Contacts of the strand formed by residues 182 - 190 (chain A) in PDB entry 4N20
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 SER 182 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ILE 3.0 25.8 + - - -
151A LEU* 3.7 16.8 - - - +
152A LEU* 4.4 3.6 + - - +
181A MET* 1.3 73.0 - - - +
183A GLN* 1.3 64.0 + - - +
251A PHE* 3.3 5.5 - - - -
252A VAL* 2.8 38.9 + - - +
292A PHE* 4.2 15.7 - - - -
363A LYS* 4.6 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A VAL* 4.3 11.3 - - - +
123A ASP* 4.7 1.9 + - - +
130A VAL* 4.0 31.4 - - + +
175A LYS* 5.4 2.8 - - - +
181A MET 5.0 2.5 - - - +
182A SER* 1.3 77.2 - - - +
184A MET* 1.3 62.6 + - - +
185A ILE* 4.5 5.2 - - - +
249A LEU* 3.7 26.4 - - + +
250A PHE 3.5 3.6 - - - -
251A PHE* 3.6 34.9 - - + -
252A VAL* 5.2 0.2 - - - -
292A PHE* 4.8 2.1 - - - -
363A LYS* 5.7 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LEU* 3.7 26.7 - - + -
121A ASP 3.4 11.4 - - - +
122A VAL* 3.9 8.5 - - + -
182A SER 3.9 0.2 + - - -
183A GLN* 1.3 76.4 - - - +
185A ILE* 1.3 65.6 - - - +
186A LEU 4.2 0.2 - - - -
202A LEU* 4.1 12.1 - - + -
214A VAL* 4.2 3.1 - - + -
250A PHE* 2.8 61.4 + - + +
252A VAL* 3.8 24.0 - - + -
268A ILE* 3.8 33.7 - - + -
290A VAL* 3.9 16.4 - - - -
292A PHE* 4.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A SER 3.4 3.5 - - - +
120A LEU* 4.4 3.1 - - - -
121A ASP* 2.8 41.5 + - - +
130A VAL* 4.1 25.6 - - + -
183A GLN* 4.5 4.7 - - - +
184A MET* 1.3 79.3 - - - +
186A LEU* 1.3 60.4 + - - +
187A ARG* 3.5 36.1 + - + +
247A GLU* 3.7 34.8 - - + +
248A LEU 3.3 10.8 - - - +
249A LEU* 3.9 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ILE* 4.0 19.7 - - + -
119A SER 3.5 20.9 - - - +
120A LEU* 4.1 9.4 - - + +
185A ILE* 1.3 70.1 - - - +
187A ARG* 1.3 60.8 + - - +
188A THR* 3.9 15.4 + - + +
200A ILE* 4.1 13.7 - - + -
202A LEU* 6.0 1.3 - - + -
239A VAL* 4.1 25.6 - - + -
246A ALA 3.9 0.9 - - - +
247A GLU* 3.4 3.3 - - - -
248A LEU* 2.9 50.1 + - + +
250A PHE* 3.9 21.4 - - + -
270A VAL* 4.1 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLU* 3.8 11.2 - - - +
118A ILE* 3.5 1.9 + - - -
119A SER* 2.9 40.3 + - - +
121A ASP* 2.8 42.4 + - - +
130A VAL* 2.9 20.2 + - - +
131A GLU 3.2 22.4 + - - -
132A LYS* 3.6 30.7 - - - +
185A ILE* 3.7 37.8 - - + +
186A LEU* 1.3 71.0 - - - +
188A THR* 1.3 64.1 + - - +
246A ALA 3.5 5.4 - - - +
247A GLU* 2.8 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLU* 3.1 16.8 - - - +
118A ILE* 4.4 12.6 - - + -
186A LEU* 4.2 24.4 + - + +
187A ARG* 1.3 79.3 - - - +
189A LYS* 1.3 64.0 + - - +
200A ILE* 4.7 10.8 - - + -
241A TYR* 4.3 14.3 - - + -
242A THR 4.0 10.0 + - - -
244A GLY 4.1 0.4 - - - -
245A SER* 3.5 2.6 - - - -
246A ALA* 2.9 46.5 + - - +
248A LEU* 5.6 4.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 6.1 0.4 - - + -
83A GLN* 6.5 0.2 - - - -
84A ALA* 3.6 23.1 - - + +
85A SER 5.8 0.2 - - - +
116A ILE* 3.2 7.4 - - - +
117A GLU* 2.8 52.8 + - + +
188A THR* 1.3 78.1 - - - +
190A GLY* 1.3 62.1 + - - +
241A TYR* 4.2 2.9 - - - -
244A GLY 3.2 8.1 - - - +
245A SER* 3.5 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ALA* 4.2 4.0 - - - -
85A SER 3.3 14.3 - - - +
86A THR* 5.0 1.9 - - - +
115A ALA 4.2 2.0 - - - -
116A ILE* 4.3 1.1 - - - -
189A LYS* 1.3 78.1 - - - +
191A PRO* 1.3 74.5 - - - +
241A TYR* 3.1 8.8 + - - -
244A GLY* 2.9 28.9 + - - -
----------------------------------------------------------
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