Contacts of the helix formed by residues 15 - 23 (chain E) in PDB entry 3STJ
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 LEU 15 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E SER* 1.4 76.5 + - - +
16E ALA* 1.3 57.9 + - - +
17E PRO* 3.4 2.5 - - - -
18E MET* 3.3 19.0 + - + +
19E LEU* 2.9 33.8 + - + +
142E VAL* 3.8 25.1 - - + -
156E SER* 3.9 16.4 - - - +
194E LEU* 3.6 29.2 - - + +
138F GLY* 3.0 21.7 + - - +
140F PHE* 3.9 17.7 - - + -
158F ILE* 4.0 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 16 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E SER* 3.1 15.8 + - - +
15E LEU* 1.3 76.2 - - - +
17E PRO* 1.4 64.0 - - + +
19E LEU 4.5 0.2 - - - +
20E GLU* 2.9 27.4 + - - +
136F ARG* 3.5 39.3 - - + +
137F VAL 3.2 23.7 - - - +
138F GLY* 3.7 3.2 - - - -
139F ASP* 3.6 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 17 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E SER* 3.4 24.5 - - - +
15E LEU 3.5 1.8 - - - -
16E ALA* 1.4 92.8 - - + +
18E MET* 1.4 60.0 - - - +
20E GLU* 3.5 23.7 - - - +
21E LYS* 3.6 21.6 - - - +
136F ARG* 4.0 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 18 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E LEU* 3.3 19.8 + - + +
17E PRO* 1.4 77.1 - - - +
19E LEU* 1.4 93.4 + - + +
21E LYS* 3.2 29.2 + - - +
22E VAL* 3.3 18.7 + - + +
142E VAL* 4.0 20.4 - - + -
192E LEU* 4.8 2.2 - - + -
193E ASN 3.5 22.4 - - - +
194E LEU* 3.6 21.8 - - - +
195E ASN 4.8 6.1 - - - +
196E GLY* 3.5 25.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 19 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E LEU* 2.9 23.5 + - + +
16E ALA 4.1 2.9 - - - +
18E MET* 1.4 96.8 - - + +
20E GLU* 1.3 59.7 + - - +
22E VAL* 4.5 2.9 - - + +
23E LEU* 2.9 67.4 + - + +
142E VAL* 4.2 19.3 - - + -
144E VAL* 4.3 0.9 - - + -
154E ALA* 4.3 15.9 - - + -
192E LEU* 4.3 12.1 - - + -
137F VAL* 3.9 9.4 - - + +
138F GLY* 3.7 29.4 - - - +
158F ILE* 5.0 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 20 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E ALA 2.9 12.7 + - - +
17E PRO* 3.5 13.2 - - - +
19E LEU* 1.3 76.0 - - - +
21E LYS* 1.4 61.3 + - + +
23E LEU* 5.2 2.4 - - - +
24E PRO* 3.7 14.7 - - - +
136F ARG* 3.0 47.0 + - - -
137F VAL 5.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 21 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E PRO* 3.6 23.8 + - - +
18E MET* 3.2 17.3 + - + +
19E LEU 3.2 0.6 - - - -
20E GLU* 1.4 77.2 - - + +
22E VAL* 1.3 63.9 + - + +
23E LEU 3.9 0.2 - - - -
24E PRO* 3.8 7.9 - - - +
125E THR* 4.1 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 22 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E MET* 3.3 19.4 + - - +
19E LEU* 3.3 4.2 + - + +
21E LYS* 1.3 82.2 - - + +
23E LEU* 1.3 67.4 + - - +
24E PRO* 3.3 3.6 - - - -
25E ALA* 3.0 26.7 + - - +
26E VAL* 4.2 3.9 + - + +
125E THR* 5.4 0.7 - - - -
127E ILE* 4.2 9.9 - - + -
192E LEU* 3.5 32.5 - - + -
195E ASN 4.6 4.0 - - - +
196E GLY* 3.3 33.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E LEU* 2.9 62.1 + - + +
20E GLU* 4.8 1.8 - - - +
22E VAL* 1.3 72.7 - - + +
24E PRO* 1.4 63.7 - - + +
25E ALA 3.0 1.9 + - - -
26E VAL* 3.0 10.7 + - - +
95E ASN* 3.6 7.9 - - - +
144E VAL* 3.6 31.6 - - + -
152E GLN* 3.0 40.0 - - + +
154E ALA* 4.6 7.2 - - + -
137F VAL* 3.9 24.9 - - + +
----------------------------------------------------------
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