Contacts of the strand formed by residues 30 - 37 (chain A) in PDB entry 3W1Y
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 HIS 30 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 2.7 38.7 + - - -
27A TYR* 3.0 38.3 + + + +
29A LYS* 1.3 94.2 - - + +
31A ILE* 1.3 59.6 + - - +
32A PRO* 3.6 0.9 - - - +
68A LEU* 3.7 30.9 + - + +
69A LEU 3.2 7.5 - - - +
70A PRO* 3.6 33.4 - - + +
90B GLU* 5.2 5.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 3.7 13.2 - - - +
30A HIS* 1.3 74.0 - - - +
32A PRO* 1.3 66.1 - - - +
33A ILE* 3.6 23.7 - - + +
68A LEU* 3.4 4.8 - - - -
69A LEU 2.7 33.7 + - - +
71A GLU* 3.7 27.8 - - + +
109A LEU* 4.0 10.3 - - + +
110A GLY* 3.8 19.5 - - - +
113A TYR* 3.5 56.1 - - + -
123A LEU* 4.2 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A THR* 4.1 17.9 - - + -
23A ALA* 4.8 6.3 - - + -
24A ARG* 4.2 11.0 - - + -
30A HIS 3.6 8.7 - - - +
31A ILE* 1.3 82.2 - - - +
33A ILE* 1.3 58.8 + - - +
67A PHE 3.5 6.3 - - - +
68A LEU* 3.8 13.2 - - + -
113A TYR* 4.0 17.9 - - + +
121A GLY 3.5 17.0 - - - +
122A PHE* 3.6 19.4 - - + -
123A LEU* 2.8 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE* 3.6 24.9 - - + +
32A PRO* 1.3 79.0 - - - +
34A LEU* 1.3 61.3 + - - +
35A CYS* 3.8 23.6 - - - -
66A LYS* 3.1 9.0 - - - +
67A PHE* 2.9 36.9 + - + +
69A LEU* 4.1 17.5 - - + -
78A PHE* 3.8 15.3 - - + -
109A LEU* 3.9 31.4 - - + -
122A PHE* 4.0 4.0 - - - -
123A LEU* 3.3 16.8 - - + +
125A VAL* 3.8 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A TYR* 4.9 0.2 - - + -
7A TYR* 3.8 25.8 - - + -
33A ILE* 1.3 74.7 - - - +
35A CYS* 1.3 61.3 + - - +
36A GLU* 3.7 33.2 - - + +
64A CYS* 3.4 25.8 - - - -
65A ASN 3.8 0.7 - - - -
66A LYS* 3.5 21.3 - - + -
122A PHE* 3.8 16.1 - - + -
123A LEU 2.9 7.8 + - - +
124A TYR* 3.5 34.3 - - + -
125A VAL 2.9 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 3.8 10.8 - - - -
34A LEU* 1.3 72.4 - - - +
36A GLU* 1.3 62.9 + - - +
63A ASP 3.8 1.4 - - - +
64A CYS* 3.3 6.6 - - - -
65A ASN* 2.7 44.0 + - + +
67A PHE* 3.8 10.3 - - - -
78A PHE* 3.4 38.8 - - - -
82A LEU* 4.5 6.5 - - + -
125A VAL* 3.1 12.3 - - + +
127A TYR* 3.7 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A TYR* 3.4 24.9 - - + -
6A ARG* 2.9 30.9 + - - +
7A TYR* 2.7 36.7 + - - +
34A LEU* 3.7 11.4 - - + +
35A CYS* 1.3 77.7 - - - +
37A PRO* 1.3 80.5 - - + +
63A ASP 4.3 0.2 - - - -
64A CYS* 4.3 14.8 - - + +
125A VAL 2.9 6.1 + - - -
126A SER* 3.2 7.3 - - - -
127A TYR* 3.0 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A TYR* 5.9 0.5 - - - -
36A GLU* 1.3 95.7 - - + +
38A THR* 1.3 67.1 + - - +
39A SER* 3.2 27.5 + - - +
60A ARG 5.6 0.2 - - - +
63A ASP* 3.5 45.8 - - + +
126A SER* 4.9 1.6 + - - -
127A TYR* 3.3 23.5 - - + +
----------------------------------------------------------
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