Contacts of the helix formed by residues 96 - 105 (chain B) in PDB entry 1EJD
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 ALA 96 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PHE* 3.7 24.4 - - + -
33B LEU* 4.5 7.6 - - + -
56B LEU* 4.4 14.4 - - + -
82B ALA* 5.2 2.9 - - + -
93B SER 3.0 15.5 + - - +
95B TRP* 1.3 76.9 - - - +
97B LEU* 1.3 64.7 + - - +
98B GLY 3.5 0.2 - - - -
99B PRO* 3.4 3.1 - - - +
100B LEU* 3.1 42.0 + - + +
109B VAL* 4.5 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ILE* 3.1 21.3 + - + +
96B ALA* 1.3 78.5 - - - +
98B GLY* 1.3 64.1 + - - +
100B LEU* 3.3 5.4 + - - +
101B VAL* 3.0 25.3 + - - +
107B GLY* 3.3 35.0 - - - +
108B GLN* 3.9 7.0 - - - +
109B VAL* 4.3 10.8 - - + +
125B HIS* 5.7 1.3 - - + -
126B ILE* 4.0 15.5 - - + -
129B LEU* 3.8 23.6 - - + -
143B VAL* 4.0 29.6 - - + +
145B ALA* 3.9 14.8 - - + +
168B THR* 5.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ILE 4.5 1.2 + - - -
95B TRP 4.3 1.0 + - - -
97B LEU* 1.3 77.6 - - - +
99B PRO* 1.3 70.5 - - - +
101B VAL* 3.3 9.2 - - - +
102B ALA* 2.9 25.8 + - - +
129B LEU* 4.0 19.3 - - - +
168B THR* 4.5 12.1 + - - +
172B ALA* 3.9 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PHE 3.6 26.0 - - - +
31B ALA* 4.4 7.2 - - - -
33B LEU* 3.9 16.6 - - + +
34B LEU* 3.7 21.4 - - + +
95B TRP 3.0 28.3 - - - +
96B ALA* 3.4 7.0 - - - +
98B GLY* 1.3 84.2 - - - +
100B LEU* 1.3 57.4 + - - +
103B ARG* 2.9 34.1 + - - +
104B PHE* 4.6 0.6 - - - -
168B THR* 5.7 2.0 - - - +
171B SER* 4.6 15.7 - - - -
172B ALA* 5.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 4.2 17.3 - - + -
60B LEU* 4.3 17.9 - - + -
77B VAL* 4.4 4.9 - - + -
80B PHE* 3.9 39.7 - - + +
81B SER 5.8 0.2 - - - -
82B ALA* 5.9 0.7 - - + +
96B ALA* 3.1 32.1 + - + +
97B LEU* 3.8 3.8 - - - +
99B PRO* 1.3 78.2 - - - +
101B VAL* 1.3 57.7 + - - +
104B PHE* 2.8 54.4 + - + +
105B GLY 3.2 4.3 + - - -
106B GLN 3.4 13.2 - - - +
107B GLY* 3.9 7.0 - - - -
108B GLN 4.9 3.4 - - - +
109B VAL* 5.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU 3.0 17.0 + - - +
98B GLY* 3.3 15.0 - - - +
100B LEU* 1.3 77.8 - - - +
102B ALA* 1.3 65.0 + - - +
105B GLY* 2.9 24.8 + - - -
106B GLN 3.6 7.8 + - - +
107B GLY 4.7 0.2 - - - +
129B LEU* 4.3 15.5 - - + -
134B ALA* 4.3 5.8 - - + -
145B ALA* 3.8 20.0 - - + +
146B SER* 3.7 38.8 - - - +
147B VAL* 3.7 17.6 - - + +
151B LEU* 4.4 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 4.2 11.2 - - + -
98B GLY 2.9 17.5 + - - +
99B PRO 3.9 2.7 - - - +
101B VAL* 1.3 79.3 - - - +
103B ARG* 1.3 60.6 + - - +
105B GLY 4.9 0.2 + - - -
150B ARG* 5.5 4.5 - - - +
151B LEU* 3.8 21.8 + - + +
172B ALA* 3.5 30.3 - - - +
175B LEU* 3.9 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU 2.8 35.3 + - - +
34B LEU* 3.7 16.5 + - + -
35B ALA 3.2 16.9 + - - -
36B GLU* 4.0 33.2 + - + +
74B ALA* 3.0 30.1 + - - +
75B SER* 4.3 8.3 + - - +
99B PRO 2.9 15.7 + - - +
102B ALA* 1.3 80.2 - - - +
104B PHE* 1.3 89.4 + - + +
105B GLY 3.6 0.4 - - - -
175B LEU* 3.8 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 3.9 10.5 - - + -
74B ALA 4.4 0.7 - - - -
75B SER 6.2 0.2 - - - -
77B VAL* 3.6 38.8 - - + -
80B PHE* 3.5 32.1 - + + -
99B PRO 5.1 0.2 - - - -
100B LEU* 2.8 38.3 + - + +
103B ARG* 1.3 125.9 - - + +
105B GLY* 1.3 62.9 + - - +
106B GLN* 3.3 9.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU 3.2 0.2 + - - -
101B VAL* 2.9 22.0 + - - -
103B ARG 3.6 1.2 - - - -
104B PHE* 1.3 76.9 - - - +
106B GLN* 1.3 61.6 + - - +
146B SER* 3.1 4.5 - - - -
147B VAL* 2.9 44.2 + - - +
149B GLY 5.2 2.9 - - - -
----------------------------------------------------------
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