Contacts of the strand formed by residues 44 - 50 (chain S) in PDB entry 3RWR
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 44 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37S LEU* 3.4 29.2 - - + -
38S VAL 3.6 2.0 - - - +
39S SER* 3.1 15.9 - - - +
43S GLN* 1.3 79.3 - - - +
45S TRP* 1.3 70.2 + - - +
125S LEU* 3.5 16.1 - - + +
126S ALA* 2.9 38.4 + - + -
131S VAL* 3.4 34.3 - - + -
135S LEU* 5.1 8.5 - - + -
628W PRO* 5.8 0.6 - - - +
636W ILE* 4.4 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 45 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23S LEU* 5.0 2.2 - - + -
37S LEU* 3.5 9.2 - - - +
38S VAL* 2.5 52.9 + - + +
39S SER* 4.0 3.6 - - - -
40S ASP* 3.5 40.2 - - + -
43S GLN* 3.6 37.2 - - + +
44S VAL* 1.3 77.2 + - - +
46S HIS* 1.3 64.6 + - - +
99S CYS* 3.6 28.9 - - + -
102S ASP* 3.9 10.9 + - - -
103S ALA 4.0 2.2 + - - -
104S LEU* 3.4 50.9 - - + +
123S CYS* 3.9 13.2 - - - -
124S MET* 3.4 23.3 - - - -
125S LEU* 3.9 2.4 - - - +
126S ALA* 4.1 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 46 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1S MET* 5.6 0.4 - - + -
5S GLU* 4.0 13.3 + - - -
8S LEU* 4.6 6.8 - - + +
35S ALA* 4.7 6.6 - - + +
36S LEU 3.6 13.7 + - - -
37S LEU* 4.4 16.4 - - + -
38S VAL 5.0 0.2 - - - +
45S TRP* 1.3 77.2 - - - +
47S GLU* 1.3 95.3 + - - +
48S GLN* 3.9 16.7 + - + +
123S CYS* 3.3 4.4 - - - +
124S MET* 2.8 36.4 + - - +
125S LEU 5.2 0.4 - - - +
126S ALA* 4.1 10.5 - - + -
130S LEU* 3.5 47.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34S TYR* 2.6 30.0 + - - +
35S ALA* 3.7 2.1 - - - -
36S LEU* 3.2 32.9 + - + +
46S HIS* 1.3 87.8 + - - +
48S GLN* 1.3 66.3 + - - +
57S ARG* 2.7 27.6 + - - +
121S PHE* 3.0 19.3 - - - +
122S HIS 2.6 39.1 + - - +
123S CYS* 3.5 14.1 - - + +
124S MET* 5.6 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 48 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555I SER* 6.0 0.9 - - - +
559I LYS* 3.5 41.2 + - + +
565I LEU 5.4 0.9 - - - +
1S MET* 3.9 28.8 - - + +
34S TYR 4.2 3.4 - - - -
35S ALA* 4.8 0.2 - - - +
46S HIS* 3.9 13.7 - - + +
47S GLU* 1.3 76.2 - - - +
49S VAL* 1.3 75.7 + - - +
50S ASP* 3.6 19.6 + - - -
53S VAL* 4.5 5.4 - - - +
57S ARG* 5.0 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1S MET* 4.2 3.7 - - - -
4S LEU* 3.7 2.8 - - - +
33S GLY* 3.4 1.0 - - - -
34S TYR* 2.9 69.3 + - + +
47S GLU* 4.6 0.9 - - - -
48S GLN* 1.3 86.2 - - - +
50S ASP* 1.3 61.7 + - - +
53S VAL* 3.5 29.4 - - + -
54S VAL* 3.3 36.1 - - + +
57S ARG* 3.8 20.2 - - - +
119S TRP* 4.8 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 50 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107F ARG* 3.1 41.3 + - - +
565I LEU 5.0 6.2 - - - +
566I THR* 4.6 2.1 + - - -
1S MET* 4.4 25.1 - - + +
4S LEU* 4.8 1.8 - - + -
32S GLN* 6.1 3.1 - - + -
33S GLY* 4.2 4.7 - - - -
48S GLN* 3.6 14.2 + - - -
49S VAL* 1.3 73.9 - - - +
51S THR* 1.3 55.4 + - - +
52S SER* 2.4 22.8 + - - -
53S VAL* 2.8 29.0 + - - +
----------------------------------------------------------
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