Contacts of the strand formed by residues 202 - 206 (chain A) in PDB entry 3AEF
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 ILE 202 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TYR* 3.8 28.5 - - + +
14A PRO* 3.1 16.4 + - - +
15A VAL* 3.4 13.0 - - + -
16A VAL* 3.0 22.7 + - - +
180A LEU* 4.8 5.2 - - + -
193A ILE* 3.8 31.9 - - + -
194A ALA 3.4 8.5 - - - +
195A LEU* 4.6 9.4 - - + -
200A GLY 4.2 7.4 - - - +
201A SER* 1.3 78.4 - - - +
203A HIS* 1.3 64.6 + - - +
204A ARG 5.2 0.2 - - - +
451A VAL* 3.7 33.2 - - + -
454A LEU* 4.3 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 3.4 29.8 - - + +
18A HIS* 2.9 32.9 + + + -
177A TYR* 3.5 39.6 + + + -
193A ILE* 3.5 3.1 - - - -
194A ALA 2.8 37.4 + - - +
196A CYS* 3.8 0.9 - - + -
201A SER* 3.1 33.5 + - - -
202A ILE* 1.3 79.2 - - - +
204A ARG* 1.3 63.0 + - - +
205A ILE* 3.5 14.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 4.6 25.0 - - + +
16A VAL 3.1 6.5 + - - +
17A ASP* 3.4 36.8 + - - +
18A HIS* 2.9 28.1 + - - +
183A LEU* 4.0 15.6 - - + +
192A VAL 3.6 5.6 - - - -
193A ILE* 3.7 23.8 - - + +
202A ILE 4.4 0.2 + - - -
203A HIS* 1.3 69.4 - - - +
205A ILE* 1.3 63.1 + - - +
206A ARG* 5.1 1.9 - - + +
442A ILE* 4.1 11.6 - - + +
443A LYS 2.6 30.3 + - - -
444A PRO* 3.0 25.9 + - - +
446A ALA* 3.1 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A HIS* 4.1 19.1 - - + -
20A PHE* 3.6 27.4 - - + -
23A VAL* 3.8 27.8 - - + +
46A ALA* 4.0 3.4 - - + -
48A VAL* 3.9 23.3 - - + -
174A PHE* 4.3 16.4 - - + -
177A TYR* 5.3 1.1 - - + -
183A LEU* 4.1 2.0 - - - +
191A GLY* 3.4 2.3 - - - -
192A VAL* 2.9 46.6 + - + +
194A ALA* 4.3 8.1 - - + -
203A HIS* 3.7 24.7 - - + +
204A ARG* 1.3 72.8 - - - +
206A ARG* 1.3 61.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASP* 5.0 11.4 + - - +
18A HIS 3.2 19.2 + - - +
19A GLU* 3.3 37.0 + - - +
20A PHE* 2.8 29.6 + - - +
23A VAL* 4.7 0.4 - - - -
183A LEU* 4.6 10.8 - - + -
190A ARG* 3.3 13.2 - - + +
204A ARG* 5.1 2.2 - - + +
205A ILE* 1.3 74.8 - - - +
207A ALA* 1.3 62.1 + - - +
438A LYS* 5.9 1.8 - - - +
439A VAL* 3.1 24.9 + - + +
440A PRO 3.0 30.9 + - - +
441A SER* 3.5 13.1 - - - +
442A ILE* 4.6 16.8 - - + +
----------------------------------------------------------
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