Contacts of the helix formed by residues 303 - 315 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ALA* 3.5 19.9 - - - +
35A GLU* 4.8 2.0 - - - -
43A ARG* 4.2 6.1 - - - -
272A SER* 3.6 7.2 + - - +
301A SER 4.1 1.0 + - - -
302A TYR* 1.3 75.3 - - - +
304A ARG* 1.3 64.2 + - - +
305A ALA 3.3 0.2 - - - -
306A LEU* 3.4 6.1 + - - +
307A GLN* 2.9 29.5 + - - +
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Residues in contact with ARG 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ARG* 2.8 68.8 - - - +
46A GLN* 2.6 35.0 - - - +
272A SER* 4.0 5.5 + - - +
273A GLY 5.4 5.4 - - - +
275A GLN 5.7 4.5 - - - +
303A GLY* 1.3 69.5 - - - +
305A ALA* 1.3 54.6 + - - +
306A LEU 2.7 17.1 + - - -
307A GLN* 2.8 2.6 + - - -
308A ALA* 2.8 47.4 + - + +
311A LEU* 5.3 5.0 - - + +
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Residues in contact with ALA 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A SER* 3.2 32.0 + - - -
275A GLN 4.8 4.8 + - - +
276A SER 4.6 2.0 - - - +
277A GLU* 3.5 29.4 - - - +
280A ALA* 3.8 13.5 - - + -
302A TYR* 3.4 17.7 - - + -
303A GLY 3.3 1.0 - - - -
304A ARG* 1.3 76.3 - - - +
306A LEU* 1.3 58.6 + - - +
331A ARG* 3.6 15.8 + - - +
335A ASN* 4.0 4.5 + - - -
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Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ILE 3.7 15.0 - - - +
31A LEU* 3.7 32.8 - - + -
74A ILE* 4.7 2.5 - - + -
277A GLU* 4.0 6.5 - - - +
300A PHE* 3.8 14.4 - - + -
302A TYR* 3.7 23.5 - - + +
303A GLY 3.4 8.6 + - - +
304A ARG 2.7 5.8 + - - -
305A ALA* 1.3 76.0 - - - +
307A GLN* 1.3 57.8 + - - +
308A ALA 3.7 0.9 - - - -
310A ALA* 4.4 0.5 - - - +
328A PHE* 3.6 32.2 - - + -
331A ARG* 3.7 6.5 - - + +
332A ALA* 3.6 38.6 - - + +
335A ASN* 3.7 17.3 - - - +
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Residues in contact with GLN 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 3.8 15.4 - - - +
32A ALA 3.3 16.0 + - - -
33A ALA* 4.2 0.8 - - - +
35A GLU* 3.3 27.4 + - - +
40A MET* 5.6 0.3 - - - +
43A ARG* 4.2 5.0 + - - +
59A TYR* 2.7 45.4 + - - +
60A ARG* 4.8 0.3 + - - -
63A LEU* 3.6 21.4 - - + +
303A GLY 2.9 21.8 + - - +
304A ARG* 2.8 7.1 + - + -
306A LEU* 1.3 80.5 - - - +
308A ALA* 1.3 59.2 + - - +
309A SER 3.6 1.3 - - - -
310A ALA* 3.8 7.6 - - + -
311A LEU* 2.8 33.7 + - + +
328A PHE* 5.5 0.4 - - + -
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Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A GLU* 3.3 21.0 + - + +
304A ARG* 2.8 39.0 + - + +
307A GLN* 1.3 72.7 - - - +
309A SER* 1.3 59.9 + - - +
311A LEU* 3.5 5.3 - - - +
312A ASN* 2.9 30.5 + - - +
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Residues in contact with SER 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A GLU* 2.8 27.7 + - - -
308A ALA* 1.3 78.3 - - - +
310A ALA* 1.3 59.2 + - - +
312A ASN* 3.1 9.3 + - - +
313A ALA* 2.8 31.5 + - - +
327A GLU* 3.1 27.3 - - - +
331A ARG* 4.0 8.8 - - - +
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Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A TYR* 4.8 2.9 - - + +
63A LEU* 4.6 6.7 - - + -
306A LEU 4.4 0.2 - - - +
307A GLN* 3.5 19.9 + - + +
308A ALA 3.1 0.2 - - - -
309A SER* 1.3 82.0 + - - +
311A LEU* 1.3 62.0 + - - +
313A ALA* 3.2 0.3 + - - +
314A TRP* 3.0 20.1 + - - +
324A ALA* 3.2 30.3 - - + +
327A GLU* 3.5 11.9 - - - -
328A PHE* 3.8 23.1 - - + +
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Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A MET* 4.9 1.3 - - + -
43A ARG* 4.0 39.3 - - + +
44A LEU* 4.4 5.6 - - + -
47A ILE* 3.6 38.0 - - + +
59A TYR* 3.3 48.4 + - + +
304A ARG* 5.3 5.8 - - + +
307A GLN* 2.8 21.8 + - + +
308A ALA* 3.5 4.5 - - - +
310A ALA* 1.3 76.6 - - - +
312A ASN* 1.3 63.1 + - - +
314A TRP* 3.5 5.7 + - + +
315A ARG 3.1 19.8 + - - -
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Residues in contact with ASN 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ILE* 4.5 8.2 - - - +
308A ALA 2.9 16.4 + - - +
309A SER* 3.4 11.0 - - - +
311A LEU* 1.3 79.1 - - - +
313A ALA* 1.3 59.8 + - - +
315A ARG* 2.8 50.3 + - - +
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Residues in contact with ALA 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A SER 2.8 16.2 + - - +
310A ALA* 3.5 4.9 - - - +
311A LEU 3.2 0.2 - - - -
312A ASN* 1.3 77.2 - - - +
314A TRP* 1.3 68.7 + - - +
315A ARG* 3.2 3.8 + - - +
320A ASN* 3.3 19.8 - - - +
323A ALA* 4.4 11.0 - - + +
324A ALA* 3.8 18.8 - - - +
327A GLU* 4.7 8.1 - - + -
289H ARG* 4.8 19.3 + - - +
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Residues in contact with TRP 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU* 3.8 19.5 - - + -
47A ILE* 3.7 15.9 - - + -
49A VAL* 4.1 11.7 - - + -
55A ASN* 3.5 21.5 - - + -
58A LEU* 4.0 16.9 + - + +
59A TYR* 3.6 40.2 - + + -
62A VAL* 3.9 23.1 - - + +
310A ALA 3.0 9.0 + - - +
311A LEU* 3.8 3.6 - - + +
313A ALA* 1.3 79.1 - - - +
315A ARG* 1.3 60.7 + - - +
316A GLY* 2.9 39.1 + - - -
317A GLN 2.9 37.1 + - - -
318A ARG* 5.0 2.6 - - - +
320A ASN* 3.3 14.9 - - - +
321A ALA* 4.2 10.4 - - - +
324A ALA* 3.5 19.8 - - + +
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Residues in contact with ARG 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLN 4.5 4.8 + - - -
47A ILE* 3.8 44.5 + - - +
49A VAL* 4.1 7.1 + - - +
311A LEU 3.1 13.5 + - - -
312A ASN* 2.8 40.4 + - - +
313A ALA 3.5 7.4 - - - +
314A TRP* 1.3 79.6 - - - +
316A GLY* 1.3 55.6 + - - +
317A GLN* 3.2 4.2 + - - -
320A ASN* 4.4 2.2 - - - +
247H GLU* 5.8 8.6 - - - +
251H MET* 5.0 7.0 - - - +
289H ARG 4.0 7.4 - - - -
290H CYS* 4.9 0.2 - - - +
291H PRO* 2.2 74.3 - - + +
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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