Contacts of the helix formed by residues 199 - 207 (chain T) in PDB entry 5IY8
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 199 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197T TYR 3.8 1.4 + - - -
198T ASN* 1.3 80.9 + - - +
200T LYS* 1.3 56.7 + - + +
202T LEU* 3.2 10.5 + - + +
203T VAL* 3.0 35.7 + - + +
210T VAL* 3.8 27.8 - - + -
213T LEU* 4.3 13.9 - - + -
214T LYS* 3.9 20.6 - - + -
217T LEU* 3.9 28.3 - - + -
231T ASN* 4.1 5.4 + - + +
233T TRP* 4.4 17.7 - - + +
68Y C 5.7 4.3 - - - +
69Y C 4.2 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 200 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B HIS* 6.3 5.2 - - + -
74B ALA* 5.4 0.4 - - - +
198T ASN* 3.2 22.4 - - - +
199T LEU* 1.3 77.9 - - + +
201T ASP* 1.3 60.4 + - - +
203T VAL* 3.5 8.9 + - - +
204T ASP* 3.1 26.9 + - - +
230T LYS* 5.6 4.2 - - - +
67Y C 4.2 19.0 + - - -
68Y C 3.3 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 201 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B HIS* 5.1 8.0 + - - -
74B ALA* 3.0 37.7 - - + +
197T TYR* 4.8 14.8 - - + -
198T ASN* 3.1 30.2 + - - +
200T LYS* 1.3 78.9 - - - +
202T LEU* 1.3 59.8 + - - +
204T ASP* 3.5 2.9 + - - +
205T ILE* 3.0 43.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 202 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187T LEU* 4.5 17.0 - - + -
190T ALA* 4.8 13.7 - - + -
197T TYR* 4.4 26.7 - - + +
198T ASN 3.4 12.5 + - - +
199T LEU* 3.2 12.0 + - - +
201T ASP* 1.3 75.4 - - - +
203T VAL* 1.3 60.7 + - - +
205T ILE* 3.6 9.8 - - + +
206T THR* 2.7 37.9 + - - +
213T LEU* 3.7 19.3 - - + -
217T LEU* 4.1 34.8 - - + -
233T TRP* 4.9 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 203 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175T ARG* 5.0 10.2 + - - +
199T LEU* 3.0 26.6 + - + +
200T LYS* 3.7 11.0 - - - +
202T LEU* 1.3 76.3 - - - +
204T ASP* 1.3 61.8 + - - +
206T THR* 4.5 2.5 - - - -
207T LYS* 3.2 23.1 + - - +
208T GLN* 4.5 10.5 + - - +
210T VAL* 3.6 32.1 - - + -
213T LEU* 4.6 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 204 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B HIS 3.9 10.9 - - - +
74B ALA* 4.7 4.0 - - + +
75B SER* 3.8 25.3 + - - -
200T LYS 3.1 14.4 + - - +
201T ASP* 3.7 9.4 - - - +
202T LEU 3.4 0.2 - - - -
203T VAL* 1.3 79.0 - - - +
205T ILE* 1.3 62.9 + - + +
206T THR 3.6 0.3 + - - -
207T LYS* 3.9 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 205 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ALA* 5.4 4.0 - - + +
75B SER* 4.4 16.2 - - - +
186T MET* 4.1 16.8 - - + +
190T ALA* 4.6 26.2 - - + -
197T TYR* 5.7 7.2 - - + -
201T ASP* 3.0 36.4 + - + +
202T LEU* 3.2 10.5 + - + +
204T ASP* 1.3 77.7 - - + +
206T THR* 1.3 70.8 + - + +
207T LYS* 4.8 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 206 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176T ALA* 5.0 3.6 - - - +
183T VAL* 4.6 11.9 - - + +
186T MET* 4.0 30.2 - - + +
187T LEU* 4.1 22.2 - - + -
202T LEU* 2.7 26.8 + - + +
203T VAL* 4.5 0.9 - - - -
205T ILE* 1.3 89.4 - - + +
207T LYS* 1.3 73.2 + - - +
208T GLN* 3.0 33.0 + - - +
213T LEU* 4.3 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 207 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195P LYS* 6.2 2.5 - - - +
175T ARG* 3.0 45.2 - - + +
176T ALA* 3.8 4.3 + - - +
203T VAL 3.2 12.7 + - - +
204T ASP 3.9 17.3 - - - +
205T ILE 4.8 4.5 - - - +
206T THR* 1.3 80.0 - - - +
208T GLN* 1.3 56.6 + - - +
----------------------------------------------------------
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