Contacts of the strand formed by residues 216 - 223 (chain C) in PDB entry 4I6N
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 PHE 216 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C PHE* 3.7 15.7 - + + -
52C LEU* 3.3 10.3 - - - +
53C PHE* 3.5 28.3 - - + -
54C ARG 4.9 0.2 - - - -
205C LYS* 5.8 0.2 - - + -
206C ILE* 3.9 20.9 - - + -
209C TYR* 3.6 43.3 - + + -
213C GLU* 3.4 35.0 - - + -
214C VAL 2.9 9.0 + - - +
215C ARG* 1.3 75.5 - - - +
217C ASN* 1.3 62.7 + - - +
8D LEU* 4.1 22.9 - - + +
9D THR* 3.3 25.6 - - + -
71D LEU* 3.6 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 217 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C SER* 3.5 30.5 + - - +
32C GLU* 2.9 28.4 + - - -
50C ILE 3.9 0.2 - - - +
51C PHE* 3.3 7.5 - - - -
52C LEU* 2.9 40.0 + - + -
216C PHE* 1.3 76.2 - - - +
218C LEU* 1.3 63.0 + - - +
219C MSE 3.4 31.7 - - - +
8D LEU* 4.2 3.1 - - - -
70D VAL* 4.9 0.8 - - - +
71D LEU* 2.9 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 218 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C GLU* 3.8 3.1 - - - +
33C LEU* 2.9 54.4 + - + +
36C LEU* 3.5 29.4 - - + -
49C PHE* 3.9 20.4 - - + -
50C ILE 3.6 13.7 - - - +
51C PHE* 4.1 11.9 - - + -
199C ILE* 4.1 6.7 - - + -
202C ILE* 3.6 32.1 - - + -
217C ASN* 1.3 75.7 + - - +
219C MSE 1.3 66.9 + - - +
8D LEU* 3.9 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 219 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C SER* 4.6 2.0 - - - -
12C ASP 3.9 7.2 - - - -
13C PRO* 3.7 32.3 - - + -
16C PHE* 3.8 26.7 - - + -
30C VAL* 3.6 17.9 - - + -
31C GLU 3.4 4.3 - - - +
32C GLU* 4.2 15.7 - - + -
33C LEU* 4.2 3.1 - - - -
49C PHE* 3.3 8.2 - - - -
50C ILE* 2.8 65.8 + - + +
52C LEU* 6.0 0.4 - - + -
162C PHE* 4.2 8.3 - - + -
217C ASN* 3.4 23.1 - - - +
218C LEU* 1.3 75.2 - - - +
220C ALA* 1.3 61.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 220 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C VAL* 3.3 3.9 - - - +
31C GLU 2.7 37.0 + - - +
33C LEU* 3.6 20.8 - - + +
43C LEU* 4.6 9.0 - - + -
46C ILE* 4.0 12.8 - - + -
48C GLY 3.6 4.9 - - - -
49C PHE* 3.8 14.8 - - + -
219C MSE 1.3 73.9 - - - +
221C VAL* 1.3 62.2 + - - +
222C ILE* 3.7 12.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 221 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ILE* 4.2 15.0 - - + -
28C LEU* 3.7 33.7 - - + -
29C GLN 3.5 7.2 - - - +
30C VAL* 4.3 13.0 - - + +
46C ILE* 3.7 0.3 - - - -
47C HIS* 2.8 29.7 + - + +
48C GLY 2.9 16.3 + - - +
50C ILE* 4.2 16.8 - - + -
90C LEU* 4.8 2.5 - - + -
93C LEU* 3.8 34.3 - - + -
94C LEU* 5.1 0.4 - - + -
220C ALA* 1.3 72.9 - - - +
222C ILE* 1.3 62.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 222 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 3.2 7.3 - - - +
29C GLN* 2.7 60.0 + - + +
31C GLU* 4.0 20.9 - - + +
43C LEU* 3.8 41.7 - - + +
45C PRO 3.9 2.2 - - - +
46C ILE* 4.0 11.4 - - + -
47C HIS* 3.7 10.5 - - - -
220C ALA* 4.0 22.4 - - + +
221C VAL* 1.3 80.2 - - - +
223C SER* 1.3 67.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 223 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C GLY 3.5 7.9 - - - -
29C GLN* 3.3 9.1 + - - -
43C LEU 5.1 0.8 + - - -
45C PRO* 4.0 14.0 + - - +
47C HIS* 2.8 26.5 + - - -
101C ASP* 2.9 28.4 + - - +
222C ILE* 1.3 86.5 - - - +
224C ASP* 1.3 72.0 + - - +
----------------------------------------------------------
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