Contacts of the strand formed by residues 210 - 220 (chain C) in PDB entry 1YA8
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 GLY 210 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C ASN 3.6 0.2 + - - -
132C ARG* 3.9 6.8 - - - +
133C LEU 3.3 6.7 - - - -
135C VAL* 3.8 12.6 - - - -
164C VAL* 4.1 5.6 - - - -
205C ILE* 3.1 18.3 + - - -
206C ALA* 3.0 23.4 + - - +
208C PHE 3.4 1.0 + - - -
209C GLY* 1.3 81.7 - - - +
211C ASN* 1.3 60.2 + - - -
212C PRO* 3.2 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 211 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C ARG* 3.2 36.8 + - + +
133C LEU 2.7 13.8 + - - +
134C PRO* 5.0 0.2 - - + -
135C VAL* 3.7 6.5 - - - +
205C ILE* 4.1 2.0 - - - -
210C GLY* 1.3 70.6 - - - -
212C PRO* 1.3 62.6 - - - +
213C GLY* 2.9 22.8 + - - -
214C SER* 2.9 47.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 212 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C ARG* 4.8 4.3 - - + -
202C GLN* 3.2 57.2 + - - +
205C ILE* 3.6 15.9 - - + -
206C ALA* 4.1 14.4 - - + -
210C GLY 3.2 11.6 - - - +
211C ASN* 1.3 85.8 - - - +
213C GLY* 1.3 55.7 + - - +
214C SER 3.3 0.4 - - - -
215C VAL* 4.1 7.3 - - + +
241C HIS* 3.3 8.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 213 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C ASN* 2.9 16.4 + - - -
212C PRO* 1.3 78.7 - - - +
214C SER* 1.3 60.1 + - - +
241C HIS* 3.0 28.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
134C PRO* 3.8 11.0 - - - +
135C VAL 3.1 22.7 + - - +
211C ASN* 2.9 29.3 + - - +
213C GLY* 1.3 80.3 - - - +
215C VAL* 1.3 59.7 + - - +
216C THR* 3.9 3.4 + - - -
241C HIS* 3.4 6.3 - - - -
242C ARG* 4.0 14.4 + - - -
504C ALA 3.5 17.8 + - - +
505C ARG* 4.4 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 215 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C VAL* 3.4 24.9 - - + +
137C VAL* 3.6 28.3 - - + -
198C LEU* 4.7 2.2 - - + -
201C VAL* 3.9 15.0 - - + -
202C GLN* 3.8 17.7 - - - +
211C ASN 4.1 6.1 - - - +
212C PRO* 4.1 4.3 - - + +
214C SER* 1.3 74.2 - - - +
216C THR* 1.3 65.7 + - - +
217C ILE* 4.6 3.1 - - + -
239C LEU 4.0 20.2 - - - +
240C PHE* 3.5 4.4 - - + -
241C HIS* 2.8 41.7 + - + -
242C ARG* 3.6 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 216 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C VAL 2.7 14.4 + - - -
136C MET* 3.4 9.9 - - + -
137C VAL* 2.8 29.5 + - - +
214C SER 4.5 1.0 + - - -
215C VAL* 1.3 75.5 - - - +
217C ILE* 1.3 70.0 + - - +
218C PHE* 4.1 1.5 + - + -
242C ARG* 3.3 31.1 - - + +
243C ALA 4.4 0.9 - - - +
244C ILE* 4.6 9.9 - - + -
503C PHE* 4.5 10.5 - - + -
504C ALA* 3.2 42.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 217 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C VAL* 3.4 13.9 - - + +
139C ILE* 5.1 5.6 - - + -
198C LEU* 3.6 32.3 - - + -
215C VAL* 4.3 1.1 - - + -
216C THR* 1.3 77.9 - - - +
218C PHE* 1.3 61.0 + - - +
227C VAL* 3.7 24.5 - - + +
230C LEU* 3.8 31.4 - - + -
240C PHE* 3.8 35.9 - - + -
242C ARG 3.0 12.6 + - - +
243C ALA* 3.2 4.7 - - + -
244C ILE 2.8 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 218 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C MET* 3.7 44.9 - - + -
137C VAL 3.1 27.6 + - - -
138C TRP* 3.1 47.8 - + + -
139C ILE* 3.0 20.1 + - - +
157C LEU* 4.4 9.4 - - + -
165C VAL* 5.3 1.8 - - + -
216C THR* 4.2 4.3 - - + -
217C ILE* 1.3 74.7 - - - +
219C GLY* 1.3 59.3 + - - +
227C VAL* 3.7 4.7 - - - -
244C ILE* 3.1 35.4 - - + -
246C GLU* 3.7 8.7 - - - +
475C VAL* 4.0 13.5 - - + -
476C PHE* 3.9 13.9 - + - -
500C TRP* 4.1 9.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 219 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C TRP* 3.7 10.0 - - - -
139C ILE 3.1 16.8 - - - -
218C PHE* 1.3 75.8 - - - +
220C GLU* 1.3 59.9 + - - -
223C GLY 3.5 9.9 - - - -
224C GLY* 3.5 9.1 - - - -
227C VAL* 3.4 4.0 - - - +
244C ILE 3.2 5.7 + - - -
246C GLU* 3.1 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 220 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C PHE* 3.5 24.4 - - - -
138C TRP* 3.5 22.9 - - + -
139C ILE 3.5 5.9 + - - -
141C GLY* 3.2 15.5 + - - +
152C TYR* 5.2 0.7 + - - -
219C GLY* 1.3 74.2 - - - +
221C SER* 1.3 75.4 + - - +
222C ALA 3.0 1.7 + - - -
223C GLY 2.6 23.6 + - - -
224C GLY 3.2 2.6 - - - +
246C GLU* 3.3 8.7 - - + +
247C SER* 4.0 2.9 - - - -
468C HIS* 3.2 31.6 + - - -
469C GLY* 3.8 17.0 + - - -
471C GLU* 3.1 26.4 - - - +
472C LEU* 3.9 7.9 - - + +
----------------------------------------------------------
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