Contacts of the strand formed by residues 74 - 80 (chain E) in PDB entry 3SDI
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 74 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E LYS 4.0 0.2 - - - -
70E CYS* 2.9 24.1 + - + -
71E ASP* 3.0 18.4 + - + +
72E GLU 3.6 0.6 - - - -
73E HIS* 1.3 97.3 - - + +
75E GLY* 1.3 60.6 + - - +
92E LEU* 4.5 9.9 - - - -
96E CYS* 4.0 17.5 - - - -
107E LEU* 3.5 26.0 - - + +
108E ALA 4.0 0.2 - - - +
109E VAL* 3.6 27.1 - - + -
112E ALA* 3.8 24.0 - - + -
138E ILE* 4.0 17.7 - - + -
139E ILE 3.3 14.8 - - - +
140E GLY* 4.7 0.7 - - - -
221E PHE* 3.9 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 75 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E LEU* 4.4 0.2 - - - -
68E ILE 3.3 13.0 - - - -
70E CYS* 3.9 7.9 - - - -
74E MET* 1.3 76.5 - - - +
76E LEU* 1.3 61.2 + - - -
138E ILE* 3.4 6.3 - - - +
139E ILE* 2.9 33.3 + - - +
221E PHE* 3.3 20.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E LEU* 3.4 7.3 - - - +
67E ILE* 3.4 5.4 - - - +
68E ILE* 2.8 65.7 + - + +
70E CYS* 3.9 9.6 - - - -
75E GLY* 1.3 75.7 - - - +
77E SER* 1.3 61.3 + - - +
88E LEU 5.3 0.2 - - - -
89E SER* 3.9 17.9 - - - +
92E LEU* 4.1 24.9 - - + -
116E LEU* 5.2 0.2 - - + -
136E LEU* 3.9 38.8 - - + -
137E LEU 3.0 12.3 - - - +
138E ILE* 3.9 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 77 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E THR* 3.0 30.6 + - - +
48E LEU* 3.4 26.2 - - - +
50E ALA* 4.8 0.9 - - - -
66E LYS 3.0 11.2 - - - -
67E ILE* 3.9 10.3 - - - -
76E LEU* 1.3 75.5 - - - +
78E LEU* 1.3 61.6 + - - +
136E LEU* 3.2 9.6 - - - +
137E LEU* 2.8 39.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
37E THR* 4.0 5.6 - - - +
64E GLN* 4.7 2.9 - - - +
65E LYS* 3.9 11.9 - - + +
66E LYS* 2.8 68.6 + - + +
68E ILE* 3.8 18.6 - - + -
76E LEU* 5.9 0.7 - - + -
77E SER* 1.3 75.5 - - - +
79E ALA* 1.3 63.1 + - - +
80E GLY 4.6 7.9 - - - +
82E ALA* 4.0 33.7 - - + +
85E ALA* 3.7 26.7 - - + -
134E VAL* 4.2 2.7 - - + -
135E GLY 3.4 4.0 - - - -
136E LEU* 4.0 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E ILE* 3.5 15.9 - - + +
34E GLY* 4.9 0.9 - - - -
35E SER 4.1 14.8 - - - +
37E THR* 4.2 2.7 - - + -
66E LYS* 3.9 6.1 - - - +
78E LEU* 1.3 76.8 - - - +
80E GLY* 1.3 56.0 + - - +
134E VAL* 3.9 1.3 - - - -
135E GLY 2.7 36.1 + - - -
165E ILE* 3.8 28.0 - - + -
166E GLY* 4.3 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 80 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E ALA* 3.6 24.2 - - - -
34E GLY* 4.3 10.2 - - - -
66E LYS* 5.0 1.4 - - - +
78E LEU* 4.3 6.0 - - - +
79E ALA* 1.3 73.3 - - - +
81E LEU* 1.3 65.8 + - - -
82E ALA* 3.2 5.0 + - - +
133E GLY 3.7 6.5 - - - -
134E VAL* 4.1 1.3 - - - +
----------------------------------------------------------
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