Contacts of the strand formed by residues 61 - 68 (chain B) in PDB entry 1YDY
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 TYR 61 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ILE* 3.8 33.9 - - + -
33B VAL 3.3 1.8 + - - -
34B ILE* 3.5 19.0 - - + -
35B ALA 2.9 25.8 + - - -
59B ALA* 3.3 2.8 - - - +
60B ASP* 1.3 93.4 - - + +
62B LEU* 1.3 67.5 + - - +
166B ILE* 4.4 0.4 - - - -
167B GLY* 3.4 14.8 - - - -
168B ILE 3.4 19.5 - - - -
169B TYR* 4.1 13.5 - + + -
203B ASP 5.0 0.5 + - - -
204B LYS* 3.8 51.2 + - + +
205B VAL 4.3 0.5 + - - -
206B TYR* 3.5 28.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ALA* 4.2 4.5 - - + -
51B LYS* 3.8 44.6 - - + +
54B ALA* 4.1 15.0 - - + -
55B TYR* 4.2 20.9 - - + +
59B ALA* 4.0 17.3 - - + -
61B TYR* 1.3 80.6 - - - +
63B GLU* 1.3 58.7 + - - +
64B GLN* 3.0 17.5 + - - +
154B PHE* 4.9 2.0 - - + -
155B VAL* 3.7 26.0 - - + -
166B ILE* 4.1 12.1 - - + -
167B GLY 3.0 10.2 + - - +
168B ILE* 3.4 1.6 - - - -
169B TYR* 3.0 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE* 4.4 7.6 - - + +
35B ALA 3.3 21.9 + - - +
36B HIS* 3.4 12.0 - - - -
37B ARG* 2.9 28.4 + - - +
46B HIS* 3.4 5.4 - - - -
51B LYS* 3.1 26.6 + - - +
61B TYR 4.1 0.2 - - - -
62B LEU* 1.3 73.8 - - - +
64B GLN* 1.3 64.9 + - - +
65B ASP* 3.5 7.0 - - - +
169B TYR* 3.3 18.4 - - - +
208B GLN* 3.0 16.3 + - - +
344B PHE* 4.0 11.4 - - + -
901B GOL 3.1 6.8 + - - -
903B CA 2.4 29.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B HIS* 3.7 6.1 - - - -
62B LEU* 3.0 23.0 + - - +
63B GLU* 1.3 76.1 - - - +
65B ASP* 1.3 58.2 + - - +
66B LEU* 4.0 17.9 - - + -
76B VAL* 4.1 5.8 - - + -
148B PHE* 4.0 16.7 - - + -
151B GLU* 2.9 41.2 + - + +
152B ILE* 5.2 0.2 - - - -
155B VAL* 5.1 0.4 - - - +
168B ILE* 3.5 22.8 - - - +
169B TYR 3.1 11.2 + - - +
170B PRO* 3.2 26.6 - - + +
171B GLU* 2.8 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ARG* 3.9 6.4 + - - +
46B HIS* 2.7 31.0 + - - +
63B GLU* 3.5 2.5 - - - +
64B GLN* 1.3 73.4 - - - +
66B LEU* 1.3 61.0 + - - +
76B VAL* 3.1 8.0 - - - +
77B LEU 2.9 39.7 + - - +
78B HIS* 3.6 24.6 - - - +
171B GLU* 2.9 18.7 - - - +
173B LYS* 3.8 6.9 - - + +
903B CA 2.4 30.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLN* 4.0 13.0 - - + -
65B ASP* 1.3 79.9 - - - +
67B VAL* 1.3 63.8 + - - +
74B LEU* 4.2 13.7 - - + -
75B VAL 3.4 8.7 - - - +
76B VAL* 4.1 4.0 - - + -
148B PHE* 3.7 48.0 - - + -
170B PRO* 4.0 12.3 - - + -
171B GLU 2.9 20.2 + - - +
172B ILE* 4.8 0.9 - - + -
173B LYS* 3.1 27.7 + - - +
185B ILE* 3.3 9.5 - - + +
189B THR* 3.7 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 1.3 80.1 - - - +
68B MET* 1.3 65.3 + - - +
74B LEU* 3.4 3.4 - - - -
75B VAL* 2.9 48.0 + - + +
77B LEU* 3.7 31.4 - - + +
79B ASP 3.6 17.5 - - - +
80B HIS* 3.9 14.6 - - + -
104B ALA* 3.9 13.2 - - + -
173B LYS* 3.8 15.5 - - + -
178B HIS* 3.8 8.3 - - + +
185B ILE* 3.8 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B VAL* 1.3 76.1 - - - +
69B THR* 1.3 66.3 + - - +
72B ASP* 3.8 40.8 - - + +
73B ASN 3.2 5.4 - - - +
74B LEU* 3.7 20.6 - - + -
104B ALA* 3.8 5.1 - - - +
105B ILE* 3.4 25.3 + - - +
178B HIS* 3.0 21.2 + - + -
183B LYS* 3.8 25.6 - - + -
184B ASP 4.8 3.4 - - - +
185B ILE* 3.6 31.6 - - + -
188B LYS* 4.2 16.6 - - + -
----------------------------------------------------------
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