Contacts of the strand formed by residues 72 - 82 (chain E) in PDB entry 5HK5
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 TRP 72 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E LYS* 5.2 8.3 - - - +
70E SER 4.3 7.0 - - - +
71E ASP* 1.3 76.6 - - - +
73E CYS* 1.3 70.2 + - - +
74E LYS* 4.6 17.7 - - + -
98E TYR* 3.4 54.3 - + - -
99E GLY* 3.7 4.5 - - - -
100E GLN* 2.9 75.5 + - + +
157E CYS* 3.8 2.0 - - - -
69F LYS* 4.5 15.5 - - + -
100F GLN* 4.7 6.0 + - - -
26G PRO* 4.8 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 73 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E TRP* 1.3 80.5 - - - +
74E LYS* 1.3 62.3 + - - +
98E TYR 3.6 4.3 - - - -
123E CYS* 2.1 47.8 - - + -
155E CYS* 3.4 16.8 - - - +
156E ARG* 3.2 36.1 - - - -
157E CYS* 3.6 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 74 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ASP* 4.5 14.3 + - - -
35B ASP* 3.2 38.8 + - - +
72E TRP* 4.6 15.2 - - + -
73E CYS* 1.3 82.1 - - - +
75E THR* 1.3 69.2 + - + +
76E GLN* 4.3 15.4 - - - +
97E CYS* 3.6 3.5 - - - -
98E TYR 3.0 33.8 + - - +
155E CYS* 3.9 6.2 - - - +
26G PRO* 5.2 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 75 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LYS 5.7 5.4 - - - +
32B GLY* 5.8 6.1 - - - -
35B ASP* 5.7 0.2 - - - +
74E LYS* 1.3 81.6 - - + +
76E GLN* 1.3 70.8 + - - +
95E ARG* 2.5 47.4 - - - +
96E PHE 3.5 5.2 + - - -
152E VAL* 4.4 4.0 - - - +
153E LYS 4.1 15.7 + - - +
154E HIS* 5.0 4.9 - - - +
155E CYS* 4.0 12.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 76 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ASP* 4.8 5.9 + - - -
74E LYS* 4.3 23.0 - - + +
75E THR* 1.3 85.5 + - - +
77E PRO* 1.4 76.4 - - + +
95E ARG* 3.1 9.1 - - - -
96E PHE* 2.8 69.0 + - + +
98E TYR* 4.4 18.6 - - + -
63F THR* 5.5 2.3 + - - -
67F TYR* 5.7 0.9 - - - +
27G ALA 5.5 0.4 + - - -
28G GLY* 3.9 25.4 - - - -
29G ALA 4.1 5.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 77 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E GLN* 1.4 92.0 - - + +
78E LEU* 1.3 58.7 + - - +
79E ARG* 5.9 1.3 - - + -
93E LEU* 4.8 11.7 - - + -
94E ASN 4.0 6.7 - - - +
95E ARG* 5.0 1.3 - - + -
96E PHE* 3.5 16.2 - - + -
62F VAL 4.2 6.4 - - - +
29G ALA* 3.7 22.2 - - + +
30G ILE 4.4 0.9 - - - -
31G PRO* 3.6 47.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E PRO* 1.3 75.2 - - - +
79E ARG* 1.3 69.4 + - - +
80E GLN 3.5 1.1 + - - +
93E LEU* 3.7 3.7 - - - +
94E ASN* 2.9 48.3 + - + +
95E ARG 4.1 2.0 - - - +
96E PHE* 4.1 20.4 - - + -
60F LEU* 4.0 29.4 - - + -
61F VAL 4.5 9.2 - - - +
62F VAL* 4.6 9.9 - - + +
106F ILE* 4.3 6.7 - - + -
107F PRO* 3.5 34.5 - - + -
110F VAL* 3.6 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 79 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D PHE* 3.4 19.1 - - + -
55D PRO* 3.6 23.4 - - - +
77E PRO* 5.9 1.1 - - + -
78E LEU* 1.3 74.6 - - - +
80E GLN* 1.3 59.3 + - - +
81E THR* 4.4 0.5 + - - -
91E THR* 4.3 10.5 - - + -
92E ILE 3.7 5.4 - - - -
93E LEU* 3.8 15.5 - - + +
60F LEU* 4.0 19.4 - - - +
61F VAL 5.7 1.1 + - - +
110F VAL 4.8 0.3 - - - +
32G SER* 2.8 28.3 + - - +
34G TYR 2.7 29.0 + - - -
35G LYS* 4.9 3.6 - - - +
45G TRP* 6.4 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 80 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E LEU* 3.5 0.9 + - + +
79E ARG* 1.3 73.5 - - - +
81E THR* 1.3 70.8 + - - +
82E VAL* 4.6 6.0 - - + +
91E THR* 3.4 4.9 - - - +
92E ILE* 2.7 45.7 + - + +
94E ASN* 2.7 40.2 + - + +
149E ILE* 3.5 33.8 - - - +
150E GLN 5.2 0.2 + - - -
108F ARG 3.9 6.6 + - - +
109F HIS* 3.3 26.4 + - - +
110F VAL* 3.9 26.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E ARG 4.4 0.7 + - - -
80E GLN* 1.3 74.6 - - - +
82E VAL* 1.3 65.3 + - - +
83E SER* 4.0 7.7 + - - +
89E SER* 4.0 26.5 - - - +
90E ARG 3.8 4.3 - - - +
91E THR* 4.4 10.1 + - - +
109F HIS 3.4 20.6 - - - +
110F VAL 3.5 13.0 + - - +
111F LYS* 3.9 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 82 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E GLN* 4.6 6.7 - - - +
81E THR* 1.3 75.5 - - - +
83E SER* 1.3 60.3 + - - +
89E SER* 3.3 4.3 - - - -
90E ARG 2.9 34.9 + - - +
92E ILE* 3.6 31.2 - - + -
133E VAL* 3.8 12.1 - - + -
135E LEU* 3.4 19.9 - - + +
147E LYS* 3.6 33.2 - - + -
149E ILE* 4.1 25.6 - - + -
----------------------------------------------------------
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