Contacts of the strand formed by residues 187 - 195 (chain A) in PDB entry 1ML3
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 THR 187 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A VAL* 4.0 5.7 - - - +
186A GLN* 1.3 94.2 + - + +
188A GLY* 1.3 59.3 + - - +
242A LYS* 3.3 14.1 - - + +
262A PHE* 3.3 4.3 - - - +
263A THR* 3.1 35.9 + - - +
320B LEU* 4.0 13.0 - - + -
323B GLU* 3.9 20.9 - - - +
326B PHE* 3.5 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A THR* 1.3 77.8 - - - +
189A LEU* 1.3 73.6 + - - +
242A LYS 2.8 9.9 + - - +
243A LEU* 3.5 19.5 - - - +
244A THR 3.4 16.4 + - - -
260A LEU* 4.8 3.4 - - - -
261A THR 3.3 9.6 - - - -
262A PHE* 3.9 5.8 - - - -
320B LEU* 4.2 1.9 - - - +
326B PHE* 3.8 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A GLY* 1.3 76.8 - - - +
190A MET* 1.3 58.7 + - - +
244A THR* 3.3 36.3 - - + +
245A GLY* 5.0 1.3 - - - -
259A ASP 3.9 0.9 - - - +
260A LEU* 4.1 1.7 - - - +
261A THR* 2.7 44.5 + - - +
261B THR* 4.3 7.0 - - + +
318B ASN 4.2 7.4 - - - +
319B ASN* 4.1 4.0 - - - +
320B LEU* 4.1 11.0 - - + +
326B PHE* 3.4 28.9 - - + +
327B PHE* 3.7 18.6 - - - +
328B LYS* 3.4 42.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A THR* 3.7 30.5 - - + -
171A LEU* 4.1 25.6 - - + -
189A LEU* 1.3 75.9 - - - +
191A THR* 1.3 65.9 + - - +
192A THR* 3.7 10.5 - - + -
226A THR* 4.0 16.6 - - + -
228A ALA* 4.4 5.2 - - + -
229A ALA* 3.8 24.2 - - + +
244A THR 3.0 8.1 + - - +
245A GLY* 2.9 25.0 - - - -
246A MET 2.9 29.5 + - - +
258A VAL* 4.7 11.2 - - + -
259A ASP 3.4 7.6 - - - +
260A LEU* 4.1 16.2 - - + -
328B LYS* 4.4 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A MET* 1.3 74.6 + - - +
192A THR* 1.3 62.4 + - - +
193A ILE* 4.1 15.7 + - + -
246A MET* 3.5 6.8 - - + +
248A PHE* 3.4 28.9 - - + -
257A VAL 3.9 0.3 - - - +
258A VAL* 3.9 0.9 - - - +
259A ASP* 2.7 46.4 + - + +
193B ILE* 5.0 1.3 - - + -
259B ASP* 2.7 30.2 + - - +
328B LYS* 2.8 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A THR* 4.5 5.8 - - + +
190A MET* 3.7 17.5 - - + -
191A THR* 1.3 76.4 - - - +
193A ILE* 1.3 62.3 + - - +
194A HIS* 3.1 13.4 + - + -
226A THR* 5.2 1.3 - - + +
246A MET 3.1 17.6 + - - +
247A SER* 3.3 19.5 - - - +
248A PHE 2.8 27.8 + - - -
257A VAL 3.2 13.0 + - - -
258A VAL* 4.9 2.5 - - - -
333A TYR* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A THR* 4.1 21.8 - - + +
192A THR* 1.3 71.4 - - - +
194A HIS* 1.3 58.7 + - - +
248A PHE* 3.5 6.3 - - + -
250A VAL* 3.6 22.4 - - + -
256A SER* 3.2 5.5 - - - -
257A VAL* 3.1 41.9 + - + +
259A ASP* 4.6 5.2 - - + +
191B THR* 4.9 0.4 - - + -
193B ILE* 4.0 23.8 - - + -
221B ILE* 3.3 33.8 - - + +
248B PHE* 4.1 30.7 - - + -
250B VAL* 4.2 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A CYS* 4.2 14.1 - - - -
167A THR* 3.8 11.6 + - - -
192A THR* 3.1 7.1 + - + +
193A ILE* 1.3 73.0 - - - +
195A SER* 1.3 83.3 + - - +
197A THR* 3.8 10.8 - - + -
247A SER* 3.5 23.6 - - - +
248A PHE 2.7 9.8 + - - +
249A ARG* 2.7 34.2 + - - -
250A VAL* 2.7 34.8 + - - -
255A VAL 4.8 0.2 - - - -
256A SER* 3.3 10.2 + - - -
333A TYR* 3.3 25.8 + - - -
335A ASN* 4.2 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A HIS* 1.3 93.1 + - - +
196A TYR* 1.3 68.3 + - - +
249A ARG* 3.2 4.9 + - - -
250A VAL 3.9 1.1 - - - -
252A THR* 2.9 32.8 + - - -
253A PRO 4.2 0.2 - - - -
254A ASP* 2.9 24.8 - - - -
255A VAL 2.4 28.4 + - - -
256A SER* 3.2 10.1 + - - -
335A ASN* 4.3 5.4 - - - -
----------------------------------------------------------
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