Contacts of the strand formed by residues 218 - 224 (chain D) in PDB entry 3HN3
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 VAL 218 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D GLU* 3.9 1.2 - - - -
41D LEU* 2.8 31.6 + - + +
42D ASP* 4.2 5.2 + - - +
45D TRP* 3.9 23.6 - - + -
79D VAL* 4.2 17.0 - - + +
121D LEU* 4.1 11.7 - - + -
122D ARG 3.5 4.3 - - - +
123D ILE* 3.3 43.3 - - + -
214D LEU* 4.3 14.6 - - + -
216D ARG 3.8 9.2 - - - +
217D SER* 1.3 77.3 - - - +
219D LEU* 1.3 65.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D TYR* 6.3 2.0 - - + -
30D PRO* 4.0 28.9 - - + +
38D CYS* 4.0 19.3 - - + -
39D LYS 3.3 13.5 - - - +
40D GLU* 4.0 12.1 - - + +
41D LEU* 4.2 2.7 - - - +
121D LEU* 3.6 6.5 - - - +
122D ARG* 2.8 64.5 + - + +
217D SER* 4.4 14.8 - - - +
218D VAL* 1.3 78.9 - - - +
220D LEU* 1.3 71.4 + - - +
221D TYR* 4.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 220 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D CYS* 3.5 0.5 - - - -
39D LYS* 2.7 38.5 + - + +
41D LEU* 4.1 16.4 - - + -
105D VAL* 4.2 14.1 - - + -
107D LEU* 3.9 28.7 - - + -
111D TRP* 3.8 22.4 - - + -
119D VAL* 4.6 4.9 - - + -
120D VAL 3.1 13.5 - - - +
121D LEU* 3.7 21.8 - - + -
153D ILE* 3.9 24.7 - - + -
166D LEU* 4.1 9.9 - - + -
168D ILE* 4.6 0.4 - - + -
219D LEU* 1.3 76.9 - - - +
221D TYR* 1.3 62.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 221 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D LEU 5.0 2.0 + - - -
30D PRO* 4.1 27.1 - - + -
31D GLN 6.0 1.1 - - - -
36D ARG* 4.5 13.6 + - + -
37D GLU 3.3 15.0 - - - +
38D CYS* 4.2 13.2 - - - +
111D TRP* 4.9 0.9 - - - -
118D ARG* 4.7 3.0 + - - -
119D VAL* 3.6 2.9 - - - +
120D VAL* 2.7 61.5 + - + +
122D ARG* 4.0 22.9 + - + -
150D GLU* 2.6 38.6 + - - -
219D LEU* 4.5 2.9 - - + -
220D LEU* 1.3 76.3 - - - +
222D THR* 1.3 74.3 + - - +
223D THR* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 222 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D SER 4.6 1.6 + - - -
36D ARG* 3.2 23.0 - - - +
37D GLU* 3.1 32.8 + - - +
111D TRP* 3.5 38.1 - - + +
117D THR* 3.7 24.7 - - + -
118D ARG 3.1 9.4 - - - +
119D VAL* 4.3 3.4 - - + -
221D TYR* 1.3 83.3 - - - +
223D THR* 1.3 72.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 223 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D SER 3.9 6.3 - - - -
36D ARG* 3.6 33.0 - - - +
116D ARG 4.1 0.7 - - - +
117D THR* 3.9 2.6 - - - +
118D ARG* 2.9 61.0 + - - +
120D VAL* 5.2 0.4 - - + +
221D TYR* 3.8 11.0 - - + -
222D THR* 1.3 83.3 - - - +
224D PRO* 1.3 83.4 + - - +
227D TYR* 3.6 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 224 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D SER* 3.7 11.4 - - - +
116D ARG 3.8 9.4 - - - +
118D ARG* 3.7 1.9 - - - +
223D THR* 1.3 106.9 + - - +
225D THR* 1.3 64.7 + - - +
226D THR 3.2 15.8 + - - +
227D TYR* 3.4 7.3 - - - +
316D VAL* 4.1 20.2 - - + -
317D SER 3.4 25.8 - - - +
318D ASP* 3.5 22.2 - - + +
----------------------------------------------------------
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