Contacts of the helix formed by residues 93 - 100 (chain E) in PDB entry 4PEI
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 SER 93 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E THR* 3.2 36.9 + - - +
49E LEU* 3.6 13.4 - - - +
54E ASP* 3.3 27.8 + - - +
57E TYR* 4.3 5.8 - - - -
92E GLU* 1.3 69.5 + - - +
94E SER* 1.3 59.2 + - - +
95E ASN* 3.0 20.0 + - - -
96E VAL* 3.0 24.5 + - - +
97E LEU* 3.3 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 94 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E TYR* 3.5 17.6 + - - -
92E GLU* 3.1 19.3 + - - +
93E SER* 1.3 70.6 - - - +
95E ASN* 1.3 64.7 + - - +
97E LEU* 3.3 7.4 + - - +
98E LEU* 3.0 24.4 + - - +
151E VAL* 4.9 3.5 + - - -
154E LEU* 3.7 31.3 - - - +
155E PHE* 4.1 24.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 95 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E ARG* 3.2 7.5 - - - +
54E ASP* 3.1 23.3 + - - +
57E TYR* 3.3 39.0 - - + +
93E SER* 3.0 20.7 + - - -
94E SER* 1.3 75.1 - - - +
96E VAL* 1.3 69.5 + - - +
98E LEU* 3.3 4.1 + - - +
99E HIS* 3.1 29.1 + - - -
146E PRO* 3.7 18.0 - - + +
154E LEU* 4.7 0.4 - - - -
402E SO4 3.1 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 96 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E THR* 3.8 25.6 - - - +
50E ARG* 3.5 36.8 - - - +
54E ASP* 4.0 0.2 - - - +
70E PHE* 6.4 0.2 - - + -
93E SER* 3.0 25.5 + - - +
95E ASN* 1.3 84.0 + - - +
97E LEU* 1.3 65.2 + - + +
99E HIS* 3.4 9.8 + - - +
100E LEU* 3.1 23.9 + - + +
106E VAL* 4.0 13.5 - - + -
333E PHE* 3.6 25.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E THR* 4.2 16.8 - - - +
86E PHE* 4.4 9.9 - - + -
88E GLY* 3.9 16.4 - - - -
92E GLU* 3.6 40.4 - - + +
93E SER 3.3 10.4 + - - +
94E SER* 3.8 8.1 - - - +
95E ASN 3.3 0.4 - - - -
96E VAL* 1.3 81.5 - - + +
98E LEU* 1.3 58.8 + - - +
100E LEU 3.1 5.2 - - - +
101E TYR* 3.0 26.3 + - - -
106E VAL* 5.0 1.6 - - + -
112E TYR* 3.6 43.3 + - + +
115E VAL* 5.9 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E SER 3.0 17.6 + - - +
95E ASN* 3.5 7.0 - - - +
96E VAL 3.3 0.2 - - - -
97E LEU* 1.3 71.7 - - - +
99E HIS* 1.3 67.4 + - - +
100E LEU 3.0 0.9 - - - -
101E TYR* 3.0 29.9 + - + +
115E VAL* 5.9 0.7 - - + -
142E TYR* 4.0 34.3 - - + -
143E THR 3.5 25.4 - - - +
144E TYR* 4.0 18.2 - - + -
146E PRO* 4.2 16.8 - - + -
154E LEU* 3.8 21.3 - - + -
292E PHE* 4.4 11.9 - - + -
337E PHE* 4.1 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 99 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E ARG* 4.7 4.3 - - - -
95E ASN 3.1 26.0 + - - -
96E VAL* 3.7 5.2 - - - +
98E LEU* 1.3 76.4 - - - +
100E LEU* 1.3 59.8 + - - +
101E TYR* 3.4 2.9 + - - -
102E ASN* 4.9 0.9 + - - +
144E TYR* 2.7 30.1 + + - -
145E PRO* 5.2 1.6 - - + -
146E PRO* 3.6 19.6 - - + +
333E PHE* 3.5 39.9 - - + +
334E ASP* 3.8 18.1 + - + +
337E PHE* 3.3 36.2 + - + +
402E SO4 2.7 37.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E VAL* 3.1 16.7 + - + +
97E LEU 3.1 4.9 + - - -
98E LEU 3.0 1.0 - - - -
99E HIS* 1.3 82.6 - - - +
101E TYR* 1.3 58.7 + - - +
102E ASN 3.0 4.0 - - - +
103E GLY* 2.8 34.5 + - - +
104E GLY* 4.2 9.6 - - - +
105E PHE 4.1 5.6 - - - +
106E VAL* 3.6 30.7 - - + -
112E TYR* 3.4 23.8 - - + -
333E PHE* 3.9 35.0 - - + -
336E GLN* 4.1 28.0 - - + +
----------------------------------------------------------
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