Contacts of the strand formed by residues 188 - 194 (chain A) in PDB entry 4H3E
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 ARG 188 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TYR* 3.2 61.9 - - + +
22A THR* 4.7 0.7 - - - -
162A CYS* 4.0 1.8 - - - -
163A VAL* 2.8 41.1 + - + +
165A PRO* 3.8 30.3 - - + +
169A ASN* 5.7 0.4 + - - -
186A GLY 4.3 4.6 + - - +
187A LEU* 1.3 74.5 - - - +
189A PRO* 1.3 70.8 - - - +
190A VAL* 3.5 2.6 + - - +
230A GLN 4.7 1.0 + - - -
231A ALA* 2.8 52.1 + - + -
233A LYS* 5.1 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TYR* 5.7 1.0 + - - -
22A THR* 3.6 24.9 + - + +
108A PHE* 4.2 20.2 - - + -
112A PHE* 3.5 16.5 - - + -
160A TRP* 3.6 34.8 - - + -
161A LEU 3.8 0.2 - - - +
162A CYS* 3.8 12.6 - - - -
182A PRO* 4.6 9.0 - - + -
183A LEU* 5.1 6.1 - - + +
187A LEU 3.6 9.2 - - - +
188A ARG* 1.3 86.8 - - - +
190A VAL* 1.3 61.6 + - - +
191A LEU 4.8 0.2 - - - +
227A MET* 4.0 6.8 - - - +
231A ALA* 5.5 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PHE* 3.6 10.9 - - - -
116A CYS* 4.3 0.9 - - - -
128A PHE* 4.5 3.4 - - + -
161A LEU* 2.8 45.8 + - + +
163A VAL* 4.0 15.3 - - + +
171A LEU* 4.4 6.7 - - + -
188A ARG 3.9 8.1 - - - +
189A PRO* 1.3 77.0 - - - +
191A LEU* 1.3 58.0 + - - +
224A VAL* 3.2 46.0 - - + +
227A MET* 3.8 9.1 - - - +
228A HIS* 3.6 31.0 - - + +
231A ALA* 4.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PHE* 3.7 7.1 - - - -
116A CYS* 3.9 19.3 - - + -
142A PHE* 4.3 8.5 - - + -
146A PHE* 4.0 26.5 - - + -
160A TRP* 3.2 9.9 - - - +
161A LEU* 3.0 37.6 + - + +
190A VAL* 1.3 79.9 - - - +
192A ALA* 1.3 76.4 + - - +
193A VAL* 4.4 1.6 - - + -
216A TRP* 4.1 11.4 - - + -
219A ILE* 3.9 19.3 - - + -
221A TRP* 4.1 25.4 - - + -
224A VAL* 4.1 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ASN 4.8 0.2 - - - +
112A PHE* 3.8 11.2 - - + -
113A TYR* 3.3 24.6 - - + +
116A CYS* 3.6 12.9 - - - +
158A TRP* 4.5 10.5 - - + -
159A THR 3.6 4.3 - - - -
160A TRP* 3.4 35.7 - - + -
191A LEU* 1.3 79.1 - - - +
193A VAL* 1.3 70.3 + - - +
219A ILE* 5.4 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A TYR* 3.8 2.2 - - - -
146A PHE* 3.7 30.5 - - + -
158A TRP* 3.5 3.9 - - - -
159A THR* 2.8 36.3 + - - +
191A LEU* 4.4 11.4 - - + -
192A ALA* 1.3 79.9 - - - +
194A ASP* 1.3 67.1 + - - +
195A VAL* 3.5 2.6 + - + +
211A TYR* 3.6 19.3 - - + +
212A LEU* 3.6 27.8 - - + -
215A ILE* 4.2 24.9 - - + -
216A TRP* 5.7 1.3 - - + -
219A ILE* 4.7 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A HIS* 2.8 12.0 + - - -
110A HIS* 3.5 1.6 + - - -
113A TYR* 3.5 20.3 - - + -
157A GLY 3.4 0.5 - - - +
158A TRP* 3.4 27.7 - - + -
193A VAL* 1.3 69.9 - - - +
195A VAL* 1.3 58.7 + - - +
196A TRP* 3.1 36.5 + - - +
198A HIS* 3.7 0.3 + - - -
199A ALA* 3.8 16.3 - - + +
211A TYR* 2.7 32.4 + - - -
301A FE2 2.0 31.2 - - - -
----------------------------------------------------------
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