Contacts of the strand formed by residues 198 - 204 (chain E) in PDB entry 6IAP
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 TYR 198 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E LEU* 3.7 45.5 - - + -
158E TRP* 4.2 5.6 - - + -
159E ASN* 3.4 13.0 - - - -
163E LEU* 3.7 25.4 - - + -
188E VAL* 2.9 21.4 - - + +
189E PRO 5.8 0.4 - - - -
192E SER* 2.8 31.2 + - - -
193E LEU* 5.0 7.9 - - + -
196E GLN* 3.5 40.4 - - + +
197E THR* 1.4 76.9 - - - +
199E ILE* 1.3 58.9 + - - +
200E CYS 4.2 0.4 - - - -
214E ARG* 3.5 3.3 - - - +
215E VAL* 2.7 44.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 199 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158E TRP* 3.6 4.3 - - - -
159E ASN* 2.8 50.8 + - - +
197E THR* 5.0 10.8 - - - +
198E TYR* 1.3 76.4 - - - +
200E CYS* 1.3 58.8 + - - +
201E ASN* 3.3 22.2 + - - +
212E ASP* 3.5 25.8 - - + +
213E LYS 3.4 15.7 - - - +
214E ARG* 3.8 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 200 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E VAL* 3.8 15.0 - - - -
144E CYS* 2.0 50.9 - - + -
156E VAL* 4.4 4.7 - - + -
157E SER 3.4 6.7 - - - +
158E TRP* 3.4 30.2 - - + +
199E ILE* 1.3 71.0 - - - +
201E ASN* 1.3 62.2 + - - +
202E VAL* 3.9 7.9 - - - -
211E VAL 3.6 1.7 - - - +
212E ASP* 3.5 0.9 - - - -
213E LYS 3.1 28.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 201 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E THR* 3.6 1.7 - - - +
156E VAL* 3.4 2.9 - - - -
157E SER* 2.8 51.1 + - - +
159E ASN* 4.9 0.2 - - - +
160E SER* 2.8 39.9 + - - +
199E ILE* 3.3 28.0 + - - +
200E CYS* 1.3 78.1 - - - +
202E VAL* 1.3 59.5 + - - +
203E ASN* 4.2 0.6 + - - -
210E LYS* 6.5 0.4 - - + -
212E ASP* 3.3 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 202 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E PRO* 4.6 4.7 - - + -
125E VAL* 4.0 21.1 - - + -
146E VAL* 3.7 43.7 - - + -
154E VAL* 4.0 12.3 - - + -
155E THR 3.3 8.5 - - - +
156E VAL* 4.0 11.9 - - + -
200E CYS* 3.9 22.9 - - - -
201E ASN* 1.3 75.7 - - - +
203E ASN* 1.3 62.1 + - - +
209E THR 4.1 0.5 - - - +
210E LYS* 3.4 5.0 - - - +
211E VAL* 2.8 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 203 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153E PRO 4.6 0.3 - - - +
154E VAL* 3.3 7.0 - - - +
155E THR* 2.8 64.0 + - + +
201E ASN 5.5 0.9 - - - +
202E VAL* 1.3 74.1 - - - +
204E HIS* 1.3 72.0 + - - +
205E LYS* 3.8 13.9 + - - +
209E THR 3.4 11.4 - - - +
210E LYS* 4.9 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 204 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E LYS 3.2 22.2 + - - -
122E GLY* 4.2 0.2 - - - -
123E PRO* 4.0 10.1 - - + -
149E TYR* 3.5 20.3 - + - -
150E PHE 3.5 12.1 - - - -
151E PRO 2.8 21.8 + - - -
153E PRO 3.3 20.0 - - - -
154E VAL* 3.7 10.3 - - + -
203E ASN* 1.3 75.5 + - - +
205E LYS* 1.3 64.2 + - - +
206E PRO* 3.5 10.0 - - + +
207E SER* 2.9 36.8 + - - -
208E ASN* 3.1 2.8 + - - -
209E THR* 2.9 43.7 + - - +
----------------------------------------------------------
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