Contacts of the helix formed by residues 92 - 102 (chain E) in PDB entry 5EIB
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 HIS 92 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404D PHE* 5.5 0.2 - - - -
55E ALA 3.1 24.9 - - - +
56E THR 3.0 20.2 + - - -
57E TYR 3.8 2.4 - - - -
58E GLY* 3.2 27.1 + - - -
87E ALA* 3.0 9.4 + - - +
90E ILE* 3.3 24.4 - - + +
91E GLY* 1.3 77.1 + - - +
93E LEU* 1.3 59.8 + - - +
94E GLU 3.5 2.0 - - - -
95E ILE* 3.2 21.8 + - + +
96E VAL* 2.9 29.6 + - - +
128E ILE* 3.9 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E GLY 3.4 6.6 + - - +
92E HIS* 1.3 68.9 - - - +
94E GLU* 1.3 70.7 + - + +
96E VAL* 3.3 5.9 + - + +
97E GLU* 3.1 34.3 + - + +
127E GLU* 3.3 32.5 - - + +
128E ILE* 3.9 33.2 - - + +
131E VAL* 3.9 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E LEU* 3.8 33.2 - - + +
92E HIS 3.5 0.2 - - - -
93E LEU* 1.3 83.6 - - + +
95E ILE* 1.3 63.5 + - + +
97E GLU* 3.3 9.6 + - - +
98E VAL* 3.1 28.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 95 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E ALA 4.0 7.9 - - - +
55E ALA* 4.1 13.7 - - + +
58E GLY* 3.5 39.7 - - - -
59E HIS 3.8 2.9 - - - +
60E LEU* 3.7 31.2 - - + +
63E VAL* 4.1 12.6 - - + -
87E ALA* 3.8 17.5 - - + -
92E HIS* 3.2 21.6 + - + +
93E LEU 3.2 0.4 - - - -
94E GLU* 1.3 75.6 - - + +
96E VAL* 1.3 66.5 + - - +
98E VAL* 3.2 3.4 + - - +
99E LEU* 2.9 34.7 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
84E LEU* 3.9 18.3 - - + +
87E ALA* 3.9 22.0 - - + +
88E ALA* 4.1 2.7 - - - +
92E HIS 2.9 19.3 + - - +
93E LEU* 3.4 9.6 - - + +
95E ILE* 1.3 75.7 - - - +
97E GLU* 1.3 59.0 + - + +
99E LEU* 3.3 2.5 + - - +
100E LEU* 2.9 47.5 + - + +
128E ILE* 3.8 32.5 - - + -
131E VAL* 4.2 12.8 - - + -
132E LEU* 4.4 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 97 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E LEU* 3.1 28.7 + - + +
94E GLU* 3.8 8.6 - - - +
95E ILE 3.1 0.8 - - - -
96E VAL* 1.3 75.3 - - + +
98E VAL* 1.3 61.9 + - + +
100E LEU* 3.4 6.6 + - + +
101E LYS* 2.9 28.8 + - - +
131E VAL* 3.7 39.5 - - + +
135E HIS* 5.4 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E LEU* 3.8 15.5 - - + -
63E VAL* 4.2 5.6 - - + -
64E GLU* 3.7 35.0 - - + +
67E LEU* 3.7 22.7 - - + -
94E GLU* 3.1 15.7 + - + +
95E ILE* 3.2 8.3 + - - +
97E GLU* 1.3 74.8 - - + +
99E LEU* 1.3 65.3 + - - +
101E LYS* 3.2 11.4 + - - +
102E HIS* 3.1 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E LEU* 4.3 12.1 - - + -
55E ALA* 4.5 1.3 - - + -
63E VAL* 4.4 7.9 - - + -
67E LEU* 4.3 12.1 - - + -
73E VAL* 3.7 22.1 - - + +
83E PRO* 3.8 22.4 - - + +
84E LEU* 3.8 33.9 - - + +
87E ALA* 4.0 5.6 - - + -
95E ILE* 2.9 36.9 + - + +
96E VAL 3.6 3.6 - - - +
98E VAL* 1.3 76.6 - - - +
100E LEU* 1.3 62.7 + - - +
102E HIS 3.1 10.2 + - - -
103E GLY 3.3 0.7 + - - -
104E ALA* 3.0 31.2 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
84E LEU* 3.9 24.2 - - + -
96E VAL* 2.9 39.6 + - + +
97E GLU* 3.7 5.2 - - - +
98E VAL 3.3 0.2 - - - -
99E LEU* 1.3 76.0 - - - +
101E LYS* 1.3 62.8 + - - +
103E GLY* 3.1 13.5 + - - -
104E ALA* 3.9 16.7 + - - +
106E VAL* 4.2 15.7 - - + -
131E VAL* 3.8 14.8 - - + -
132E LEU* 4.3 7.2 - - + -
135E HIS* 3.8 44.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 101 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E GLU* 5.4 6.5 + - - -
97E GLU 2.9 18.5 + - - +
98E VAL* 3.2 13.0 + - - +
100E LEU* 1.3 76.0 - - - +
102E HIS* 1.3 80.2 + - + +
103E GLY 3.3 2.3 + - - -
135E HIS* 5.5 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 102 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E GLU* 5.3 3.6 + - - +
67E LEU* 3.9 48.9 + - + +
68E LYS* 5.2 9.6 - - + -
73E VAL* 3.4 17.6 - - + +
98E VAL* 3.1 38.6 + - + +
99E LEU 3.1 6.0 + - - +
101E LYS* 1.3 101.3 + - + +
103E GLY* 1.3 55.1 + - - -
104E ALA 3.6 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