Contacts of the helix formed by residues 303 - 315 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32E ALA* 3.5 20.8 - - - +
35E GLU* 4.8 2.0 - - - -
43E ARG* 4.2 5.8 - - - -
272E SER* 3.6 6.8 + - - -
301E SER 4.1 1.0 + - - -
302E TYR* 1.3 75.7 - - - +
304E ARG* 1.3 65.1 + - - +
305E ALA 3.3 0.2 - - - -
306E LEU* 3.4 5.9 + - - +
307E GLN* 2.9 29.2 + - - +
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Residues in contact with ARG 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E ARG* 2.8 67.6 - - - +
46E GLN* 2.6 35.2 + - - +
272E SER* 4.0 5.2 + - - +
273E GLY 5.4 5.8 - - - +
275E GLN 5.7 4.5 - - - +
303E GLY* 1.3 69.3 - - - +
305E ALA* 1.3 54.3 + - - +
306E LEU 2.7 17.1 + - - -
307E GLN* 2.8 3.3 + - + -
308E ALA* 2.8 48.8 + - + +
311E LEU* 5.3 4.4 - - + +
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Residues in contact with ALA 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E SER* 3.2 31.3 + - - -
275E GLN 4.8 4.3 + - - +
276E SER 4.6 2.0 - - - +
277E GLU* 3.5 29.5 - - - +
280E ALA* 3.8 13.5 - - + -
302E TYR* 3.4 18.4 - - + -
303E GLY 3.3 0.4 - - - -
304E ARG* 1.3 76.1 - - - +
306E LEU* 1.3 58.1 + - - +
331E ARG* 3.6 15.6 + - - +
335E ASN* 4.0 4.7 + - - -
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Residues in contact with LEU 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E ILE 3.7 15.3 - - - +
31E LEU* 3.7 31.9 - - + -
74E ILE* 4.7 2.9 - - + -
277E GLU* 4.0 7.3 - - - +
300E PHE* 3.8 15.5 - - + -
302E TYR* 3.7 23.5 - - + +
303E GLY 3.4 8.2 + - - +
304E ARG 2.7 5.3 + - - -
305E ALA* 1.3 76.4 - - - +
307E GLN* 1.3 58.8 + - - +
308E ALA 3.7 0.7 - - - -
310E ALA* 4.4 0.9 - - - +
328E PHE* 3.6 31.5 - - + -
331E ARG* 3.7 6.7 - - + +
332E ALA* 3.6 38.8 - - + +
335E ASN* 3.7 15.9 - - - +
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Residues in contact with GLN 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E LEU* 3.8 16.5 - - + +
32E ALA 3.3 15.2 + - - -
33E ALA* 4.2 1.0 - - - +
35E GLU* 3.3 27.3 + - - +
40E MET* 5.6 0.2 - - - +
43E ARG* 4.2 4.9 + - - +
59E TYR* 2.7 44.8 + - - +
60E ARG* 4.8 0.3 + - - -
63E LEU* 3.6 22.7 - - + +
303E GLY 2.9 22.3 + - - +
304E ARG* 2.8 6.4 + - + -
306E LEU* 1.3 81.3 - - + +
308E ALA* 1.3 59.4 + - - +
309E SER 3.6 1.1 - - - -
310E ALA* 3.8 8.5 - - + -
311E LEU* 2.8 33.7 + - + +
328E PHE* 5.5 0.2 - - + -
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Residues in contact with ALA 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277E GLU* 3.3 20.8 + - + +
304E ARG* 2.8 38.1 + - + +
307E GLN* 1.3 73.7 - - - +
309E SER* 1.3 59.8 + - - +
311E LEU* 3.5 5.5 - - - +
312E ASN* 2.9 29.6 + - - +
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Residues in contact with SER 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277E GLU* 2.8 26.8 + - - -
308E ALA* 1.3 77.7 - - - +
310E ALA* 1.3 58.9 + - - +
312E ASN* 3.4 9.1 - - - +
313E ALA* 2.8 32.2 + - - +
327E GLU* 3.1 27.1 - - - +
331E ARG* 4.0 8.5 - - - +
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Residues in contact with ALA 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E TYR* 4.8 2.7 - - + +
63E LEU* 4.6 6.5 - - + -
277E GLU* 4.4 0.2 + - - -
306E LEU 4.4 0.2 - - - +
307E GLN* 3.7 19.9 - - + +
308E ALA 3.1 0.4 - - - -
309E SER* 1.3 82.1 + - - +
311E LEU* 1.3 61.7 + - - +
313E ALA* 3.2 0.3 + - - +
314E TRP* 3.0 20.4 + - - +
324E ALA* 3.2 30.3 - - + +
327E GLU* 3.5 11.7 - - - -
328E PHE* 3.8 23.8 - - + +
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Residues in contact with LEU 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E MET* 4.9 0.7 - - + -
43E ARG* 4.0 39.7 - - + +
44E LEU* 4.4 5.2 - - + -
47E ILE* 3.6 39.8 - - + +
59E TYR* 3.3 48.8 + - + +
304E ARG* 5.3 5.4 - - + +
307E GLN* 2.8 21.3 + - + +
308E ALA* 3.5 5.4 - - - +
310E ALA* 1.3 76.5 - - - +
312E ASN* 1.3 62.8 + - - +
314E TRP* 3.5 6.3 + - + +
315E ARG 3.1 19.4 + - - -
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Residues in contact with ASN 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E ILE* 4.4 7.8 - - - +
308E ALA 2.9 16.8 + - - +
309E SER* 3.4 11.2 - - - +
311E LEU* 1.3 79.0 - - - +
313E ALA* 1.3 59.5 + - - +
315E ARG* 2.8 50.5 + - - +
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Residues in contact with ALA 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309E SER 2.8 16.8 + - - +
310E ALA* 3.5 4.7 - - - +
312E ASN* 1.3 77.2 - - - +
314E TRP* 1.3 69.3 + - - +
315E ARG* 3.2 3.6 + - - +
320E ASN* 3.3 19.8 - - - +
323E ALA* 4.4 11.7 - - + +
324E ALA* 3.8 18.2 - - - +
327E GLU* 4.7 8.5 - - + +
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Residues in contact with TRP 314 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E LEU* 3.8 20.2 - - + -
47E ILE* 3.7 15.3 - - + -
49E VAL* 4.1 11.2 - - + -
55E ASN* 3.5 23.3 - - - -
58E LEU* 4.0 16.7 - - + +
59E TYR* 3.6 39.7 - + + -
62E VAL* 3.9 23.5 - - + +
310E ALA 3.0 8.4 + - - +
311E LEU* 3.8 3.8 - - + +
313E ALA* 1.3 79.8 - - - +
315E ARG* 1.3 60.5 + - - +
316E GLY* 2.9 37.8 + - - -
317E GLN 2.9 38.0 + - - -
318E ARG* 4.8 2.2 - - - +
320E ASN* 3.3 15.7 - - - +
321E ALA* 4.2 9.5 - - - +
324E ALA* 3.5 19.4 - - + +
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Residues in contact with ARG 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E GLN 4.5 5.1 + - - -
47E ILE* 3.8 47.8 + - - +
49E VAL* 4.1 7.5 - - - +
311E LEU 3.1 13.3 + - - -
312E ASN* 2.8 42.0 + - - +
313E ALA 3.5 7.0 - - - +
314E TRP* 1.3 80.1 - - - +
316E GLY* 1.3 55.5 + - - +
317E GLN* 3.2 15.7 + - + +
320E ASN* 4.4 5.8 - - - +
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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