Contacts of the helix formed by residues 276 - 289 (chain I) 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 SER 276 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274I GLY 3.8 0.8 + - - -
275I GLN* 1.3 75.7 - - - +
277I GLU* 1.3 68.0 + - - +
278I GLU* 3.0 6.1 + - - +
279I GLU* 3.0 32.6 + - - +
280I ALA* 2.9 21.1 + - - +
305I ALA* 4.9 1.1 - - - -
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Residues in contact with GLU 277 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276I SER* 1.3 73.9 - - - +
278I GLU* 1.3 61.8 + - + +
280I ALA* 3.8 3.1 + - - +
281I SER* 2.9 13.5 + - - -
305I ALA* 3.5 24.4 - - - +
306I LEU 4.0 2.4 - - - -
308I ALA* 3.3 25.6 + - + +
309I SER* 2.8 49.7 + - - -
331I ARG* 2.8 52.9 + - - +
335I ASN* 4.9 0.2 + - - -
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Residues in contact with GLU 278 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276I SER* 3.1 5.2 + - - +
277I GLU* 1.3 77.6 - - + +
279I GLU* 1.3 57.9 + - - +
280I ALA 3.1 1.8 - - - -
281I SER* 2.9 3.9 + - - -
282I PHE* 2.7 74.9 + - + -
331I ARG* 2.5 35.0 + - - -
343I TYR* 3.1 13.3 + - - -
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Residues in contact with GLU 279 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274I GLY 4.7 1.2 - - - +
275I GLN* 3.5 26.7 - - - +
276I SER* 3.0 36.1 + - - +
278I GLU* 1.3 76.0 - - - +
280I ALA* 1.3 56.9 + - - +
282I PHE* 3.9 5.3 - - - +
283I ASN* 3.0 44.7 + - - +
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Residues in contact with ALA 280 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272I SER* 4.4 2.7 - - - -
275I GLN* 3.6 20.1 + - + +
276I SER 2.9 15.7 + - - +
277I GLU 3.9 1.8 - - - +
279I GLU* 1.3 77.8 - - - +
281I SER* 1.3 57.4 + - - +
283I ASN* 3.9 1.0 - - - +
284I LEU* 2.8 26.5 + - - +
302I TYR* 3.1 40.7 + - + -
305I ALA* 3.8 14.6 - - + -
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Residues in contact with SER 281 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277I GLU 2.9 14.9 + - - -
278I GLU* 2.9 8.2 + - - -
280I ALA* 1.3 78.6 - - - +
282I PHE* 1.3 57.4 + - - +
285I ASN* 2.9 31.8 + - - +
331I ARG* 3.0 17.6 + - - -
334I VAL* 3.7 19.5 - - - +
335I ASN* 2.7 26.6 + - - -
338I ALA* 3.3 8.0 - - - +
343I TYR* 4.4 8.5 - - - -
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Residues in contact with PHE 282 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246I PRO* 4.5 16.2 - - + +
278I GLU* 2.7 54.4 + - + +
279I GLU* 3.9 5.8 - - - +
281I SER* 1.3 71.6 - - - +
283I ASN* 1.3 62.3 + - - +
285I ASN* 3.2 7.6 + - - +
286I ALA* 2.8 30.3 + - - +
343I TYR* 3.8 22.2 - + - -
344I GLU 6.0 3.6 - - - -
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Residues in contact with ASN 283 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233I MET* 3.7 20.0 - - - +
235I THR* 5.2 1.0 - - - +
246I PRO* 3.1 33.7 - - - +
249I ILE* 3.8 30.0 - - + +
250I ALA* 4.6 0.5 - - - +
275I GLN* 2.7 21.3 - - - +
279I GLU* 3.0 27.3 + - - +
280I ALA 3.9 0.7 - - - +
282I PHE* 1.3 77.3 - - - +
284I LEU* 1.3 64.5 + - - +
286I ALA* 3.2 6.4 + - - +
287I ILE* 2.9 29.4 + - - +
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Residues in contact with LEU 284 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233I MET* 4.1 5.5 - - + +
270I PHE* 4.2 14.1 - - + -
280I ALA 2.8 21.6 + - - +
281I SER 3.8 3.8 - - - +
283I ASN* 1.3 73.3 - - - +
285I ASN* 1.3 64.4 + - - +
287I ILE* 3.1 8.3 + - + +
288I ASN* 3.0 22.4 + - - +
298I LEU 3.3 26.0 - - - +
299I THR 3.8 12.8 - - - +
300I PHE* 3.7 41.5 - - + -
302I TYR* 3.5 8.7 - - + +
335I ASN* 4.0 14.4 - - - +
338I ALA* 3.7 13.0 - - + +
339I ALA* 4.1 3.4 - - - +
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Residues in contact with ASN 285 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281I SER 2.9 18.3 + - - +
282I PHE* 3.4 7.6 - - - +
284I LEU* 1.3 74.8 - - - +
286I ALA* 1.3 64.7 + - - +
288I ASN* 2.9 14.7 + - - +
289I ARG* 3.0 44.6 + - - +
338I ALA* 3.2 15.4 - - + +
341I GLY* 3.0 14.2 + - - -
343I TYR* 2.9 53.7 + - + +
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Residues in contact with ALA 286 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246I PRO* 3.2 38.8 - - + +
247I GLU* 4.1 13.7 - - - +
250I ALA* 3.5 7.5 - - + +
282I PHE 2.8 16.1 + - - +
283I ASN 3.4 7.4 - - - +
285I ASN* 1.3 73.8 - - - +
287I ILE* 1.3 58.1 + - - +
289I ARG* 2.9 26.1 + - - +
290I CYS* 3.0 10.7 + - - -
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Residues in contact with ILE 287 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233I MET* 4.0 23.3 - - + -
249I ILE* 5.5 1.1 - - + -
250I ALA* 3.4 26.4 - - - +
253I THR* 3.8 14.1 - - + +
254I VAL* 3.8 10.1 - - + +
270I PHE* 3.8 35.9 - - + -
283I ASN* 2.9 19.2 + - + +
284I LEU* 3.1 10.5 + - + +
286I ALA* 1.3 75.0 - - - +
288I ASN* 1.3 57.9 + - - +
290I CYS* 3.0 25.3 + - - +
294I ARG* 3.6 6.8 - - - -
298I LEU* 3.4 28.9 - - + -
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Residues in contact with ASN 288 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284I LEU* 3.0 15.2 + - - +
285I ASN 2.9 4.9 + - - +
287I ILE* 1.3 72.9 - - - +
289I ARG* 1.3 58.9 + - - +
294I ARG* 2.8 33.8 + - - +
298I LEU* 2.8 39.5 + - - +
338I ALA 2.9 20.3 + - - +
339I ALA* 3.2 21.2 - - - +
340I GLN* 3.9 4.5 - - - +
341I GLY* 3.4 23.0 - - - +
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Residues in contact with ARG 289 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247I GLU* 5.0 8.9 + - - -
285I ASN* 3.0 26.1 + - - +
286I ALA* 2.9 14.9 + - - +
288I ASN* 1.3 80.1 - - - +
290I CYS* 1.3 66.4 + - - +
291I PRO* 3.5 5.5 - - - +
294I ARG* 4.6 0.2 - - - +
341I GLY* 2.8 32.2 + - - +
344I GLU* 5.2 8.3 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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