Contacts of the helix formed by residues 303 - 315 (chain K) in PDB entry 1XFB
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 303 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K ALA* 3.5 21.7 - - - +
35K GLU* 4.8 1.6 - - - -
43K ARG* 4.2 5.4 - - - -
272K SER* 3.6 6.4 + - - -
301K SER 4.1 1.2 + - - -
302K TYR* 1.3 74.9 - - - +
304K ARG* 1.3 65.4 + - - +
305K ALA 3.3 0.2 - - - -
306K LEU* 3.4 5.9 + - - +
307K GLN* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 304 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43K ARG* 2.8 68.0 - - - +
46K GLN* 2.6 35.2 - - - +
272K SER* 4.0 5.2 + - - +
273K GLY 5.4 5.6 - - - +
275K GLN 5.7 4.7 - - - +
303K GLY* 1.3 69.3 - - - +
305K ALA* 1.3 53.6 + - - +
306K LEU 2.7 17.1 + - - -
307K GLN* 2.8 3.3 + - + -
308K ALA* 2.8 47.3 + - + +
311K LEU* 5.3 5.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 305 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272K SER* 3.2 32.0 + - - -
275K GLN 4.8 4.6 + - - +
276K SER 4.6 2.0 - - - +
277K GLU* 3.5 29.4 - - - +
280K ALA* 3.8 13.5 - - + -
302K TYR* 3.4 17.7 - - + -
303K GLY 3.3 0.4 - - - -
304K ARG* 1.3 77.5 - - - +
306K LEU* 1.3 57.2 + - - +
331K ARG* 3.6 15.4 + - - +
335K ASN* 4.0 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K ILE 3.7 15.7 - - - +
31K LEU* 3.7 32.5 - - + -
74K ILE* 4.7 2.5 - - + -
277K GLU* 4.0 6.7 - - - +
300K PHE* 3.8 15.0 - - + -
302K TYR* 3.7 22.9 - - + +
303K GLY 3.4 8.4 + - - +
304K ARG 2.7 5.5 + - - -
305K ALA* 1.3 75.4 - - - +
307K GLN* 1.3 58.5 + - - +
308K ALA 3.7 0.7 - - - -
310K ALA* 4.4 0.7 - - - +
328K PHE* 3.6 31.2 - - + -
331K ARG* 3.7 6.5 - - + +
332K ALA* 3.6 38.4 - - + +
335K ASN* 3.7 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 307 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31K LEU* 3.8 16.1 - - + +
32K ALA 3.3 15.0 + - - -
33K ALA* 4.2 1.2 - - - +
35K GLU* 3.3 27.8 + - - +
40K MET* 5.6 0.2 - - - +
43K ARG* 4.2 4.9 + - - +
59K TYR* 2.7 44.2 + - - +
60K ARG* 4.8 0.3 + - - -
63K LEU* 3.6 22.3 - - + +
303K GLY 2.9 21.8 + - - +
304K ARG* 2.8 6.6 + - + -
306K LEU* 1.3 80.9 - - + +
308K ALA* 1.3 59.7 + - - +
309K SER 3.6 1.1 - - - -
310K ALA* 3.8 8.1 - - + -
311K LEU* 2.8 33.5 + - + +
328K PHE* 5.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 308 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277K GLU* 3.3 20.4 + - + +
304K ARG* 2.8 38.7 + - + +
307K GLN* 1.3 73.4 - - - +
309K SER* 1.3 59.1 + - - +
311K LEU* 3.5 5.1 - - - +
312K ASN* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 309 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277K GLU* 2.8 26.7 + - - -
308K ALA* 1.3 78.3 - - - +
310K ALA* 1.3 59.2 + - - +
312K ASN* 3.4 8.9 - - - +
313K ALA* 2.8 31.7 + - - +
327K GLU* 3.1 26.9 - - - +
331K ARG* 4.0 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 310 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59K TYR* 4.8 2.7 - - + +
63K LEU* 4.6 6.5 - - + -
306K LEU 4.4 0.2 - - - +
307K GLN* 3.7 19.9 - - + +
308K ALA 3.1 0.2 - - - -
309K SER* 1.3 82.7 + - - +
311K LEU* 1.3 62.5 + - - +
313K ALA* 3.5 0.2 - - - +
314K TRP* 3.0 20.6 + - - +
324K ALA* 3.2 29.6 - - + +
327K GLU* 3.5 11.2 - - - -
328K PHE* 3.8 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 311 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40K MET* 4.9 0.7 - - + -
43K ARG* 4.0 40.2 - - + +
44K LEU* 4.4 5.2 - - + -
47K ILE* 3.6 39.3 - - + +
59K TYR* 3.3 48.4 + - + +
304K ARG* 5.3 5.6 - - + +
307K GLN* 2.8 21.6 + - + +
308K ALA* 3.5 5.2 - - - +
310K ALA* 1.3 76.2 - - - +
312K ASN* 1.3 62.4 + - - +
314K TRP* 3.8 5.9 - - + +
315K ARG 3.1 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 312 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47K ILE* 4.4 7.3 - - - +
308K ALA 2.9 17.4 + - - +
309K SER* 3.4 10.7 - - - +
311K LEU* 1.3 79.4 - - - +
313K ALA* 1.3 59.3 + - - +
315K ARG* 2.8 50.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 313 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309K SER 2.8 17.1 + - - +
310K ALA* 3.5 4.5 - - - +
311K LEU 3.2 0.2 - - - -
312K ASN* 1.3 76.5 - - - +
314K TRP* 1.3 69.3 + - - +
315K ARG* 3.2 3.5 + - - +
320K ASN* 3.3 19.8 - - - +
323K ALA* 4.4 10.8 - - + +
324K ALA* 3.8 18.4 - - - +
327K GLU* 4.7 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 314 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44K LEU* 3.8 20.0 - - + -
47K ILE* 3.7 15.9 - - + -
49K VAL* 4.1 11.7 - - + -
55K ASN* 3.5 22.4 - - + -
58K LEU* 4.0 16.9 + - + +
59K TYR* 3.6 39.3 - + + -
62K VAL* 3.9 23.3 - - + +
310K ALA 3.0 8.8 + - - +
311K LEU* 3.8 3.6 - - + +
313K ALA* 1.3 79.1 - - - +
315K ARG* 1.3 61.5 + - - +
316K GLY* 2.9 38.3 + - - -
317K GLN 2.9 37.7 + - - -
318K ARG* 4.8 2.2 - - - +
320K ASN* 3.3 15.2 - - - +
321K ALA* 4.2 9.5 - - - +
324K ALA* 3.5 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 315 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46K GLN 4.5 4.9 + - - -
47K ILE* 3.8 47.5 + - - +
49K VAL* 4.1 7.3 - - - +
311K LEU 3.1 13.9 + - - -
312K ASN* 2.8 41.4 + - - +
313K ALA 3.5 7.2 - - - +
314K TRP* 1.3 79.9 - - - +
316K GLY* 1.3 56.2 + - - +
317K GLN* 3.2 15.9 + - + +
320K ASN* 4.4 6.1 - - - +
----------------------------------------------------------
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