Contacts of the strand formed by residues 34 - 39 (chain H) in PDB entry 2R9R
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 ARG 34 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H SER 3.4 8.9 + - - +
33H GLU* 1.3 85.6 - - - +
35H VAL* 1.3 66.4 + - - +
36H VAL* 4.3 4.0 + - + +
45H GLU* 2.7 34.1 + - - +
46H THR* 3.4 19.9 - - - +
47H GLN* 4.2 9.4 - - + -
74H ASN* 5.5 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 35 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H GLU* 5.5 2.9 - - - +
34H ARG* 1.3 79.7 - - - +
36H VAL* 1.3 66.1 + - - +
37H ILE* 4.0 13.2 + - + +
45H GLU* 3.2 6.6 - - - +
46H THR* 2.8 37.6 + - + +
48H LEU* 3.7 42.0 - - + -
51H LEU* 4.1 19.5 - - + -
65H ARG* 5.9 1.1 - - - +
76H TYR* 3.7 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 36 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H ARG* 4.3 3.8 + - + +
35H VAL* 1.3 78.7 - - - +
37H ILE* 1.3 68.0 + - - +
38H ASN* 5.3 0.2 - - + -
43H ARG* 3.7 48.2 - - + +
44H PHE 3.4 8.3 - - - +
45H GLU* 4.0 13.2 - - + +
74H ASN* 3.8 14.7 + - - +
75H GLU* 3.4 27.1 - - + +
76H TYR* 2.9 28.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 37 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H VAL* 4.1 13.0 - - + +
36H VAL* 1.3 80.0 - - - +
38H ASN* 1.3 60.2 + - - +
39H ILE* 3.8 17.5 - - + -
42H LEU 3.6 1.2 - - - +
44H PHE* 2.7 52.1 + - + +
46H THR* 4.9 7.4 - - + -
51H LEU* 4.3 20.0 - - + -
59H LEU* 3.8 32.1 - - + -
76H TYR* 3.5 9.9 - - + -
78H PHE* 3.9 15.5 - - + -
85H PHE* 3.8 26.5 - - + -
89H LEU* 5.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 38 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H VAL* 4.1 0.8 - - + -
37H ILE* 1.3 72.3 - - - +
39H ILE* 1.3 61.6 + - - +
41H GLY* 2.7 42.4 + - - +
42H LEU 3.5 4.9 - - - -
43H ARG* 4.7 4.0 - - + +
73H ARG* 3.8 16.8 - - - +
75H GLU* 2.9 38.6 + - - +
76H TYR 2.8 11.9 + - - +
77H PHE* 3.5 21.8 - - + -
78H PHE 2.9 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 39 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H ILE* 3.8 7.0 - - + -
38H ASN* 1.3 70.9 + - - +
40H SER* 1.3 70.8 + - - +
41H GLY 3.1 0.2 - - - -
42H LEU* 2.8 28.3 + - + +
44H PHE* 3.8 15.0 - - + -
78H PHE* 3.5 30.1 - - + +
80H ARG 3.4 24.9 - - - +
81H ASN 3.4 18.4 - - - +
82H ARG* 3.9 7.5 - - - +
85H PHE* 3.5 35.4 - - + -
116H TYR* 3.5 23.1 - - - +
----------------------------------------------------------
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