3.6 25.0 - - - +
----------------------------------------------------------
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