Contacts of the helix formed by residues 73 - 85 (chain B) in PDB entry 4XJO
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 73 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B HIS* 3.7 26.5 - - + +
70B GLY 4.2 1.8 + - - +
71B HIS 3.2 3.7 + - - -
72B GLY* 1.3 74.8 - - - +
74B PRO* 1.3 75.6 - - + +
75B ALA* 3.1 36.4 + - + +
76B LEU* 3.0 21.7 + - + -
77B ASP* 2.8 26.9 + - - +
289B TYR* 2.9 4.9 + - - +
335B LEU* 3.5 39.7 - - + +
413B ILE* 5.0 8.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLY 3.4 7.1 - - - +
73B HIS* 1.3 96.8 - - + +
75B ALA* 1.3 57.3 + - - +
77B ASP* 3.8 7.3 - - + +
78B GLN* 2.9 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B HIS* 3.1 22.7 + - + +
74B PRO* 1.3 78.7 - - - +
76B LEU* 1.3 67.5 + - + +
78B GLN* 3.6 6.0 + - - +
79B ALA* 3.0 26.9 + - - +
331B ALA* 4.3 4.9 - - + +
335B LEU* 4.7 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B HIS* 3.9 26.0 - - + -
70B GLY 5.1 0.4 - - - +
73B HIS* 3.0 20.2 + - + +
75B ALA* 1.3 77.4 - - + +
77B ASP* 1.3 64.9 + - - +
79B ALA* 3.3 2.6 + - - +
80B LEU* 3.2 20.4 + - - +
286B THR 4.7 0.4 - - - +
287B GLY* 4.4 5.8 - - - +
289B TYR* 3.5 38.1 - - + +
328B VAL* 3.6 19.1 - - + +
331B ALA* 3.6 12.6 - - + +
332B SER* 3.5 38.6 - - - +
335B LEU* 4.0 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 3.7 32.5 - - + +
85A ARG* 5.5 1.2 - - - -
72B GLY* 3.4 18.9 - - - +
73B HIS 2.8 16.5 + - - +
74B PRO* 3.8 7.1 - - + +
76B LEU* 1.3 75.7 - - - +
78B GLN* 1.3 61.6 + - - +
80B LEU* 3.3 4.4 + - - +
81B THR* 3.1 29.2 + - + +
289B TYR* 2.7 34.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B PRO 2.9 20.6 + - - +
75B ALA* 3.7 6.7 - - - +
77B ASP* 1.3 74.3 - - - +
79B ALA* 1.3 60.9 + - - +
81B THR* 2.8 18.1 + - - -
82B THR* 2.8 54.6 + - - +
85B ARG* 4.2 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ALA 3.0 10.5 + - - +
76B LEU 3.6 5.4 - - - +
78B GLN* 1.3 76.5 - - - +
80B LEU* 1.3 62.5 + - - +
82B THR* 3.5 6.1 + - - -
83B GLN* 3.1 23.6 + - - +
327B ALA* 4.0 16.9 - - + +
328B VAL* 4.3 3.6 - - - -
331B ALA* 3.4 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 4.7 17.9 - - + -
84A LEU* 3.7 30.5 - - + -
324A LEU* 4.0 17.9 - - + -
76B LEU 3.2 10.5 + - - +
77B ASP* 3.6 8.3 - - - +
78B GLN 3.3 0.2 - - - -
79B ALA* 1.3 79.2 - - - +
81B THR* 1.3 56.6 + - + +
83B GLN* 3.2 3.8 + - - +
84B LEU* 2.9 30.0 + - + +
289B TYR* 4.4 7.4 - - + -
290B LEU* 4.1 13.5 - - + -
324B LEU* 3.7 50.7 - - + +
328B VAL* 4.8 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A THR* 3.9 20.4 - - + -
84A LEU* 3.7 19.7 - - + -
77B ASP* 3.1 15.6 + - + +
78B GLN* 2.8 34.3 + - - -
80B LEU* 1.3 74.8 - - - +
82B THR* 1.3 60.9 + - - +
84B LEU* 3.4 10.1 + - - +
85B ARG* 3.4 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLN* 2.8 40.1 + - - +
79B ALA* 3.7 7.0 - - - +
81B THR* 1.3 77.6 + - - +
83B GLN* 1.3 60.8 + - - +
85B ARG* 3.4 23.2 + - - +
86B VAL* 3.7 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ALA 3.1 11.1 + - - +
80B LEU* 3.2 4.0 + - - +
82B THR* 1.3 74.3 - - - +
84B LEU* 1.3 65.9 + - - +
86B VAL* 3.0 20.5 + - - +
87B MET* 2.9 59.6 + - - +
99B PRO* 3.5 26.0 - - - +
323B PRO* 3.7 25.8 - - - +
324B LEU* 3.9 10.1 - - + -
327B ALA* 3.6 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A HIS* 5.8 0.2 - - - -
72A GLY* 5.2 4.9 - - - -
77A ASP* 3.6 58.4 - - + +
80A LEU* 3.8 25.1 - - + -
81A THR* 3.7 21.8 - - + -
289A TYR* 3.7 20.4 - - + -
80B LEU* 2.9 18.0 + - + +
81B THR* 3.5 9.9 - - - +
82B THR 3.3 0.2 - - - -
83B GLN* 1.3 77.1 - - - +
85B ARG* 1.3 61.6 + - + +
86B VAL 3.4 0.9 + - - -
87B MET 4.2 5.4 + - - -
88B ASN* 4.6 6.0 + - + +
324B LEU* 3.7 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A HIS* 3.3 20.8 - - - -
77A ASP* 5.7 1.3 - - - -
78B GLN* 4.2 16.6 + - - -
81B THR* 3.4 31.6 + - - +
82B THR* 3.4 13.1 + - - +
83B GLN 3.1 1.0 - - - -
84B LEU* 1.3 78.3 - - + +
86B VAL* 1.3 62.6 + - + +
504B CL 4.5 14.6 - - - -
----------------------------------------------------------
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