Contacts of the strand formed by residues 154 - 158 (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 VAL 154 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E PRO* 4.1 3.8 - - + -
146E VAL* 3.8 22.9 - - + -
149E TYR* 3.7 15.3 + - + +
152E GLU* 4.4 2.0 + - - +
153E PRO* 1.3 75.6 - - - +
155E THR* 1.3 60.6 + - - +
156E VAL* 4.1 10.4 + - + +
182E LEU* 3.7 35.1 - - + +
202E VAL* 4.0 12.1 - - + -
203E ASN 3.3 17.3 - - - +
204E HIS* 3.7 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 155 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153E PRO* 5.6 2.6 - - - +
154E VAL* 1.3 73.9 + - - +
156E VAL* 1.3 70.3 + - - +
157E SER* 5.0 5.6 - - - +
201E ASN 3.6 1.5 - - - +
202E VAL* 3.3 3.8 - - - +
203E ASN* 2.8 65.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 156 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144E CYS* 5.7 0.2 - - + -
146E VAL* 3.8 27.4 - - + -
154E VAL* 4.1 5.0 + - + +
155E THR* 1.3 83.2 - - - +
157E SER* 1.3 70.9 + - - +
158E TRP* 4.0 4.7 - - - +
167E VAL* 5.6 0.9 - - - +
169E THR* 4.0 25.6 + - + +
182E LEU* 4.1 15.7 - - + -
184E SER* 3.3 28.3 - - - +
200E CYS* 4.4 5.2 - - + -
201E ASN 3.4 5.2 - - - +
202E VAL* 4.0 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 157 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E THR* 5.5 5.8 - - - -
156E VAL* 1.3 74.6 - - - +
158E TRP* 1.3 66.4 + - - +
160E SER* 4.0 3.0 - - - -
161E GLY* 3.8 16.7 + - - -
167E VAL* 6.2 0.7 - - - -
200E CYS* 3.4 4.7 - - - -
201E ASN* 2.8 56.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 158 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E LEU* 3.6 21.8 - - + -
143E GLY* 3.5 23.8 - - - -
144E CYS 3.9 1.3 - - - -
156E VAL* 4.0 2.9 - - + +
157E SER* 1.3 79.3 - - - +
159E ASN* 1.3 70.8 + - - +
160E SER 3.3 0.9 - - - -
161E GLY* 3.0 12.3 + - - +
162E ALA 3.1 9.0 + - - -
163E LEU* 3.3 32.7 + - + +
167E VAL* 3.6 28.5 - - + +
184E SER* 2.7 46.7 + - - -
186E VAL* 4.4 14.9 - - + +
198E TYR* 4.2 9.0 - - + -
199E ILE 3.6 9.2 - - - -
200E CYS* 3.4 41.5 - - + -
215E VAL* 3.8 12.6 - - + -
----------------------------------------------------------
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