Contacts of the strand formed by residues 191 - 196 (chain N) in PDB entry 1MMJ
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 PRO 191 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14N SER* 5.3 0.7 - - - +
15N GLN* 3.4 24.0 - - - +
32N GLY 4.0 7.4 - - - +
33N THR* 3.4 23.8 - - + +
128N TYR 4.1 0.3 - - - +
129N ILE* 3.7 10.4 - - - +
130N THR* 3.5 27.3 + - - +
190N GLY* 1.4 86.1 - - - +
192N LEU* 1.3 59.5 + - - +
193N HIS* 3.4 35.2 - - + +
202N VAL* 3.9 12.6 - - + -
204N GLY 3.6 6.3 - - - +
206N THR* 4.6 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127N CYS* 3.9 13.7 - - + -
128N TYR 3.7 19.5 - - - +
129N ILE* 4.1 4.7 - - + +
150N LEU* 4.4 4.7 - - + +
152N THR* 4.8 0.2 - - + -
173N VAL* 4.3 18.4 - - + -
175N ALA* 4.1 24.9 - - + -
191N PRO* 1.3 74.8 - - - +
193N HIS* 1.3 58.5 + - - +
194N CYS* 3.7 24.3 + - - -
201N ALA 3.6 0.2 - - - +
202N VAL* 3.4 3.0 - - - -
203N HIS* 2.9 29.5 + - + -
204N GLY* 3.1 21.7 + - - +
223N PHE* 3.8 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 193 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12N TRP* 3.4 49.6 - + + -
14N SER* 4.4 13.5 - - - -
15N GLN 5.5 0.7 - - - -
127N CYS* 3.0 1.7 - - - -
128N TYR* 2.7 51.5 + - + +
130N THR* 2.9 37.0 + - + +
191N PRO* 3.4 24.5 - - + +
192N LEU* 1.3 70.3 - - - +
194N CYS* 1.3 62.7 + - - +
200N TYR* 3.8 14.1 - - + +
201N ALA 3.5 7.6 - - - -
202N VAL* 4.3 8.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 194 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121N LEU* 3.5 21.1 - - + -
125N SER* 5.4 0.9 - - - -
126N PRO 3.3 3.8 - - - +
127N CYS* 2.0 46.2 - - - -
192N LEU* 3.8 15.7 - - - -
193N HIS* 1.3 75.8 - - - +
195N LEU* 1.3 63.9 + - - +
196N VAL* 3.5 7.6 + - + +
199N GLN 3.3 0.9 - - - +
200N TYR* 3.2 5.5 - - - -
201N ALA 2.8 35.6 + - - +
203N HIS* 3.7 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125N SER* 5.5 2.1 + - - -
126N PRO* 2.9 42.4 + - + +
194N CYS* 1.3 71.1 - - - +
196N VAL* 1.3 68.1 + - - +
198N GLY* 3.6 40.2 - - - +
199N GLN 3.6 10.8 - - - +
200N TYR* 3.6 37.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 196 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119N THR* 5.9 5.4 - - + -
121N LEU* 4.6 9.2 - - + -
125N SER* 6.2 0.2 - - - +
194N CYS* 3.9 14.8 - - + +
195N LEU* 1.3 80.5 - - - +
197N ASN* 1.3 75.0 - - + +
198N GLY 3.4 0.2 - - - -
199N GLN* 2.9 36.8 + - - +
201N ALA* 5.3 4.3 - - + -
203N HIS* 3.7 30.3 - - + +
----------------------------------------------------------
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