Contacts of the strand formed by residues 218 - 223 (chain A) in PDB entry 1AHF
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 LEU 218 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 4.2 9.6 - - + -
184A ASP 3.0 7.7 + - - +
185A VAL* 3.5 32.6 - - + +
186A VAL 2.9 22.9 + - - -
216A GLY 4.2 0.8 + - - -
217A TRP* 1.3 72.1 - - - +
219A PRO* 1.3 82.2 - - + +
220A LEU* 3.6 0.9 + - + -
249A GLU* 3.9 28.0 - - + +
250A LEU* 4.0 4.3 - - - +
251A ILE* 3.5 29.6 - - + -
5B MET* 4.0 27.5 - - + +
6B PHE* 4.4 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A VAL* 3.5 8.1 - - + +
188A PHE* 4.3 3.6 - - + -
212A SER* 4.4 2.5 - - - +
217A TRP* 3.1 11.2 - - + +
218A LEU* 1.3 95.9 - - + +
220A LEU* 1.3 59.0 + - - +
221A PHE* 4.0 11.2 - - + -
243A PHE* 3.6 31.2 - - + -
247A HIS* 3.3 35.4 - - + +
249A GLU 3.8 3.4 - - - +
250A LEU* 3.7 9.6 - - + +
251A ILE* 3.1 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 4.1 17.0 - - + -
115A ALA* 4.5 12.1 - - + -
119A LEU* 4.2 18.8 - - + -
147A PHE* 4.3 19.3 - - + -
185A VAL* 3.8 27.6 - - + -
186A VAL 3.0 8.1 + - - +
187A LEU* 3.4 23.3 - - + +
188A PHE* 2.8 27.0 + - - +
218A LEU* 5.7 0.2 - - + -
219A PRO* 1.3 74.5 - - - +
221A PHE* 1.3 75.3 + - - +
251A ILE* 3.4 21.5 - - + +
253A ALA* 4.7 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A PHE* 3.2 15.9 - + + -
190A GLY* 4.0 20.4 - - - +
205A TRP* 3.9 24.0 - + - -
219A PRO* 4.0 12.1 - - + -
220A LEU* 1.3 81.4 - - - +
222A ASP* 1.3 60.5 - - - +
223A PHE* 3.6 2.0 - - + +
240A LEU* 3.9 40.2 - - + -
243A PHE* 3.7 51.4 - + + -
250A LEU* 5.2 4.0 - - + -
251A ILE 2.9 14.0 + - - +
252A VAL* 3.7 18.3 - - + +
253A ALA* 2.6 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A GLY* 5.8 0.3 - - - -
112A LEU* 3.9 11.7 - - + +
143A HIS* 2.8 29.0 + - + +
187A LEU* 4.2 9.8 - - + +
188A PHE 2.8 12.5 + - - +
189A HIS* 3.3 8.6 - - - +
190A GLY 2.9 20.6 + - - -
191A CYS 5.5 0.7 - - - +
220A LEU* 3.9 0.6 + - - +
221A PHE* 1.3 72.9 - - - +
223A PHE* 1.3 60.4 + - - +
224A ALA* 3.8 8.0 + - - +
253A ALA* 3.4 9.2 - - - +
410A PLP 2.4 48.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 4.4 12.3 - - + -
190A GLY* 3.9 18.4 - - - -
191A CYS* 3.6 28.3 - - - -
221A PHE* 4.9 1.6 - - + -
222A ASP* 1.3 72.6 + - - +
224A ALA* 1.3 59.5 + - - +
225A TYR 4.6 0.2 - - - -
226A GLN* 3.7 35.1 + - + +
236A ASP 3.1 27.8 - - - -
237A ALA* 4.1 9.2 - - + -
240A LEU* 3.9 35.4 - - + -
252A VAL* 4.2 8.5 - - + -
253A ALA 2.7 14.0 + - - +
254A SER* 3.0 12.7 - - - -
255A SER 3.0 23.4 + - - +
----------------------------------------------------------
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