Contacts of the strand formed by residues 71 - 77 (chain K) 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 K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35K PHE* 3.2 7.2 - - - +
36K VAL* 3.0 49.8 + - + +
37K ARG* 5.1 0.4 - - - -
44K ILE* 3.6 28.5 - - + -
45K GLN* 3.5 23.6 - - - +
48K VAL* 3.5 27.8 + - + +
50K LYS* 5.0 0.2 - - - -
51K VAL* 3.5 34.3 - - + -
53K PHE* 3.4 8.8 - - + -
66K CYS* 4.0 19.7 - - + -
67K LYS 4.4 3.3 + - - -
68K ASP* 3.7 23.0 - - - -
69K PRO* 3.6 24.9 - - + +
70K PRO* 1.3 68.4 - - + +
72K LYS* 1.3 58.5 + - - +
202K SO4 5.3 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16K ARG* 5.7 1.4 - - - +
33K MET* 3.6 26.4 - - + +
34K VAL 3.4 5.6 - - - +
35K PHE* 4.9 0.2 - - + -
53K PHE* 4.5 0.4 - - - -
66K CYS* 3.5 15.8 - - - -
70K PRO* 3.1 32.7 + - + +
71K TYR* 1.3 75.2 - - - +
73K VAL* 1.3 71.4 - - - +
74K GLU* 3.8 32.0 + - + +
202K SO4 3.4 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 73 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K TRP* 3.7 25.5 - - + -
33K MET* 3.2 4.3 - - - +
34K VAL* 2.9 41.9 + - + -
53K PHE* 3.4 37.7 - - + -
55K LEU* 4.1 13.0 - - + -
64K ARG* 4.0 20.9 - - + +
66K CYS* 5.1 1.6 - - - -
72K LYS* 1.3 79.4 - - - +
74K GLU* 1.3 65.1 + - - +
75K GLU* 4.1 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 74 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16K ARG* 5.6 3.1 + - - -
32K TRP 3.6 5.4 - - - +
33K MET* 3.8 22.6 - - + +
64K ARG* 4.9 0.9 + - - -
72K LYS* 3.8 22.8 + - + +
73K VAL* 1.3 76.3 - - - +
75K GLU* 1.3 74.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 75 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31K ASP* 3.6 2.9 - - - +
32K TRP* 2.9 67.2 + - + +
55K LEU* 4.3 1.1 - - + -
59K PHE* 4.0 19.6 - - + -
60K PRO* 5.8 2.2 - - - +
61K ARG* 5.0 3.3 + - - -
64K ARG* 2.6 41.0 + - - +
73K VAL* 4.1 4.0 + - + -
74K GLU* 1.3 81.5 - - - +
76K SER* 1.3 69.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 76 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K ARG* 4.3 4.3 + - - -
24K THR* 4.4 8.0 - - - +
28K PHE* 3.7 33.6 - - - -
30K HIS 3.2 7.9 - - - -
31K ASP* 2.9 24.3 + - - -
32K TRP* 4.4 3.6 - - - +
59K PHE* 3.7 15.1 - - - -
75K GLU* 1.3 82.0 + - - +
77K GLY* 1.3 58.3 + - - +
18M KCR 4.2 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 77 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28K PHE* 3.9 10.7 - - - +
29K THR 3.0 6.4 + - - -
30K HIS* 2.9 36.0 + - - -
32K TRP* 4.2 11.9 - - - +
59K PHE* 4.7 0.2 - - - -
76K SER* 1.3 75.2 - - - +
78K TYR* 1.3 61.5 + - - -
79K ALA 3.7 2.5 - - - -
106K LEU* 5.0 0.9 - - - -
18M KCR 3.2 14.8 - - - -
----------------------------------------------------------
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