Contacts of the strand formed by residues 72 - 78 (chain D) in PDB entry 5GJQ
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 MET 72 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D LYS 4.0 0.2 - - - -
68D LEU* 3.0 20.9 + - + -
69D ASN* 2.9 39.5 + - + +
70D GLU 3.7 0.4 - - - -
71D ASP* 1.3 80.9 - - + +
73D ALA* 1.3 65.6 + - - +
105D ILE* 3.6 21.8 - - + +
106D PRO 4.4 0.2 - - - -
107D CYS* 3.4 46.2 - - - +
110D LEU* 3.4 31.2 - - + -
111D VAL* 5.8 0.2 - - - -
136D TYR* 5.4 7.6 - - + -
137D ILE 3.2 20.0 - - - +
138D GLY* 4.0 2.0 - - - -
139D TRP 4.9 2.5 - - - +
216D LEU* 4.3 0.4 - - - -
225D ILE* 3.7 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D ILE* 4.9 7.6 - - + -
66D TYR 3.3 14.1 - - - +
67D LYS* 4.2 4.9 - - - -
68D LEU* 4.1 4.5 - - - +
72D MET* 1.3 78.1 - - - +
74D CYS* 1.3 65.1 + - - +
136D TYR* 3.7 1.6 - - - +
137D ILE* 2.9 49.8 + - + +
225D ILE* 3.9 25.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D LEU* 4.0 5.2 - - - -
65D ILE* 3.5 3.6 - - - +
66D TYR* 2.7 61.9 + - - +
68D LEU* 3.6 26.2 - - + -
73D ALA* 1.3 79.0 - - - +
75D SER* 1.3 61.2 + - - +
76D VAL* 5.5 0.2 - - - -
87D THR* 3.9 12.3 - - - -
90D LEU* 4.6 0.7 - - - -
134D LEU* 4.2 15.7 - - + -
135D LEU 3.2 11.9 - - - +
136D TYR* 4.3 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D CYS* 3.0 32.2 - - - -
45D LEU* 3.7 20.8 - - - +
47D ALA* 4.4 0.3 - - - +
64D LYS* 2.7 26.5 + - - +
65D ILE* 3.7 8.2 - - - +
66D TYR* 5.1 0.2 - - - -
74D CYS* 1.3 76.9 - - - +
76D VAL* 1.3 66.6 + - - +
134D LEU* 3.4 6.9 - - - +
135D LEU* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D CYS* 4.5 4.0 - - - +
64D LYS* 3.3 35.5 + - + +
66D TYR* 4.1 19.7 - - + +
74D CYS* 5.5 0.2 - - - -
75D SER* 1.3 81.0 + - - +
77D ALA* 1.3 72.0 + - - +
78D GLY 5.2 0.9 - - - +
79D ILE 6.3 0.2 - - - -
80D THR* 5.6 6.7 - - + -
83D ALA* 3.6 32.3 - - + +
87D THR* 5.6 1.1 - - + -
132D VAL* 3.5 29.2 - - + -
133D SER 3.6 4.5 - - - +
134D LEU* 3.9 14.1 - - + +
164D ILE* 5.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D ILE* 3.6 11.8 - - + +
31D ALA* 4.2 13.7 - - + -
32D GLY 4.4 9.2 - - - +
34D CYS* 5.1 0.7 - - + -
64D LYS* 5.2 1.8 - - - +
76D VAL* 1.3 83.7 - - - +
78D GLY* 1.3 57.6 + - - +
132D VAL* 3.4 4.0 - - - -
133D SER 2.9 32.2 + - - +
164D ILE* 3.4 31.6 - - + -
165D GLY* 4.8 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ALA 4.9 2.7 - - - -
28D ILE* 4.3 10.8 - - - -
31D ALA* 3.6 22.0 - - - +
76D VAL* 5.2 1.8 - - - +
77D ALA* 1.3 75.3 - - - +
79D ILE* 1.3 68.5 + - - -
80D THR* 3.5 10.6 + - - +
131D GLY 3.2 10.1 - - - -
132D VAL* 4.9 0.2 - - - +
----------------------------------------------------------
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