Contacts of the strand formed by residues 43 - 50 (chain B) in PDB entry 6J7Z
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 MET 43 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LEU* 4.7 8.7 - - + -
178A ARG* 3.6 31.2 - - - +
179A TRP* 4.9 1.1 - - - +
41B GLN 4.2 4.5 - - - +
42B ARG* 1.3 77.5 - - - +
44B VAL* 1.3 63.4 + - - +
45B TRP* 3.4 32.8 - - + +
67B ILE* 3.4 7.3 - - - +
68B THR* 2.9 35.7 + - - +
69B ASP 4.2 1.3 - - - +
70B SER* 3.6 20.6 - - - +
72B LEU* 3.8 22.4 - - + -
138B PRO* 3.9 7.4 - - + +
140B ALA* 4.4 4.3 - - + -
167B ILE* 3.6 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B MET* 1.3 71.6 - - - +
45B TRP* 1.3 58.8 + - - +
46B VAL* 4.1 9.2 - - + -
65B CYS* 3.7 26.5 - - - -
66B LEU 3.6 2.9 - - - -
67B ILE* 3.6 17.7 - - + -
128B VAL* 4.1 11.9 - - + -
132B THR* 3.8 17.9 - - + +
137B CYS* 4.1 7.2 - - + -
138B PRO 3.0 11.8 + - - +
139B LEU* 3.3 7.4 - - - +
140B ALA 2.9 22.4 + - - -
158B PHE* 4.3 6.1 - - + -
162B LEU* 3.6 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B MET* 3.4 20.6 - - + +
44B VAL* 1.3 71.5 - - - +
46B VAL* 1.3 60.0 + - - +
65B CYS* 3.2 5.9 - - - -
66B LEU* 2.9 41.7 + - + +
68B THR* 3.0 41.2 + - + +
72B LEU* 3.8 22.7 - - + -
140B ALA* 3.3 18.2 - - + -
141B GLY 3.7 17.5 - - - -
167B ILE* 5.2 0.7 - - + -
169B VAL* 3.5 33.2 - - + -
200B ILE* 3.6 24.8 - - + +
203B SER* 3.9 3.4 - - - -
204B ILE* 3.5 40.4 - - + -
207B LEU* 3.7 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B VAL* 3.7 2.2 + - + -
45B TRP* 1.3 79.5 - - - +
47B ASP* 1.3 63.3 + - - +
48B LEU* 3.6 26.5 - - + -
63B MET* 4.0 6.3 - - + -
64B ALA 3.3 6.1 - - - +
65B CYS* 3.9 22.0 - - + -
139B LEU* 3.6 25.6 - - + -
140B ALA 3.0 15.6 + - - +
141B GLY* 4.4 1.7 - - - -
144B VAL* 3.9 11.4 - - - +
147B ASP* 4.3 6.8 - - + +
151B LEU* 3.9 15.3 - - + -
158B PHE* 4.0 15.3 - - + -
200B ILE* 3.5 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL* 1.3 74.2 - - - +
48B LEU* 1.3 70.9 + - - +
49B GLU* 3.3 10.6 - - - +
63B MET* 3.4 3.8 - - - -
64B ALA 3.0 32.2 + - - +
142B ASN 5.3 1.0 + - - +
147B ASP* 3.8 8.3 - - - +
196B ALA* 3.3 32.5 - - - +
199B ALA* 3.2 27.0 - - - +
200B ILE* 3.9 14.0 - - + +
301B MG 3.7 1.2 - - - -
302B MG 2.9 20.4 - - - -
11C U 4.6 1.0 - - - +
12C U 3.6 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL* 3.6 15.9 - - + -
47B ASP* 1.3 87.4 - - - +
49B GLU* 1.3 66.9 + - - +
50B MET* 3.7 13.7 - - + -
60B ILE* 3.7 39.5 - - + -
62B GLU 3.4 2.9 - - - +
63B MET* 3.5 26.5 - - + -
147B ASP* 3.0 34.0 + - + +
150B PHE* 3.8 20.0 - - + -
151B LEU* 4.1 6.1 - - + -
12C U 3.5 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ASP* 3.3 5.4 - - - +
48B LEU* 1.3 77.4 - - - +
50B MET* 1.3 55.4 + - - +
60B ILE* 3.8 2.1 - - - +
61B ILE* 2.8 30.8 + - + +
62B GLU* 2.9 49.0 + - + +
101B HIS* 3.9 4.4 - - + -
106B LEU* 3.9 13.7 - - + -
194B HIS* 3.2 19.2 - - - +
195B ARG 3.3 17.0 - - - -
196B ALA* 3.9 4.5 - - + +
301B MG 2.4 30.8 - - - -
12C U 2.9 22.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 3.7 27.8 - - + +
49B GLU* 1.3 75.1 - - - +
51B THR* 1.3 58.0 + - - +
52B GLY 3.1 19.1 - - - +
53B LEU* 4.4 3.1 - - + -
58B ASP* 5.0 0.2 - - + -
59B GLN 3.2 16.2 - - - +
60B ILE* 4.2 9.6 - - + -
61B ILE* 3.9 6.1 - - - -
101B HIS* 3.0 17.2 + - - -
146B GLU* 4.2 15.7 - - + -
147B ASP* 5.2 2.5 - - - +
150B PHE* 3.6 45.1 - - + -
11C U 4.7 0.9 - - - +
12C U 2.5 50.3 + - - +
----------------------------------------------------------
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