Contacts of the strand formed by residues 71 - 77 (chain C) in PDB entry 5HJD
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 TYR 71 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C PHE* 3.3 2.5 - - - +
36C VAL 2.9 46.0 + - - +
37C ARG* 5.4 0.7 - - - -
44C ILE* 3.5 26.7 - - + -
45C GLN* 3.4 28.3 + - - +
48C VAL* 3.8 28.4 + - + +
49C GLU 5.0 0.4 - - - -
50C LYS* 4.7 0.9 - - - -
51C VAL* 3.5 33.0 - - + -
53C PHE* 3.2 11.3 - - + -
66C CYS* 3.9 21.5 - - + -
67C LYS 4.5 7.7 + - - -
68C ASP 4.0 14.4 - - - -
69C PRO* 4.0 23.3 - - + +
70C PRO* 1.3 70.8 - - + +
72C LYS* 1.3 57.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C MET* 3.7 29.2 - - + -
34C VAL 3.3 10.1 - - - +
35C PHE* 4.0 5.4 - - + -
53C PHE* 4.2 0.7 - - - -
66C CYS* 3.2 19.1 - - - -
70C PRO* 3.2 40.1 + - + +
71C TYR* 1.3 75.6 - - - +
73C VAL* 1.3 64.1 + - - +
74C GLU* 3.6 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C TRP* 3.3 24.5 - - + -
33C MET* 3.3 2.1 - - - -
34C VAL* 2.8 43.2 + - + -
53C PHE* 3.5 33.8 - - + -
55C LEU* 4.4 16.2 - - + -
64C ARG* 4.1 22.4 - - + +
66C CYS* 4.5 4.3 - - - -
72C LYS* 1.3 77.6 - - - +
74C GLU* 1.3 69.4 + - - +
75C GLU* 4.5 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C TRP 3.5 7.2 - - - +
33C MET* 3.8 20.1 - - + +
72C LYS* 3.6 32.4 + - + +
73C VAL* 1.3 74.2 - - - +
75C GLU* 1.3 76.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ASP* 3.3 2.5 - - - +
32C TRP* 2.5 66.3 + - + +
59C PHE* 3.4 27.8 - - + -
60C PRO* 5.6 3.5 - - - +
64C ARG* 2.9 31.9 + - - +
73C VAL* 4.1 5.3 + - + +
74C GLU* 1.3 83.1 - - - +
76C SER* 1.3 67.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ARG* 4.1 15.7 + - - -
28C PHE* 3.5 34.8 - - - -
30C HIS 3.3 17.5 - - - -
31C ASP* 3.2 16.4 - - - +
32C TRP* 4.4 2.7 - - - -
59C PHE* 3.9 6.9 - - - -
75C GLU* 1.3 87.1 - - - +
77C GLY* 1.3 57.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C PHE* 4.1 11.0 - - - +
29C THR 3.6 2.4 + - - -
30C HIS* 3.2 34.3 + - - +
32C TRP* 4.1 13.9 - - - +
59C PHE* 4.8 0.4 - - - -
76C SER* 1.3 75.5 - - - +
78C TYR* 1.3 60.7 + - - -
79C ALA 3.7 2.0 - - - -
106C LEU* 6.0 0.9 - - - -
18D KCR 3.9 16.4 - - - -
----------------------------------------------------------
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