Contacts of the strand formed by residues 47 - 54 (chain C) in PDB entry 1YA8
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 VAL 47 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C PHE* 3.4 3.2 - - - -
38C VAL* 2.8 37.5 + - - +
40C LEU 5.7 1.6 - - - +
43C PHE* 6.4 0.4 - - + -
45C GLN 4.3 5.2 - - - +
46C PRO* 1.3 77.9 - - + +
48C ALA* 1.3 63.3 + - - +
49C ILE* 3.7 5.4 + - + +
122C TYR* 4.1 10.1 - - + -
123C THR 3.1 34.1 - - - +
124C PRO* 3.9 10.8 - - + -
155C LEU* 3.6 27.4 - - + -
158C ALA* 4.2 9.0 - - + -
159C ALA* 4.2 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C PRO* 4.0 13.7 - - + -
36C LYS 3.4 5.2 - - - -
37C PHE* 4.1 10.8 - - + -
46C PRO 4.2 0.6 + - - -
47C VAL* 1.3 73.7 - - - +
49C ILE* 1.3 62.0 + - - +
50C PHE* 3.9 16.5 - - + -
121C ILE 3.6 3.1 - - - +
122C TYR* 3.7 0.2 - - - -
123C THR* 3.1 47.4 + - + +
125C ALA 5.8 1.3 + - - +
127C LEU* 4.0 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C GLY* 3.4 3.1 - - - -
36C LYS* 2.7 51.5 + - + +
38C VAL* 3.4 34.3 - - + -
47C VAL* 4.1 9.9 - - + +
48C ALA* 1.3 79.4 - - - +
50C PHE* 1.3 65.1 + - - +
51C LEU* 3.7 29.8 + - + +
80C ALA 4.1 2.4 - - - +
81C THR* 5.1 0.2 - - - +
121C ILE 3.4 7.0 - - - +
122C TYR* 3.8 32.5 - - + -
153C ASP* 5.2 0.9 - - - +
155C LEU* 5.1 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C PRO* 4.0 19.3 - - + -
26C VAL* 3.8 14.6 - - + -
33C VAL* 3.6 35.7 - - + -
34C LEU 4.1 2.2 - - - -
35C GLY* 3.4 28.7 - - - -
48C ALA* 3.9 23.3 - - + -
49C ILE* 1.3 76.1 - - - +
51C LEU* 1.3 65.6 + - - +
52C GLY 4.3 0.2 - - - -
53C ILE* 3.7 20.4 - - + -
80C ALA* 3.6 6.7 - - + -
119C LEU 4.3 0.3 - - - +
120C ASN* 3.3 5.0 - - - -
121C ILE* 2.9 42.4 + - + +
123C THR* 4.7 2.7 - - + -
127C LEU* 4.6 0.4 - - + -
208C PHE* 3.6 31.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LYS* 5.1 13.0 - - - +
49C ILE* 3.7 24.9 - - + +
50C PHE* 1.3 80.1 - - - +
52C GLY* 1.3 61.8 + - - +
53C ILE 3.6 0.4 - - - -
80C ALA* 2.8 34.6 + - - +
81C THR* 3.7 14.0 + - + +
82C SER 3.6 18.0 - - - +
83C TYR* 3.9 48.9 - - + +
120C ASN* 3.2 24.7 - - + +
122C TYR* 4.0 5.8 - - - +
1382C SIA 3.5 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 1.3 74.1 - - - +
53C ILE* 1.3 61.9 + - - +
54C PRO* 3.3 6.2 - - - +
78C LYS* 5.2 0.7 - - - +
80C ALA* 5.0 1.2 - - - +
84C PRO* 3.9 7.3 - - - +
118C TYR* 2.9 31.0 - - - -
119C LEU 3.5 0.8 + - - -
120C ASN* 3.0 13.7 + - - -
1382C SIA 3.1 31.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C THR* 5.6 0.2 - - + -
33C VAL* 4.3 17.0 - - + -
50C PHE* 3.7 33.4 - - + -
52C GLY* 1.3 75.5 - - - +
54C PRO* 1.3 79.6 - - + +
74C TRP* 5.3 4.5 - - + -
78C LYS* 5.8 0.4 - - - -
80C ALA* 4.1 12.3 - - + -
118C TYR* 3.3 0.7 - - - -
119C LEU* 3.0 41.6 + - + +
121C ILE* 3.9 13.7 - - + -
200C TRP* 3.6 24.0 - - + +
208C PHE* 3.8 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A GLU* 5.2 4.0 - - - +
184A HIS* 6.2 2.5 - - + +
30C HIS* 5.6 1.2 - - - -
52C GLY 3.3 9.4 - - - +
53C ILE* 1.3 97.2 - - + +
55C PHE* 1.3 59.9 + - - +
56C ALA 3.5 13.7 - - - +
58C PRO* 6.4 0.2 - - + -
71C ALA* 4.6 10.3 - - + +
74C TRP* 4.0 25.8 - - + -
78C LYS* 4.1 23.6 - - + +
117C LEU 3.6 2.9 - - - +
118C TYR* 3.5 25.8 - - + +
200C TRP* 4.0 7.3 + - - -
----------------------------------------------------------
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