Contacts of the strand formed by residues 189 - 196 (chain A) in PDB entry 3AIH
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 GLU 189 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU 3.5 5.2 - - - -
175A TYR 3.6 9.6 - - - +
176A GLY* 4.5 4.5 - - - -
177A ASN 5.3 0.2 - - - +
186A ARG* 3.4 19.7 - - - +
187A PRO 4.6 0.4 - - - +
188A ARG* 1.3 75.8 - - - +
190A ALA* 1.3 60.5 + - - +
216A CYS 3.1 2.6 + - - -
217A SER* 3.1 18.8 + - - +
218A TYR* 2.9 29.5 + - - -
184B ASN* 5.6 0.2 - - - +
186B ARG* 2.8 42.8 + - - -
189B GLU* 3.6 1.0 - - - +
214B LEU* 3.7 16.4 - - + +
215B SER 5.5 0.2 - - - -
217B SER* 2.8 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ILE* 4.0 26.2 - - + -
145A LEU* 4.3 11.9 - - + +
174A THR* 3.6 2.6 - - - -
175A TYR* 2.8 40.8 + - + +
189A GLU* 1.3 77.6 - - - +
191A GLU* 1.3 63.8 + - - +
218A TYR* 3.2 21.1 - - + +
220A LEU* 4.0 5.4 - - + -
214B LEU* 4.1 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A GLN 3.5 7.9 - - - +
174A THR* 4.2 20.3 - - + +
190A ALA* 1.3 79.3 - - - +
192A VAL* 1.3 63.9 + - - +
193A ARG* 2.8 30.9 + - - +
218A TYR 2.9 6.8 + - - +
219A VAL* 3.3 5.2 - - - -
220A LEU* 2.9 25.5 + - - +
213B PRO 3.5 8.3 - - - +
214B LEU* 3.4 26.5 - - + +
215B SER* 3.0 32.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A PHE* 4.0 7.0 - - + -
128A ILE* 3.9 15.3 - - + -
172A SER* 3.6 10.4 - - - -
173A GLN* 3.0 25.8 + - + +
175A TYR* 3.6 34.3 - - + -
191A GLU* 1.3 78.5 - - - +
193A ARG* 1.3 67.4 + - - +
194A PHE* 3.5 23.1 - - + -
220A LEU* 3.2 11.2 - - + +
222A ILE* 3.5 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A HIS 4.7 1.6 - - - -
172A SER* 5.5 0.7 - - - +
191A GLU* 2.8 38.2 + - - +
192A VAL* 1.3 82.1 + - - +
194A PHE* 1.3 61.0 + - - +
195A LEU* 4.7 11.4 - - + -
219A VAL* 3.7 31.5 - - + +
220A LEU 2.8 6.7 + - - +
221A THR* 3.9 19.5 - - + +
222A ILE 2.8 26.0 + - - -
213B PRO* 2.7 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A PHE* 3.9 16.8 - + - -
124A TYR* 3.9 19.1 - + - -
171A HIS* 3.2 50.5 + + + +
173A GLN* 3.9 19.5 - - + -
192A VAL* 3.5 31.2 - - + -
193A ARG* 1.3 74.8 - - - +
195A LEU* 1.3 69.0 + - - +
205A ASP* 5.6 3.6 - - - -
222A ILE* 3.4 33.2 - - + -
224A THR* 4.5 9.4 - - + -
227A LEU* 3.3 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ARG* 4.7 10.1 - - + -
194A PHE* 1.3 84.7 - - - +
196A CYS* 1.3 64.5 + - - +
221A THR* 3.6 22.4 - - + +
222A ILE 2.9 7.4 + - - +
223A ARG* 3.3 42.8 - - - +
224A THR* 3.0 23.6 + - - +
227A LEU* 3.8 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU* 1.3 71.8 - - - +
197A ASP* 1.3 66.7 + - - +
198A GLU* 3.1 28.6 + - - +
223A ARG* 2.8 32.2 + - - +
224A THR 3.6 4.5 - - - -
227A LEU* 3.7 12.1 + - - +
228A CYS* 2.1 56.8 - - - -
229A PRO* 4.2 9.9 - - + -
----------------------------------------------------------
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