Contacts of the strand formed by residues 87 - 94 (chain E) in PDB entry 4J9G
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 LYS 87 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E LEU* 4.0 27.4 - - + +
66E PHE 3.5 7.0 - - - +
67E VAL* 5.4 4.7 - - + -
85E GLY 4.7 4.3 - - - +
86E GLU* 1.3 73.3 - - - +
88E LEU* 1.3 62.3 + - - +
104E THR* 3.6 19.8 - - - +
105E LYS 5.0 0.7 + - - -
201E SO4 2.4 44.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E ASN 3.6 0.2 - - - +
65E LEU* 3.5 8.1 - - - +
66E PHE* 2.9 39.7 + - + +
67E VAL 3.7 6.7 - - - -
68E ALA* 3.4 35.0 - - + +
82E ILE* 3.9 25.8 - - + -
86E GLU* 3.5 6.3 - - + +
87E LYS* 1.3 74.5 - - - +
89E ARG* 1.3 64.3 + - - +
90E VAL* 4.0 1.3 - - + -
102E ALA* 3.7 27.8 - - + -
103E GLN 3.3 9.9 - - - +
104E THR* 3.7 17.5 - - + -
111E VAL* 4.6 2.5 - - + -
116E ILE* 4.0 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 89 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E ASN* 3.4 25.8 - - - +
65E LEU* 5.0 9.0 - - + +
88E LEU* 1.3 77.4 - - - +
90E VAL* 1.3 61.7 + - - +
91E LEU* 3.9 0.8 + - + -
102E ALA* 3.3 2.0 - - - -
103E GLN* 2.7 63.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 90 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C HIS* 3.8 18.1 + - + +
64E ASN* 2.8 34.9 + - - +
66E PHE* 3.3 51.8 - - + -
88E LEU* 4.9 1.6 - - + -
89E ARG* 1.3 73.9 - - - +
91E LEU* 1.3 64.6 + - - +
92E GLY* 3.5 25.6 - - - +
93E TYR* 4.4 4.9 - - + -
100E CYS* 4.6 4.7 - - + -
101E GLU 3.7 5.2 - - - +
102E ALA* 4.5 8.1 - - + -
116E ILE* 3.8 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ASN* 3.8 15.2 - - - +
95C HIS* 3.9 3.4 + - - +
110C TRP* 4.9 3.6 - - - -
1D ALA* 5.2 4.5 + - - +
64E ASN* 5.0 7.2 - - - +
89E ARG 4.7 1.3 - - - +
90E VAL* 1.3 78.7 - - - +
92E GLY* 1.3 55.1 + - - +
101E GLU* 2.7 30.9 + - + +
103E GLN* 4.0 28.7 - - + +
108E GLN* 3.7 36.1 - - - +
202E GOL 3.4 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 92 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C TYR 3.0 13.7 - - - -
94C ASN 3.9 8.7 - - - -
90E VAL* 3.5 9.9 - - - +
91E LEU* 1.3 83.1 - - - +
93E TYR* 1.3 62.8 + - - -
100E CYS* 3.3 5.0 - - - +
101E GLU 2.8 26.5 + - - -
202E GOL 3.4 12.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 93 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C GLY* 3.2 0.2 - - - -
93C TYR* 2.8 37.5 + - + +
94C ASN 3.5 13.7 - - - -
95C HIS* 3.3 28.4 + - - -
66E PHE* 3.3 28.3 - + - -
90E VAL* 4.4 4.0 - - + -
92E GLY* 1.3 76.2 - - - -
94E ASN* 1.3 66.3 + - - +
97E GLY* 4.1 13.5 - - - -
99E TRP 3.3 8.5 - - - +
100E CYS* 2.5 35.4 - - - +
110E TRP* 4.1 2.5 - - - -
113E SER* 3.8 14.9 + - - -
118E PRO* 5.3 1.7 - - - +
202E GOL 3.0 13.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 94 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LEU 3.5 8.1 - - - +
92C GLY* 3.9 0.4 - - - -
93C TYR* 3.9 10.6 - - - -
93E TYR* 1.3 77.2 - - - +
95E HIS* 1.3 74.0 + - - +
96E ASN* 2.9 26.4 + - - +
97E GLY* 2.9 31.2 + - - -
98E GLU 3.0 7.8 + - - -
99E TRP* 3.0 32.8 + - - -
110E TRP* 3.7 8.4 - - + -
202E GOL 4.8 0.2 - - - -
1F ALA* 3.6 27.6 - - + +
2F PRO 4.8 3.0 + - - -
----------------------------------------------------------
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