Contacts of the strand formed by residues 297 - 305 (chain C) in PDB entry 6C3P
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 THR 297 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ILE* 3.7 33.0 - - + +
290B VAL* 4.1 25.9 - - + +
291B VAL 5.0 0.3 - - - +
292B GLU 4.5 9.7 - - - +
295B GLY* 4.2 9.7 + - - -
174C ALA* 4.4 8.8 - - - +
288C GLU* 5.0 1.1 - - + -
289C GLY 3.1 23.8 - - - +
290C VAL* 3.5 17.8 - - - +
295C GLY 4.7 0.7 + - - -
296C ILE* 1.3 78.4 - - - +
298C THR* 1.3 63.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 298 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ILE* 4.8 2.9 - - - -
174C ALA* 4.3 14.2 - - - +
175C HIS* 4.0 9.8 + - - +
177C ARG* 5.0 3.6 - - + -
178C ALA* 3.3 31.2 - - + +
181C LEU* 4.9 11.0 - - + -
210C ILE* 4.1 11.9 - - + -
287C LEU 3.9 0.3 - - - +
288C GLU* 3.5 3.5 - - - -
289C GLY 3.0 28.6 + - - +
291C VAL* 4.0 20.9 - - + -
296C ILE 4.2 0.2 + - - -
297C THR* 1.3 78.2 - - - +
299C GLN* 1.3 67.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 299 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B MET* 3.9 8.2 - - - +
210B ILE 3.8 9.9 - - - +
211B ILE* 3.4 27.1 - - + +
250B PHE* 3.3 19.3 - - - -
292B GLU* 6.4 0.6 - - + +
175C HIS* 5.8 0.5 - - - +
178C ALA* 3.8 11.6 - - - +
286C ILE* 3.3 22.2 - - - +
287C LEU 3.2 11.9 - - - +
288C GLU* 3.2 21.6 + - + +
298C THR* 1.3 82.3 + - - +
300C ALA* 1.3 61.8 + - - +
301C ARG* 2.5 51.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 300 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C ALA* 3.8 23.3 - - + +
181C LEU* 4.2 20.9 - - + +
183C PHE* 4.1 23.7 - - + -
285C VAL 4.0 0.5 - - - +
286C ILE* 3.9 0.2 - - - -
287C LEU* 3.0 33.0 + - + +
299C GLN* 1.3 75.2 - - - +
301C ARG* 1.3 68.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 301 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B MET* 4.8 11.7 - - - +
211B ILE* 6.1 0.2 - - - +
250B PHE* 3.9 21.9 - - + -
292B GLU* 3.9 23.4 + - - +
36C VAL* 3.9 12.6 - - + -
38C LYS 4.8 0.2 - - - +
39C LYS* 3.9 3.5 - - - -
40C GLY* 3.3 52.3 + - - -
42C CYS* 4.8 10.5 - - - -
183C PHE* 4.8 4.5 - - - -
284C ILE* 5.3 1.6 - - + -
285C VAL 3.6 4.0 - - - +
286C ILE* 4.3 6.7 - - + -
299C GLN* 2.5 71.3 + - - +
300C ALA* 1.3 77.2 - - - +
302C THR* 1.3 63.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 302 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C VAL* 5.0 2.0 - - - -
37C SER 4.4 7.2 - - - -
38C LYS* 4.0 18.3 + - - -
183C PHE* 3.5 47.4 + - + +
284C ILE* 4.0 2.1 - - - +
285C VAL* 2.8 49.7 + - + +
301C ARG* 1.3 76.7 - - - +
303C SER* 1.3 70.1 + - - +
304C TYR* 4.2 14.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 303 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ARG* 2.3 40.0 + - - -
36C VAL* 2.4 26.6 + - - -
37C SER 4.0 3.3 + - - -
38C LYS* 3.2 14.4 - - - +
282C GLU* 3.1 22.1 + - - -
283C ILE 3.8 5.2 - - - -
284C ILE* 3.8 13.7 - - - -
302C THR* 1.3 78.2 + - - +
304C TYR* 1.3 67.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 304 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LYS* 4.0 5.6 - - - -
183C PHE* 3.7 9.5 - - - +
184C SER* 2.1 44.7 + - - -
185C LYS 3.5 17.0 - - - -
186C HIS 3.7 10.1 - - - -
187C ALA* 4.2 15.0 - - + -
198C PHE* 5.1 6.5 - + + -
200C LEU* 3.5 29.5 - - + +
282C GLU* 3.2 4.0 - - - -
283C ILE* 2.9 32.2 + - + +
285C VAL* 4.3 10.8 - - + -
302C THR* 4.2 18.3 + - + -
303C SER* 1.3 75.6 - - - +
305C LEU* 1.3 62.1 + - - +
308C GLU* 3.2 26.7 - - + +
309C ILE* 4.1 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 305 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ARG* 3.9 12.3 - - + +
33C ALA 5.7 1.6 - - - +
34C ARG* 3.1 46.3 - - + +
277C HIS* 3.4 44.0 - - + +
281C LEU 3.3 18.6 - - - +
282C GLU* 4.0 8.7 - - + +
304C TYR* 1.3 76.6 - - - +
306C ALA* 1.3 75.8 + - - +
307C ASP* 3.1 30.2 + - - +
308C GLU* 3.4 11.5 + - - +
309C ILE* 3.3 14.8 + - - +
----------------------------------------------------------
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