Contacts of the strand formed by residues 73 - 84 (chain B) in PDB entry 5LK5
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 73 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ASP* 3.5 36.5 + - - +
46B PHE 4.7 1.6 + - - -
47B GLY* 3.8 10.8 - - - +
70B GLN* 2.9 42.7 + - + +
71B LYS 3.3 14.2 + - - +
72B ALA* 1.3 81.6 + - - +
74B PHE* 1.3 59.5 + - - +
75B TYR* 3.4 24.1 - - + -
319B TRP* 3.3 10.2 - - - -
320B GLN 3.0 29.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LYS* 3.5 26.5 - - + -
45B ASP 5.2 1.2 + - - +
46B PHE* 3.3 26.9 - - + -
47B GLY 2.8 29.5 + - - -
73B ARG* 1.3 75.1 - - - +
75B TYR* 1.3 58.0 + - - +
317B ASP* 6.2 0.4 - - - -
318B LEU 3.3 7.9 - - - +
319B TRP* 3.7 45.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PHE* 4.4 3.1 - - - -
47B GLY* 3.5 34.8 - - - -
48B LYS 3.7 12.6 - - - -
49B PHE* 3.7 31.2 - + + -
68B THR* 3.5 30.5 - - + -
69B SER 3.4 2.9 + - - -
70B GLN* 2.5 42.6 + - - +
73B ARG* 3.4 27.6 - - + -
74B PHE* 1.3 74.3 - - - +
76B ALA* 1.3 65.8 + - - +
316B LEU 3.8 2.0 - - - -
317B ASP* 3.3 5.4 - - - -
318B LEU* 2.7 45.4 + - + +
320B GLN* 4.1 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLU* 3.8 4.2 - - - +
40B SER* 3.0 44.0 + - - +
46B PHE* 3.8 26.5 - - + +
47B GLY 5.2 1.2 + - - -
49B PHE* 4.5 1.6 - - - -
75B TYR* 1.3 79.2 - - - +
77B LEU* 1.3 60.7 + - - +
78B SER* 5.2 0.2 - - - -
122B MET* 4.0 11.2 - - + +
316B LEU 3.3 5.8 - - - -
317B ASP* 4.4 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TRP* 4.1 16.8 - - + -
37B TRP* 3.7 36.8 - - + -
38B ILE 3.5 15.0 - - - +
39B GLU* 3.5 30.7 - - + -
49B PHE* 3.7 33.2 - - + -
66B LEU* 3.8 20.9 - - + -
76B ALA* 1.3 74.2 - - - +
78B SER* 1.3 65.5 + - - +
122B MET* 4.9 0.2 - - - -
315B GLY* 3.6 0.3 - - - -
316B LEU* 2.8 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B TRP* 3.1 9.4 - - - -
38B ILE 2.8 38.9 + - - -
76B ALA 5.2 0.2 - - - -
77B LEU* 1.3 73.1 - - - +
79B ALA* 1.3 62.2 + - - +
119B GLN* 3.2 24.4 + - - +
122B MET* 2.6 37.1 - - - +
313B VAL* 3.6 13.9 - - - -
314B LEU 3.3 5.6 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
23B PHE* 3.6 29.6 - - + -
36B ARG 3.6 16.8 - - - +
37B TRP* 3.6 22.4 - - + +
78B SER* 1.3 76.6 - - - +
80B SER* 1.3 61.5 + - - +
81B PHE* 3.9 4.0 - - - -
119B GLN* 3.8 3.4 - - - +
313B VAL* 3.3 2.5 - - - -
314B LEU* 2.9 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE* 4.3 8.3 - - - -
36B ARG 4.2 6.1 + - - +
79B ALA* 1.3 74.5 - - - +
81B PHE* 1.3 68.3 + - - +
115B ASN* 5.2 2.4 + - - -
119B GLN* 2.7 30.1 + - - +
312B GLY 3.3 9.6 + - - -
313B VAL* 4.0 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR* 3.4 23.8 - - + +
23B PHE* 3.9 22.9 - + + -
79B ALA 3.9 4.7 - - - -
80B SER* 1.3 80.8 - - - +
82B GLU* 1.3 76.9 + - - +
83B PRO* 3.0 9.7 - - - +
84B PHE* 3.7 19.7 - + - -
112B LEU* 5.4 2.5 - - + -
115B ASN* 4.6 1.7 - - - +
311B PHE* 3.4 30.3 - - + -
312B GLY* 3.0 23.3 + - - +
313B VAL 3.6 8.5 - - - -
314B LEU* 3.5 30.5 - - + -
332B ILE* 4.4 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR* 4.8 6.6 - - - +
81B PHE* 1.3 81.9 - - - +
83B PRO* 1.3 90.6 - - - +
84B PHE* 3.6 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PHE 3.0 7.6 - - - +
82B GLU* 1.3 108.9 - - - +
84B PHE* 1.3 61.1 + - - +
115B ASN* 3.5 33.2 - - + +
310B ASN* 4.0 15.3 - - + +
311B PHE 3.0 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR* 3.5 69.5 - + + -
81B PHE* 3.7 20.9 - + - -
82B GLU 4.2 1.8 - - - +
83B PRO* 1.3 78.0 - - - +
85B SER* 1.3 76.0 + - - +
86B ASN* 4.3 4.3 - - + -
91B LEU* 3.6 22.4 - - + -
112B LEU* 5.6 0.9 - - + -
309B ASP 4.2 0.7 - - - -
310B ASN* 3.2 5.5 - - - -
311B PHE* 2.7 69.6 + + + +
332B ILE* 3.9 8.3 - - + -
----------------------------------------------------------
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