Contacts of the strand formed by residues 212 - 221 (chain C) in PDB entry 1FVU
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 ASN 212 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C CYS* 4.2 0.4 - - - -
208C SER* 3.2 7.7 - - - -
209C TYR 2.9 28.4 + - - +
210C GLU* 3.6 13.7 + - - +
211C GLY* 1.3 83.8 - - - +
213C CYS* 1.3 66.2 + - - +
214C TYR* 3.5 21.6 + - + +
243C LYS* 5.9 2.0 - - - +
329C LYS* 4.0 23.7 - - + +
330C SER 3.6 6.6 - - - +
331C PRO* 3.6 21.5 - - - +
332C PRO* 4.3 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 213 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C CYS* 2.0 57.7 - - + -
203C PRO* 4.2 5.2 - - + -
206C TRP* 3.6 14.2 - - + -
207C SER 3.4 0.7 - - - -
212C ASN* 1.3 73.2 - - - +
214C TYR* 1.3 64.5 + - - +
329C LYS* 3.3 5.2 - - - +
330C SER* 2.8 47.7 + - - +
331C PRO 4.4 0.4 - - - -
332C PRO* 3.8 26.5 - - - -
333C PRO* 4.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 214 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C GLY 4.4 0.2 - - - +
206C TRP* 3.2 7.1 - - - -
207C SER* 2.7 48.1 + - - +
209C TYR* 3.5 36.1 + + + -
212C ASN* 3.5 23.7 + - + +
213C CYS* 1.3 77.2 - - - +
215C LYS* 1.3 61.1 + - - +
240C VAL* 3.8 22.0 - - + -
248C GLU* 2.5 29.8 + - - -
251C PHE* 3.5 15.0 - + - -
252C VAL* 4.0 13.7 - - + -
255C LEU* 3.6 21.1 - - + +
327C VAL* 4.8 2.7 - - + -
328C CYS 3.4 6.7 - - - +
329C LYS* 3.4 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 215 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C SER 5.2 1.8 + - - -
205C GLY* 3.7 20.7 - - - +
206C TRP* 3.4 40.5 - - + +
214C TYR* 1.3 77.0 - - - +
216C PHE* 1.3 74.0 + - - +
217C PHE* 3.4 44.1 - - + +
233C GLN* 5.4 1.2 + - - -
255C LEU* 4.3 4.2 - - - +
327C VAL* 3.4 5.3 - - - -
328C CYS 2.9 35.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 216 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C LYS* 1.3 89.0 - - - +
217C PHE* 1.3 65.8 + - - +
218C GLN* 3.6 22.3 + - + -
255C LEU* 4.0 26.2 - - + +
256C VAL* 3.8 32.8 - - + -
259C ASN* 3.7 24.2 - - + +
260C ILE* 3.5 42.8 - - + -
267C ALA* 4.3 3.6 - - + -
325C PRO* 3.7 23.3 - - + -
326C PHE 3.5 15.0 - - - -
327C VAL* 3.9 8.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 217 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C TRP* 4.0 12.8 - + - -
215C LYS* 3.4 60.8 - - + -
216C PHE* 1.3 77.0 - - - +
218C GLN* 1.3 62.9 + - - +
219C GLN* 3.3 18.2 + - - +
229C PHE* 3.4 28.7 - + - -
233C GLN* 4.0 12.3 - - + -
325C PRO* 3.2 4.2 - - - +
326C PHE* 2.7 52.3 + + + +
328C CYS* 3.6 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 218 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C PHE* 3.6 11.1 + - + -
217C PHE* 1.3 69.2 - - - +
219C GLN* 1.3 68.4 + - + +
220C LYS* 3.4 6.9 + - - +
259C ASN 3.5 6.3 - - - +
260C ILE* 3.4 8.9 - - - +
261C GLN* 2.9 53.2 + - + +
264C ASP* 2.5 30.9 + - - -
325C PRO* 3.5 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 219 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C PHE* 3.3 16.1 - - + +
218C GLN* 1.3 82.7 - - + +
220C LYS* 1.3 62.0 + - - +
221C MET* 4.9 8.2 - - + +
229C PHE* 3.2 40.6 - - - -
325C PRO* 3.2 14.0 - - - +
326C PHE* 3.3 20.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 220 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LYS* 5.4 7.9 - - - +
63A SER* 5.9 0.8 + - - -
218C GLN* 4.1 6.1 - - - +
219C GLN* 1.3 73.9 - - - +
221C MET* 1.3 65.9 + - - +
261C GLN* 6.2 0.2 - - - +
264C ASP* 3.2 32.6 + - - -
323C LYS* 3.7 37.6 + - + +
324C ASN* 3.5 6.3 - - - -
325C PRO* 3.9 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 221 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C GLN* 3.8 10.7 + - + +
220C LYS* 1.3 81.4 - - - +
222C ASN* 1.3 67.8 + - - +
225C ASP* 3.7 31.2 - - + +
226C ALA* 4.1 4.7 - - - +
228C ARG* 5.4 3.1 - - - +
229C PHE* 3.9 37.0 - - + -
268C TRP* 2.8 22.7 + - - -
323C LYS* 3.6 10.8 - - - +
324C ASN 3.1 12.5 + - - +
326C PHE* 4.0 19.3 - - + -
----------------------------------------------------------
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