Contacts of the strand formed by residues 211 - 216 (chain C) in PDB entry 3Q3G
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 ILE 211 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C ALA* 4.6 8.5 - - + -
119C PRO* 3.5 45.8 - - + +
121C VAL* 3.8 27.2 - - + +
200C CYS 3.7 2.3 - - - +
201C GLU* 3.5 1.6 - - - -
202C ALA* 2.7 43.5 + - + +
204C HIS* 6.0 1.3 - - + -
206C THR* 5.5 1.1 - - - +
207C SER* 5.4 8.3 - - - -
209C SER 4.9 4.0 - - - +
210C PRO* 1.4 70.2 - - - +
212C VAL* 1.3 64.5 + - - +
213C LYS* 4.9 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 212 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C LYS* 6.4 0.7 - - + -
199C THR* 3.3 28.3 - - + +
200C CYS 3.8 2.5 - - - +
201C GLU* 3.6 29.6 - - + +
210C PRO* 3.4 15.3 + - + +
211C ILE* 1.3 75.7 - - - +
213C LYS* 1.3 71.8 - - - +
214C SER* 4.2 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 213 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C THR* 6.2 0.4 - - - +
121C VAL* 2.8 56.0 + - + +
122C SER* 4.4 3.2 + - - +
123C ILE* 3.7 25.3 - - + +
199C THR* 3.3 2.5 + - - -
200C CYS* 3.0 34.2 + - - +
211C ILE* 4.1 8.0 + - + -
212C VAL* 1.3 79.5 - - - +
214C SER* 1.3 61.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 214 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C ILE* 3.8 9.2 - - - +
197C SER* 3.1 19.8 + - - -
198C TYR 2.9 17.9 + - - -
199C THR* 3.4 15.6 - - - +
212C VAL* 4.2 6.2 + - - -
213C LYS* 1.3 75.8 - - - +
215C PHE* 1.3 63.7 + - - +
216C ASN* 4.8 1.7 + - - -
140D ALA 5.6 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 215 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C ILE* 3.7 27.8 - - + -
125C PRO* 3.7 37.2 - - + -
138C VAL* 3.3 28.5 - - + -
192C TYR* 3.2 36.3 - + - -
197C SER* 3.4 2.9 + - - -
198C TYR* 2.8 61.5 + + + +
214C SER* 1.3 76.2 + - - +
216C ASN* 1.3 76.6 + - - +
217C ARG* 4.1 7.6 - - - -
219C GLU* 5.3 2.2 - - - -
138D GLY* 5.4 7.9 - - - -
224D ARG* 5.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 216 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C ASN* 3.2 28.1 - - - +
197C SER* 3.5 25.9 + - - -
214C SER* 4.8 1.4 + - - -
215C PHE* 1.3 84.0 + - - +
217C ARG* 1.3 65.4 + - - +
218C ASN 4.6 1.6 - - - +
219C GLU* 3.3 52.5 + - + +
----------------------------------------------------------
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