Contacts of the strand formed by residues 117 - 121 (chain D) in PDB entry 5EJK
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 117 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D GLN 3.0 21.7 + - - +
60D ILE* 4.7 7.2 - - + -
61D TRP 3.4 11.9 + - - -
115D PRO* 3.2 7.3 - - - +
116D LYS* 1.3 80.3 - - - +
118D ILE* 1.3 70.0 + - - +
119D LYS* 4.3 0.9 - - + -
140D ILE* 3.7 2.5 - - - -
141D ALA* 3.3 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 118 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D TRP* 3.8 36.8 - - + +
63D THR* 4.2 4.5 - - - +
105D TRP* 3.5 58.1 - - + +
109D ILE* 5.1 2.0 - - + -
115D PRO* 3.6 19.1 - - + -
117D ALA* 1.3 81.6 - - - +
119D LYS* 1.3 61.4 + - - +
120D THR* 4.3 3.8 - - + -
134D TRP* 5.7 1.3 - - + -
135D MSE 4.3 14.8 - - + -
140D ILE* 4.2 10.3 - - + +
141D ALA 3.3 5.3 + - - -
142D HIS* 3.1 30.0 - - - -
143D THR 3.9 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 119 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D ILE* 4.6 23.7 - - + +
61D TRP 2.8 25.0 + - - +
62D GLN* 3.4 34.8 - - - +
63D THR 3.6 0.2 + - - -
117D ALA* 4.3 0.6 - - + -
118D ILE* 1.3 73.7 - - - +
120D THR* 1.3 63.5 + - - +
143D THR* 3.3 26.9 - - + +
144D THR 5.1 0.4 - - - +
145D GLY* 3.8 22.2 - - - -
146D ILE 5.1 1.6 - - - +
148D GLY 4.7 6.7 - - - +
149D ASN* 3.8 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 120 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D THR* 3.3 31.0 - - - +
105D TRP* 3.5 31.2 - - + -
118D ILE* 4.1 3.2 + - + -
119D LYS* 1.3 80.3 - - - +
121D ASP* 1.3 59.8 + - - +
122D ASN* 5.6 0.2 - - - -
126D PHE* 3.5 28.2 - - + +
142D HIS* 3.2 17.5 + - - +
143D THR 3.8 2.6 + - - -
144D THR* 3.3 6.4 - - - +
145D GLY* 2.6 29.1 + - - -
148D GLY 5.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 121 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D THR 3.9 10.4 - - - +
64D ASP* 3.6 27.1 - - - +
120D THR* 1.3 72.1 - - - +
122D ASN* 1.3 69.8 + - - +
123D GLY* 3.0 5.0 + - - -
126D PHE* 3.4 18.3 - - - -
145D GLY* 4.0 10.5 - - - +
148D GLY* 4.6 16.9 - - - +
----------------------------------------------------------
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