Contacts of the helix formed by residues 303 - 315 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32D ALA* 3.5 20.1 - - - +
35D GLU* 4.8 2.2 - - - -
43D ARG* 4.2 6.7 - - - -
272D SER* 3.6 7.4 + - - -
301D SER 4.1 1.0 + - - -
302D TYR* 1.3 75.3 - - - +
304D ARG* 1.3 64.3 + - - +
305D ALA 3.3 0.2 - - - -
306D LEU* 3.4 6.1 + - - +
307D GLN* 2.9 29.3 + - - +
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Residues in contact with ARG 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D ARG* 2.8 66.8 - - - +
46D GLN* 2.6 35.2 - - - +
272D SER* 4.0 5.7 + - - +
273D GLY 5.4 5.4 - - - +
275D GLN 5.7 4.7 - - - +
303D GLY* 1.3 69.2 - - - +
305D ALA* 1.3 54.8 + - - +
306D LEU 2.7 17.4 + - - -
307D GLN* 2.8 3.7 + - + -
308D ALA* 2.8 46.5 + - + +
311D LEU* 5.3 5.4 - - + +
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Residues in contact with ALA 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272D SER* 3.2 32.2 + - - +
275D GLN 4.8 4.6 + - - +
276D SER 4.6 1.8 - - - +
277D GLU* 3.5 30.0 - - - +
280D ALA* 3.8 13.5 - - + -
302D TYR* 3.4 17.9 - - + -
303D GLY 3.3 0.6 - - - -
304D ARG* 1.3 76.2 - - - +
306D LEU* 1.3 57.3 + - - +
331D ARG* 3.6 15.8 + - - +
335D ASN* 4.0 4.5 + - - -
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Residues in contact with LEU 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ILE 3.7 15.0 - - - +
31D LEU* 3.7 31.9 - - + -
74D ILE* 4.7 2.5 - - + -
277D GLU* 4.0 6.9 - - - +
300D PHE* 3.8 15.3 - - + -
302D TYR* 3.7 22.2 - - + +
303D GLY 3.4 8.8 + - - +
304D ARG 2.7 5.5 + - - -
305D ALA* 1.3 75.8 - - - +
307D GLN* 1.3 59.0 + - - +
308D ALA 3.7 1.1 - - - -
310D ALA* 4.4 0.9 - - - +
328D PHE* 3.6 31.8 - - + -
331D ARG* 3.7 6.3 - - + +
332D ALA* 3.6 38.6 - - + +
335D ASN* 3.7 17.0 - - - +
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Residues in contact with GLN 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D LEU* 3.8 15.7 - - + +
32D ALA 3.3 15.0 + - - -
33D ALA* 4.2 1.0 - - - +
35D GLU* 3.3 27.7 + - - +
40D MET* 5.6 0.2 - - - +
43D ARG* 4.2 5.2 + - - +
59D TYR* 2.7 45.4 + - - +
60D ARG* 4.8 0.3 + - - -
63D LEU* 3.6 21.7 - - + +
303D GLY 2.9 23.5 + - - +
304D ARG* 2.8 7.0 + - + -
306D LEU* 1.3 80.7 - - - +
308D ALA* 1.3 59.6 + - - +
309D SER 3.6 1.3 - - - -
310D ALA* 3.8 8.3 - - + -
311D LEU* 2.8 34.2 + - + +
328D PHE* 5.5 0.2 - - + -
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Residues in contact with ALA 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D GLU* 3.3 20.2 + - + +
304D ARG* 2.8 40.0 + - + +
307D GLN* 1.3 72.6 - - - +
309D SER* 1.3 60.6 + - - +
311D LEU* 3.5 5.7 - - - +
312D ASN* 2.9 30.3 + - - +
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Residues in contact with SER 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277D GLU* 2.8 27.5 + - - -
308D ALA* 1.3 78.7 - - - +
310D ALA* 1.3 58.8 + - - +
312D ASN* 3.1 8.8 + - - +
313D ALA* 2.8 31.7 + - - +
327D GLU* 3.1 27.0 - - - +
331D ARG* 4.0 8.8 - - - +
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Residues in contact with ALA 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D TYR* 4.8 3.4 - - + +
63D LEU* 4.6 6.7 - - + -
306D LEU 4.4 0.4 - - - +
307D GLN* 3.7 19.9 - - + +
308D ALA 3.1 0.6 - - - -
309D SER* 1.3 83.6 + - - +
311D LEU* 1.3 62.4 + - - +
313D ALA* 3.5 0.2 - - - +
314D TRP* 3.0 20.1 + - - +
324D ALA* 3.2 29.2 - - + +
327D GLU* 3.5 12.1 - - - -
328D PHE* 3.8 23.1 - - + +
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Residues in contact with LEU 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D MET* 4.9 1.3 - - + -
43D ARG* 4.0 39.0 - - + +
44D LEU* 4.4 5.6 - - + -
47D ILE* 3.6 38.4 - - + +
59D TYR* 3.3 48.2 + - + +
304D ARG* 5.3 5.4 - - + +
307D GLN* 2.8 20.9 + - + +
308D ALA* 3.5 4.5 - - - +
310D ALA* 1.3 76.2 - - - +
312D ASN* 1.3 62.9 + - - +
314D TRP* 3.8 5.3 - - + +
315D ARG 3.1 20.1 + - - -
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Residues in contact with ASN 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ILE* 4.4 8.4 - - - +
308D ALA 2.9 17.0 + - - +
309D SER* 3.4 10.7 - - - +
311D LEU* 1.3 79.1 - - - +
313D ALA* 1.3 59.5 + - - +
315D ARG* 2.8 51.9 + - - +
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Residues in contact with ALA 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309D SER 2.8 17.0 + - - +
310D ALA 3.5 4.3 - - - +
312D ASN* 1.3 77.5 - - - +
314D TRP* 1.3 69.0 + - - +
315D ARG* 3.2 3.6 + - - +
320D ASN* 3.3 19.3 - - - +
323D ALA* 4.4 11.0 - - + +
324D ALA* 3.8 18.6 - - - +
327D GLU* 4.7 8.3 - - + -
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Residues in contact with TRP 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LEU* 3.8 20.0 - - + -
47D ILE* 3.7 15.3 - - + -
49D VAL* 4.1 11.4 - - + -
55D ASN* 3.5 21.8 - - + -
58D LEU* 4.0 16.2 - - + +
59D TYR* 3.6 41.1 - + + -
62D VAL* 3.9 24.2 - - + +
310D ALA 3.0 8.3 + - - +
311D LEU* 3.8 4.3 - - + +
313D ALA* 1.3 79.0 - - - +
315D ARG* 1.3 61.5 + - - +
316D GLY* 2.9 40.4 + - - -
317D GLN 2.9 38.1 + - - -
318D ARG* 5.0 2.4 - - - +
320D ASN* 3.3 15.6 - - - +
321D ALA* 4.2 9.5 - - - +
324D ALA* 3.5 20.0 - - + +
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Residues in contact with ARG 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D GLN 4.5 4.9 + - - -
47D ILE* 3.8 48.4 + - - +
49D VAL* 4.1 7.1 - - - +
311D LEU 3.1 12.5 + - - -
312D ASN* 2.8 41.5 + - - +
313D ALA 3.2 8.0 + - - +
314D TRP* 1.3 80.1 - - - +
316D GLY* 1.3 56.1 + - - +
317D GLN* 3.2 15.6 + - + -
320D 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