Contacts of the helix formed by residues 210 - 215 (chain A) in PDB entry 1N54
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 HIS 210 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A GLN* 4.1 12.1 - - - -
206A ARG* 4.3 1.6 - - - -
207A GLN* 3.5 24.9 + - - +
208A LYS* 2.8 11.3 + - - -
209A THR* 1.3 73.1 + - - +
211A VAL* 1.3 86.2 + - + +
212A PRO* 3.2 0.2 - - - +
213A MET* 2.7 24.0 + - - +
214A LEU* 3.3 27.6 + - + -
227A GLU* 3.2 32.1 + - + +
285A PRO* 3.7 31.2 - - + +
287A VAL* 5.3 2.0 - - + -
784A GLN* 4.7 7.0 - - - +
787A ALA* 3.5 28.6 + - + +
788A LEU* 4.9 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LYS* 3.3 27.6 - - + +
210A HIS* 1.3 91.1 - - + +
212A PRO* 1.3 64.4 - - + +
214A LEU* 3.1 1.3 + - - +
215A GLN* 2.8 58.7 + - + +
225A GLN 4.6 7.2 - - - +
227A GLU* 4.0 19.3 - - + +
287A VAL* 4.2 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LYS 3.9 2.9 - - - +
209A THR 3.1 24.9 - - - +
210A HIS 2.7 1.1 - - - +
211A VAL* 1.3 89.5 - - + +
213A MET* 1.3 60.0 + - - +
214A LEU 3.3 0.7 + - - -
215A GLN* 3.0 25.3 + - - +
218A THR* 5.4 7.0 - - + +
406A ASN* 5.5 1.7 + - - -
748A GLN* 4.4 5.7 + - - +
784A GLN* 4.4 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A HIS* 2.7 15.3 + - - +
212A PRO* 1.3 76.5 - - - +
214A LEU* 1.3 58.2 + - + +
215A GLN 3.7 0.2 - - - -
362A LEU* 3.8 7.0 - - - +
748A GLN* 3.9 21.9 + - + -
751A PHE* 4.5 4.7 - - + -
752A LEU* 3.1 47.3 - - + +
781A VAL* 3.2 37.2 - - + +
784A GLN* 3.0 32.3 + - + +
785A PHE* 3.2 29.8 - - + +
788A LEU* 4.4 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A HIS* 3.4 43.1 - - + +
211A VAL 3.1 4.0 + - - +
213A MET* 1.3 84.4 - - + +
215A GLN* 1.3 65.2 + - - +
216A VAL* 3.8 3.3 + - - +
285A PRO* 3.8 22.7 - - + +
286A ARG* 5.8 0.2 - - - -
287A VAL* 3.7 31.8 + - + +
362A LEU* 3.6 43.4 + - + +
363A PRO* 4.3 6.1 - - + -
752A LEU* 4.8 5.8 - - + -
788A LEU* 4.1 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A VAL* 2.8 42.9 + - + +
212A PRO* 3.0 29.0 + - - +
214A LEU* 1.3 78.9 - - - +
216A VAL* 1.3 60.6 + - - +
217A TRP 3.2 24.2 + - - +
218A THR* 4.5 17.6 + - + +
220A ASP* 5.3 5.5 + - - -
225A GLN* 4.0 25.8 + - + +
287A VAL* 4.3 8.5 - - + -
362A LEU* 3.1 16.4 - - - +
406A ASN* 4.0 8.8 - - - +
----------------------------------------------------------
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