Contacts of the strand formed by residues 180 - 184 (chain C) in PDB entry 1IRI
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 ARG 180 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C THR* 2.8 24.6 + - - +
151C ASP* 3.0 43.5 + - - +
152C VAL* 2.8 33.6 + - - +
172C LYS* 6.1 0.2 - - - +
178C GLY 3.8 1.7 + - - +
179C PRO* 1.3 74.8 - - - +
181C VAL* 1.3 56.3 + - - +
182C TRP* 4.2 17.4 - - + +
287C HIS* 4.4 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 181 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C VAL* 3.2 23.1 - - + +
154C ASN* 6.2 0.4 - - + +
168C THR* 4.2 5.2 - - - +
172C LYS* 3.6 17.0 + - - +
179C PRO 4.7 0.7 - - - +
180C ARG* 1.3 77.9 - - - +
182C TRP* 1.3 68.8 + - - +
183C TYR* 3.9 27.9 - - + +
283C SER* 3.8 24.7 - - - +
286C LEU* 5.7 0.7 - - + -
287C HIS* 3.5 35.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 182 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C ASP* 3.0 30.0 + - + +
152C VAL 2.9 14.5 + - - +
153C ILE* 3.6 9.4 - - + +
154C ASN* 3.0 26.7 + - - +
180C ARG* 4.2 17.8 - - + +
181C VAL* 1.3 83.8 - - - +
183C TYR* 1.3 69.1 + - - +
184C VAL 4.0 0.4 - - - -
195C THR* 4.1 34.5 - - + +
198C GLN* 3.5 50.9 - - + -
199C LEU* 3.5 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 183 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C ASN* 3.5 30.5 - - + -
161C ASP* 3.6 23.6 - - - +
164C PRO* 3.2 12.6 + - + -
165C LEU* 3.8 37.9 - - + +
168C THR* 3.1 38.2 - - - +
169C GLU* 6.0 2.2 - - - -
181C VAL* 3.9 22.3 - - + +
182C TRP* 1.3 76.6 - - - +
184C VAL* 1.3 61.7 + - - +
185C SER* 4.9 0.2 + - - -
191C HIS* 3.2 22.1 + - - -
195C THR* 5.2 0.7 + - - -
283C SER* 2.8 33.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 184 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C ILE* 4.0 13.5 - - + -
154C ASN 2.9 12.2 + - - +
155C ILE* 3.3 9.0 - - + +
156C GLY 3.1 24.4 + - - +
161C ASP* 4.4 1.4 - - - +
183C TYR* 1.3 73.1 - - - +
185C SER* 1.3 64.4 + - - +
191C HIS* 4.1 9.4 - - + +
192C ILE* 3.9 37.2 - - + +
195C THR* 3.6 39.3 - - + +
221C ASN* 4.1 19.5 - - + +
----------------------------------------------------------
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