Contacts of the helix formed by residues 303 - 315 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B ALA* 3.5 20.2 - - - +
35B GLU* 4.8 1.6 - - - -
43B ARG* 4.2 6.1 - - - -
272B SER* 3.6 7.4 + - - -
301B SER 4.1 1.2 + - - -
302B TYR* 1.3 75.3 - - - +
304B ARG* 1.3 64.3 + - - +
305B ALA 3.3 0.2 - - - -
306B LEU* 3.4 6.2 + - - +
307B GLN* 2.9 29.1 + - - +
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Residues in contact with ARG 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ARG* 2.8 68.3 - - - +
46B GLN* 2.6 34.6 + - - +
272B SER* 4.0 5.7 + - - +
273B GLY 5.4 5.8 - - - +
275B GLN 5.7 4.9 - - - +
303B GLY* 1.3 68.4 - - - +
305B ALA* 1.3 54.1 + - - +
306B LEU 2.7 16.8 + - - -
307B GLN* 2.8 3.3 + - + -
308B ALA* 2.8 47.0 + - + +
311B LEU* 5.3 5.2 - - + +
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Residues in contact with ALA 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B SER* 3.2 31.5 + - - -
275B GLN 4.8 4.8 + - - +
276B SER 4.6 2.0 - - - +
277B GLU* 3.5 30.7 - - - +
280B ALA* 3.8 13.5 - - + -
302B TYR* 3.4 17.7 - - + -
303B GLY 3.3 0.8 - - - -
304B ARG* 1.3 76.2 - - - +
306B LEU* 1.3 58.7 + - - +
331B ARG* 3.6 15.6 + - - +
335B ASN* 4.0 4.3 + - - -
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Residues in contact with LEU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ILE 3.7 14.8 - - - +
31B LEU* 3.7 32.8 - - + -
74B ILE* 4.7 1.8 - - + -
277B GLU* 4.0 6.5 - - - +
300B PHE* 3.8 15.3 - - + -
302B TYR* 3.7 24.0 - - + +
303B GLY 3.4 8.8 + - - +
304B ARG 2.7 5.3 + - - -
305B ALA* 1.3 77.5 - - - +
307B GLN* 1.3 57.5 + - - +
308B ALA 3.7 1.1 - - - -
310B ALA* 4.4 0.7 - - - +
328B PHE* 3.6 31.7 - - + -
331B ARG* 3.7 6.9 - - + +
332B ALA* 3.6 38.1 - - + +
335B ASN* 3.7 17.0 - - - +
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Residues in contact with GLN 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.8 16.3 - - + +
32B ALA 3.3 15.0 + - - -
33B ALA* 4.2 0.8 - - - +
35B GLU* 3.3 27.9 + - - +
40B MET* 5.6 0.2 - - - +
43B ARG* 4.3 4.9 + - - +
59B TYR* 2.7 44.5 + - - +
60B ARG* 4.8 0.3 + - - -
63B LEU* 3.6 21.6 - - + +
303B GLY 2.9 21.6 + - - +
304B ARG* 2.8 6.7 + - + -
306B LEU* 1.3 80.9 - - + +
308B ALA* 1.3 60.4 + - - +
309B SER 3.6 1.3 - - - -
310B ALA* 3.8 8.3 - - + -
311B LEU* 2.8 34.2 + - + +
328B PHE* 5.5 0.4 - - + -
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B GLU* 3.3 21.0 + - + +
304B ARG* 2.8 39.8 + - + +
307B GLN* 1.3 73.5 - - - +
309B SER* 1.3 59.5 + - - +
311B LEU* 3.5 5.9 - - - +
312B ASN* 2.9 30.6 + - - +
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Residues in contact with SER 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B GLU* 2.8 28.0 + - - -
308B ALA* 1.3 79.5 - - - +
310B ALA* 1.3 59.4 + - - +
312B ASN* 3.4 8.4 - - - +
313B ALA* 2.8 32.2 + - - +
327B GLU* 3.1 27.7 - - - +
331B ARG* 4.0 8.3 - - - +
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Residues in contact with ALA 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B TYR* 4.8 2.2 - - + +
62B VAL* 5.7 0.2 - - + -
63B LEU* 4.6 6.5 - - + -
307B GLN* 3.5 20.5 + - + +
308B ALA 3.1 0.2 - - - -
309B SER* 1.3 84.3 + - - +
311B LEU* 1.3 62.2 + - - +
313B ALA* 3.2 0.3 + - - +
314B TRP* 3.0 19.8 + - - +
324B ALA* 3.2 30.3 - - + +
327B GLU* 3.5 10.8 - - - -
328B PHE* 3.8 23.3 - - + +
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Residues in contact with LEU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B MET* 4.9 0.7 - - + -
43B ARG* 4.0 39.7 - - + +
44B LEU* 4.4 5.6 - - + -
47B ILE* 3.6 38.8 - - + +
59B TYR* 3.3 47.3 + - + +
304B ARG* 5.3 5.6 - - + +
307B GLN* 2.8 20.3 + - + +
308B ALA* 3.5 5.2 - - - +
310B ALA* 1.3 76.3 - - - +
312B ASN* 1.3 62.6 - - - +
314B TRP* 3.8 5.3 - - + +
315B ARG 3.1 19.1 + - - -
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Residues in contact with ASN 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 4.5 8.0 - - - +
308B ALA 2.9 17.6 + - - +
309B SER* 3.4 10.7 - - - +
311B LEU* 1.3 78.7 - - - +
313B ALA* 1.3 59.6 + - - +
315B ARG* 2.8 49.8 + - - +
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Residues in contact with ALA 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B SER 2.8 15.8 + - - +
310B ALA* 3.5 4.9 - - - +
311B LEU 3.2 0.2 - - - -
312B ASN* 1.3 78.9 - - - +
314B TRP* 1.3 67.9 + - - +
315B ARG* 3.2 3.8 + - - +
320B ASN* 3.3 18.6 - - - +
323B ALA* 4.4 11.2 - - + +
324B ALA* 3.8 17.9 - - - +
327B GLU* 4.7 8.1 - - + -
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Residues in contact with TRP 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 3.8 19.5 - - + -
47B ILE* 3.7 15.5 - - + -
49B VAL* 4.1 11.0 - - + -
55B ASN* 3.5 22.7 - - + -
58B LEU* 4.0 17.3 - - + +
59B TYR* 3.6 38.8 - + + -
62B VAL* 3.9 23.4 - - + +
310B ALA 3.0 8.6 + - - +
311B LEU* 3.8 3.8 - - + +
313B ALA* 1.3 78.9 - - - +
315B ARG* 1.3 62.4 + - - +
316B GLY* 2.9 39.2 + - - -
317B GLN 2.9 36.8 + - - -
318B ARG* 5.0 2.6 - - - +
320B ASN* 3.3 15.7 - - - +
321B ALA* 4.2 9.9 - - - +
324B ALA* 3.5 19.8 - - + +
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Residues in contact with ARG 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLN 4.5 4.8 + - - -
47B ILE* 3.8 47.5 + - - +
49B VAL* 4.1 6.7 - - - +
311B LEU 3.1 13.4 + - - -
312B ASN* 2.8 41.6 + - - +
313B ALA 3.5 7.4 - - - +
314B TRP* 1.3 79.4 - - - +
316B GLY* 1.3 56.2 + - - +
317B GLN* 3.2 16.0 + - + +
320B ASN* 4.4 5.6 - - - +
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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