Contacts of the helix formed by residues 191 - 195 (chain D) in PDB entry 3KYM
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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D SER 3.4 20.6 - - - +
141D THR* 3.7 4.9 - - - -
189D THR 4.4 4.3 - - - +
190D VAL* 1.4 86.1 - - - +
192D SER* 1.3 68.8 + - - +
193D SER* 3.4 5.2 - - - +
194D ASN* 2.7 41.9 + - - +
79M GLN* 6.4 0.4 - - + -
80M SER* 5.0 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 192 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D THR* 3.3 34.9 + - - -
138D SER 3.7 2.5 + - - -
139D GLU 3.9 0.5 + - - -
140D SER* 3.5 27.8 + - - -
141D THR* 3.9 4.8 + - - +
142D ALA* 4.5 4.8 - - - +
190D VAL* 3.7 1.2 + - - +
191D PRO* 1.3 71.9 - - - +
193D SER* 1.3 55.2 + - - +
194D ASN* 2.8 13.5 + - - +
195D PHE* 3.1 40.1 + - - -
211K ARG* 4.6 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 193 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D PRO* 3.3 4.9 + - - +
192D SER* 1.3 72.2 - - - +
194D ASN* 1.3 60.1 + - - +
195D PHE 2.8 17.0 + - - -
197D THR* 4.5 4.2 - - - +
211K ARG* 3.2 33.9 + - - -
15M PRO* 5.3 1.4 - - - +
16M GLY* 4.4 22.7 + - - -
77M SER* 4.4 11.7 + - - -
78M LEU 5.2 1.7 + - - -
79M GLN* 5.6 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 194 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D VAL* 3.4 17.2 - - + +
191D PRO* 2.7 47.7 + - - +
192D SER 2.8 5.1 + - - +
193D SER* 1.3 76.6 + - - +
195D PHE* 1.3 66.2 + - - +
197D THR* 3.3 16.3 - - - +
198D GLN* 3.9 8.9 + - + +
200D TYR* 4.0 19.4 + - - +
219D ARG* 5.4 0.8 + - - -
78M LEU 5.1 0.7 - - - +
79M GLN* 3.5 45.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 195 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D PRO* 6.3 3.1 - - + -
136D SER 3.9 5.2 - - - -
137D THR* 3.8 22.0 - - - -
142D ALA* 4.3 20.6 - - + -
144D LEU* 6.3 0.2 - - + -
190D VAL* 5.8 2.9 - - + -
191D PRO 5.6 0.2 - - - -
192D SER* 3.1 29.3 + - - -
193D SER 2.8 5.1 + - - -
194D ASN* 1.3 77.5 - - - +
196D GLY* 1.3 57.3 + - - +
197D THR* 2.7 18.1 + - - -
198D GLN 3.7 12.0 - - - +
219D ARG* 3.1 43.6 + - - +
220D LYS* 3.6 20.4 - - + +
210K ASN 3.4 10.8 - - - +
211K ARG* 3.2 41.1 - - + -
----------------------------------------------------------
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