Contacts of the strand formed by residues 35 - 41 (chain A) in PDB entry 5Y03
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 GLN 35 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASP* 3.9 10.5 - - - +
34A PRO* 1.3 79.9 - - - +
36A LEU* 1.3 57.6 + - - +
55A ARG* 3.4 32.9 - - - +
56A VAL 3.1 11.2 - - - +
57A HIS* 3.4 31.2 + - + +
58A PHE* 3.8 4.5 - - - -
128A ARG* 3.5 21.3 - - - +
129A ASP* 2.7 49.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 5.5 1.1 - - + -
35A GLN* 1.3 75.6 - - - +
37A GLN* 1.3 71.4 + - - +
38A VAL* 4.2 6.3 - - + -
54A PHE* 3.8 2.3 - - + +
55A ARG* 3.4 1.8 - - - -
56A VAL* 2.8 46.9 + - + +
58A PHE* 3.6 21.5 - - + -
83A PHE* 4.6 8.7 - - + -
89A PHE* 3.8 27.6 - - + -
91A LEU* 4.0 20.4 - - + -
126A VAL* 3.8 13.2 - - + -
127A SER 3.7 6.5 - - - +
128A ARG* 4.7 0.2 - - - -
130A ILE* 3.5 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 1.3 75.7 - - - +
38A VAL* 1.3 67.1 + - - +
39A ASP* 2.9 26.1 + - - +
53A HIS* 3.3 26.8 + - + +
54A PHE 3.3 8.7 - - - +
55A ARG* 3.1 15.1 + - + -
72A TRP* 5.8 1.2 - - - -
125A GLN* 3.6 2.6 - - - +
126A VAL* 3.3 3.5 - - - -
127A SER* 2.7 53.6 + - - +
128A ARG* 2.6 48.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 3.9 21.3 - - + -
36A LEU* 4.2 11.2 - - + -
37A GLN* 1.3 79.6 - - - +
39A ASP* 1.3 65.1 + - - +
40A PHE* 3.7 28.3 - - + -
52A PHE* 3.8 1.8 - - + +
53A HIS* 3.7 0.9 - - - -
54A PHE* 2.8 46.9 + - + +
91A LEU* 4.1 16.4 - - + -
93A ILE* 4.0 11.0 - - + -
124A VAL* 3.9 15.3 - - + -
125A GLN 3.2 4.5 - - - +
126A VAL* 4.4 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLN* 2.9 28.7 + - - +
38A VAL* 1.3 75.8 - - - +
40A PHE* 1.3 62.7 + - - +
41A TYR* 3.4 31.0 + - + -
50A ILE* 3.6 17.9 - - + +
52A PHE 3.5 2.7 - - - -
53A HIS* 2.8 31.8 + - - +
72A TRP* 4.6 0.2 - - - -
124A VAL* 3.3 5.5 - - - -
125A GLN* 2.8 48.2 + - + +
127A SER* 4.8 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 3.5 23.8 - - + -
20A VAL* 3.8 17.7 - - + -
38A VAL* 3.7 13.5 - - + -
39A ASP* 1.3 73.9 - - - +
41A TYR* 1.3 61.2 + - - +
50A ILE* 3.5 3.9 - - - -
51A ALA* 2.9 27.7 + - - +
52A PHE* 2.8 31.0 + + + +
93A ILE* 3.6 40.6 - - + -
95A VAL* 4.8 1.6 - - + -
100A TYR* 3.5 41.1 - + - -
121A VAL* 3.8 14.3 - - + +
123A MET 3.8 4.9 - - - -
124A VAL* 3.8 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ASP* 3.4 32.2 + - + -
40A PHE* 1.3 73.5 - - - +
42A THR* 1.3 59.8 + - - +
43A ASP 3.3 16.6 - - - +
45A ASP 3.8 2.9 - - - -
46A GLU* 3.0 43.5 + - + +
48A SER* 3.2 23.8 - - - -
49A ASP 3.7 2.0 - - - -
50A ILE* 3.6 17.3 - - + +
67A ARG* 3.6 15.9 + - - -
121A VAL* 3.5 4.5 - - - -
122A LYS 2.9 21.5 + - - -
123A MET* 2.8 39.0 + - + +
125A GLN* 4.0 28.8 + - + -
----------------------------------------------------------
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