Contacts of the strand formed by residues 71 - 80 (chain J) in PDB entry 4EMG
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 ILE 71 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52J GLU 3.8 0.9 - - - +
53J ILE* 3.8 0.5 - - - -
54J VAL* 2.8 54.9 + - + +
70J THR* 1.3 77.5 - - - +
72J ARG* 1.3 69.5 + - - +
73J LYS* 5.5 4.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 72 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51J GLU* 2.7 30.6 + - + +
52J GLU 3.3 5.4 - - - +
53J ILE* 3.4 32.5 - - + +
70J THR* 2.7 45.6 + - + +
71J ILE* 1.3 82.5 - - - +
73J LYS* 1.3 65.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 73 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51J GLU* 3.4 5.5 - - - +
52J GLU* 2.7 48.2 + - + +
71J ILE* 5.5 5.2 - - + +
72J ARG* 1.3 78.8 - - - +
74J HIS* 1.3 65.4 + - - +
75J TYR* 3.1 41.7 + - + +
23K TYR* 3.9 17.6 - - - +
31K GLU* 4.4 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 74 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J ASP* 3.5 35.6 + - - -
50J ALA 3.3 21.8 - - - -
51J GLU* 4.7 6.5 - - + -
73J LYS* 1.3 79.8 + - - +
75J TYR* 1.3 79.8 + - - +
76J GLU* 4.2 1.3 - - - -
92K ARG* 2.5 45.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 75 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J ASP* 3.3 3.1 - - - -
50J ALA* 2.7 46.2 + - + +
52J GLU* 2.7 42.4 + - + -
73J LYS* 3.1 41.9 + - + +
74J HIS* 1.3 80.5 - - - +
76J GLU* 1.3 62.0 + - - +
77J MSE 3.8 13.9 - - - +
78J LEU* 3.9 33.9 - - + -
23K TYR* 3.2 32.5 + + + -
87K LEU* 4.4 1.8 - - + +
89K ALA* 3.5 19.5 - - + -
92K ARG* 3.8 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 76 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48J GLY* 3.5 3.8 - - - -
49J ASP* 2.7 29.3 + - - +
74J HIS* 4.5 2.5 - - - -
75J TYR* 1.3 71.5 - - - +
77J MSE 1.3 70.8 + - + +
91K PRO 5.7 0.4 - - - -
92K ARG* 3.2 43.6 + - + +
93K ASN* 3.0 46.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 77 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J HIS* 3.7 31.4 - - + +
46J VAL* 3.8 21.1 - - + -
47J LEU 3.6 1.6 - - - -
48J GLY* 4.0 5.2 - - - -
75J TYR* 3.8 4.3 - - - +
76J GLU* 1.3 96.5 + - + +
78J LEU* 1.3 60.7 + - - +
13K LEU* 4.2 16.4 - - + -
89K ALA* 3.7 9.0 - - - +
90K PRO* 3.2 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32J LEU* 3.9 38.6 - - + -
45J MSE 3.6 0.3 - - - +
46J VAL* 3.1 4.9 - - - +
47J LEU* 2.7 45.6 + - + +
50J ALA* 4.1 17.9 - - + -
75J TYR* 3.9 42.6 - - + -
77J MSE 1.3 76.6 - - - +
79J PHE* 1.3 67.4 + - - +
80J VAL* 3.8 5.2 + - + +
13K LEU* 3.9 4.2 - - - +
23K TYR* 5.5 0.2 - - + -
87K LEU* 4.1 22.9 - - + -
88K ILE 4.0 3.6 - - - +
89K ALA* 4.1 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44J ASN* 3.9 30.3 - - + -
45J MSE 3.4 9.4 - - - -
46J VAL* 4.4 1.3 - - + -
78J LEU* 1.3 71.5 - - - +
80J VAL* 1.3 71.7 - - - +
81J ARG* 3.8 7.4 - - + -
10K PRO* 3.5 25.8 - - + -
11K LEU* 3.7 23.6 - - + -
13K LEU* 3.5 15.9 - - + +
14K VAL* 4.2 9.0 - - + -
43K LEU* 3.7 32.3 - - + -
85K VAL* 5.4 0.7 - - + -
86K ILE 4.8 0.9 - - - -
87K LEU* 3.2 9.4 - - - +
88K ILE* 2.8 64.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 80 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26J LEU* 3.9 26.7 - - + -
32J LEU* 3.5 27.4 - - + -
44J ASN* 3.3 5.2 - - - +
45J MSE 2.7 45.6 + - + +
47J LEU* 4.1 15.5 - - + -
78J LEU* 4.2 9.9 - - + +
79J PHE* 1.3 80.9 - - - +
81J ARG* 1.3 72.5 + - - +
84J SER* 4.7 0.4 - - - +
85J VAL* 4.3 7.6 - - + -
86K ILE 3.8 2.2 - - - +
87K LEU* 4.1 11.4 - - + -
----------------------------------------------------------
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