Contacts of the strand formed by residues 208 - 217 (chain B) in PDB entry 1MKM
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 208 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LYS* 3.3 21.5 - - - +
139B ILE* 3.5 27.2 - - + +
142B PHE* 3.4 29.6 - - + +
143B VAL* 3.5 33.0 - - + +
200B PRO* 5.0 3.1 - - + -
201B ILE 4.0 6.5 - - - +
202B PHE* 4.0 6.5 - - + -
206B GLY 4.4 0.4 - - - +
207B TYR* 1.3 97.2 - - + +
209B VAL* 1.3 60.5 + - - +
210B ALA 3.4 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ILE* 5.0 2.2 - - + -
100B LEU* 3.8 13.1 - - + +
101B LYS* 3.0 30.0 + - + +
201B ILE 3.3 12.2 + - - +
203B ASP* 3.8 27.1 - - + +
207B TYR* 3.0 23.3 + - + +
208B PRO* 1.3 71.7 - - - +
210B ALA* 1.3 66.4 + - + +
244B LEU* 3.5 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ILE* 3.3 33.2 - - + -
98B LEU* 4.4 3.8 - - + -
99B ILE 3.3 11.4 - - - +
100B LEU* 5.0 1.3 - - - -
101B LYS* 4.2 0.2 - - - +
139B ILE* 3.2 20.4 - - - +
200B PRO* 3.6 2.4 - - - +
201B ILE* 3.3 35.5 + - + -
208B PRO 3.4 1.5 + - - -
209B VAL* 1.3 83.8 + - + +
211B GLY* 1.3 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B HIS 3.8 0.2 - - - +
98B LEU* 3.1 5.9 - - - +
99B ILE* 2.6 48.1 + - - -
135B SER* 3.8 13.3 - - - -
139B ILE* 3.6 7.3 - - - +
199B VAL 3.9 6.5 - - - -
201B ILE* 5.1 0.2 - - - -
210B ALA* 1.3 76.7 - - - +
212B VAL* 1.3 62.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 4.6 10.5 - - + -
88B ILE* 5.6 2.7 - - + -
96B VAL* 5.7 0.2 - - + -
97B HIS 3.2 7.4 - - - +
98B LEU* 3.2 26.9 - - + -
135B SER* 4.2 1.3 - - - -
198B GLY* 3.3 0.9 - - - -
199B VAL* 3.1 40.7 + - + +
201B ILE* 3.8 20.0 - - + -
211B GLY* 1.3 72.6 - - - -
213B SER* 1.3 63.9 + - - +
233B LEU* 4.0 23.9 - - + +
236B LYS* 6.2 0.4 - - + -
237B ALA* 4.6 12.6 - - + +
240B ILE* 4.5 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B VAL* 3.4 7.3 - - - +
97B HIS* 2.9 43.5 + - - +
134B ALA* 4.7 0.2 - - - -
135B SER* 3.7 20.5 + - - -
197B VAL 3.0 19.3 - - - -
198B GLY* 3.8 5.6 - - - -
212B VAL* 1.3 76.7 - - - +
214B ILE* 1.3 62.6 + - - +
215B SER* 4.0 1.9 + - - -
233B LEU* 4.0 6.2 - - - +
401B ZN 3.6 20.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ILE* 3.9 17.7 - - + -
92B THR* 3.8 22.9 - - + +
94B GLU* 3.4 30.7 - - + -
95B THR 3.5 4.9 - - - +
96B VAL* 4.8 1.3 - - + -
196B CYS* 3.2 26.2 - - - +
197B VAL 2.9 12.0 + - - +
213B SER* 1.3 74.4 - - - +
215B SER* 1.3 66.0 + - - +
221B PHE* 4.0 5.6 - - + -
229B TYR* 3.4 57.2 - - + +
232B VAL* 5.3 0.2 - - + -
233B LEU* 3.9 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLU* 3.9 5.0 - - - +
95B THR* 2.8 31.3 + - - -
97B HIS* 3.0 35.8 - - - -
118B ILE* 3.7 10.7 - - - +
120B MET* 4.0 16.3 - - - -
194B ILE* 5.1 0.4 - - - -
195B MET 3.8 4.0 - - - -
196B CYS* 3.8 14.7 - - - -
213B SER* 4.0 5.4 + - - -
214B ILE* 1.3 79.5 + - - +
216B GLY* 1.3 58.9 + - - +
221B PHE* 4.0 3.4 - - - -
401B ZN 4.0 1.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLU* 4.1 9.4 - - - -
118B ILE* 4.0 17.2 - - - +
194B ILE* 3.4 11.7 - - - +
195B MET 3.1 27.7 + - - +
215B SER* 1.3 76.8 - - - +
217B VAL* 1.3 67.1 + - - -
221B PHE* 3.6 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLN* 5.4 4.2 + - - +
117B SER 5.4 1.1 - - - +
118B ILE* 4.3 9.1 - - + +
119B PRO* 3.7 29.8 - - + -
193B GLY* 3.3 14.4 - - - +
194B ILE* 4.6 0.7 - - - +
216B GLY* 1.3 73.7 - - - -
218B ALA* 1.3 71.4 + - + +
219B ARG* 3.2 27.6 + - + +
220B LYS* 3.2 23.4 + - + +
221B PHE* 3.3 10.6 - - - -
----------------------------------------------------------
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