Contacts of the helix formed by residues 303 - 315 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32F ALA* 3.5 20.2 - - - +
35F GLU* 4.8 1.8 - - - -
43F ARG* 4.2 5.6 - - - -
272F SER* 3.6 7.1 + - - -
301F SER 4.1 1.2 + - - -
302F TYR* 1.3 75.4 - - - +
304F ARG* 1.3 63.7 + - - +
305F ALA 3.3 0.2 - - - -
306F LEU* 3.4 6.8 + - - +
307F GLN* 2.9 27.9 + - - +
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Residues in contact with ARG 304 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F ARG* 2.8 68.0 - - - +
46F GLN* 2.6 34.6 + - - +
272F SER* 4.0 5.0 + - - +
273F GLY 5.4 6.1 - - - +
275F GLN 5.7 4.9 - - - +
303F GLY* 1.3 68.6 - - - +
305F ALA* 1.3 55.0 + - - +
306F LEU 2.7 17.4 + - - -
307F GLN* 2.8 3.5 + - + -
308F ALA* 2.8 47.9 + - + +
311F LEU* 5.3 5.2 - - + +
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Residues in contact with ALA 305 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272F SER* 3.2 32.2 + - - -
275F GLN 4.8 4.4 + - - +
276F SER 4.6 1.8 - - - +
277F GLU* 3.5 29.9 - - - +
280F ALA* 3.8 12.8 - - + -
302F TYR* 3.4 17.9 - - + -
303F GLY 3.3 0.6 - - - -
304F ARG* 1.3 76.7 - - - +
306F LEU* 1.3 57.7 + - - +
331F ARG* 3.6 15.4 + - - +
335F ASN* 4.0 5.0 + - - -
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Residues in contact with LEU 306 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F ILE 3.7 15.0 - - - +
31F LEU* 3.7 32.3 - - + -
74F ILE* 4.7 2.5 - - + -
277F GLU* 4.0 6.6 - - - +
300F PHE* 3.8 15.3 - - + -
302F TYR* 3.7 23.6 - - + +
303F GLY 3.4 8.8 + - - +
304F ARG 2.7 5.5 + - - -
305F ALA* 1.3 76.0 - - - +
307F GLN* 1.3 57.7 + - - +
308F ALA 3.7 0.7 - - - -
310F ALA* 4.4 0.5 - - - +
328F PHE* 3.6 32.1 - - + -
331F ARG* 3.7 6.5 - - + +
332F ALA* 3.6 37.5 - - + +
335F ASN* 3.7 17.3 - - - +
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Residues in contact with GLN 307 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F LEU* 3.8 15.9 - - + +
32F ALA 3.3 15.2 + - - -
33F ALA* 4.2 1.0 - - - +
35F GLU* 3.3 27.5 + - - +
40F MET* 5.6 0.2 - - - +
43F ARG* 4.2 4.7 + - - +
59F TYR* 2.7 44.6 + - - +
60F ARG* 4.8 0.5 + - - -
63F LEU* 3.6 22.1 - - + +
303F GLY 2.9 22.2 + - - +
304F ARG* 2.8 6.8 + - + -
306F LEU* 1.3 80.1 - - - +
308F ALA* 1.3 58.7 + - - +
309F SER 3.6 1.1 - - - -
310F ALA* 3.8 9.4 - - + -
311F LEU* 2.8 33.6 + - + +
328F PHE* 5.5 0.7 - - + -
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Residues in contact with ALA 308 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277F GLU* 3.3 19.7 + - + +
304F ARG* 2.8 40.3 + - + +
307F GLN* 1.3 74.5 - - - +
309F SER* 1.3 59.7 + - - +
311F LEU* 3.5 5.1 - - - +
312F ASN* 2.9 29.5 + - - +
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Residues in contact with SER 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277F GLU* 2.8 28.0 + - - -
308F ALA* 1.3 79.2 - - - +
310F ALA* 1.3 59.4 + - - +
312F ASN* 3.1 8.4 + - - +
313F ALA* 2.8 32.1 + - - +
327F GLU* 3.1 27.7 + - - +
331F ARG* 4.0 8.8 - - - +
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Residues in contact with ALA 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F TYR* 4.8 1.8 - - + +
62F VAL* 5.7 0.2 - - + -
63F LEU* 4.6 7.0 - - + -
277F GLU* 4.4 0.2 + - - -
307F GLN* 3.5 19.4 + - + +
308F ALA 3.1 0.2 - - - -
309F SER* 1.3 83.5 + - - +
311F LEU* 1.3 61.6 + - - +
313F ALA* 3.2 0.3 + - - +
314F TRP* 3.0 19.9 + - - +
324F ALA* 3.2 30.5 - - + +
327F GLU* 3.5 11.2 - - - -
328F PHE* 3.8 23.3 - - + +
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Residues in contact with LEU 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F MET* 4.9 0.9 - - + -
43F ARG* 4.0 39.5 - - + +
44F LEU* 4.4 5.6 - - + -
47F ILE* 3.6 39.2 - - + +
59F TYR* 3.3 48.9 + - + +
304F ARG* 5.3 5.6 - - + +
307F GLN* 2.8 21.4 + - + +
308F ALA* 3.5 4.9 - - - +
310F ALA* 1.3 76.8 - - - +
312F ASN* 1.3 62.5 + - - +
314F TRP* 3.8 4.8 - - + +
315F ARG 3.1 20.1 + - - -
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Residues in contact with ASN 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F ILE* 4.5 7.3 - - - +
308F ALA 2.9 16.6 + - - +
309F SER* 3.1 11.0 + - - +
311F LEU* 1.3 79.0 - - - +
313F ALA* 1.3 59.7 + - - +
315F ARG* 2.8 51.0 + - - +
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Residues in contact with ALA 313 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309F SER 2.8 15.5 + - - +
310F ALA* 3.5 4.7 - - - +
312F ASN* 1.3 76.6 - - - +
314F TRP* 1.3 68.6 + - - +
315F ARG* 3.2 4.0 + - - +
320F ASN* 3.3 18.4 - - - +
323F ALA* 4.4 10.5 - - + +
324F ALA* 3.8 18.8 - - - +
327F GLU* 4.7 8.3 - - + -
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Residues in contact with TRP 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F LEU* 3.8 20.2 - - + -
47F ILE* 3.7 15.3 - - + -
49F VAL* 4.1 11.9 - - + -
55F ASN* 3.5 22.0 - - + -
58F LEU* 4.0 16.9 + - + +
59F TYR* 3.6 39.3 - + + -
62F VAL* 3.9 23.5 - - + +
310F ALA 3.0 8.6 + - - +
311F LEU* 3.8 3.4 - - + +
313F ALA* 1.3 79.4 - - - +
315F ARG* 1.3 62.9 + - - +
316F GLY* 2.9 40.0 + - - -
317F GLN 2.9 37.0 + - - -
318F ARG* 4.8 2.2 - - - +
320F ASN* 3.3 15.1 - - - +
321F ALA* 4.2 9.5 - - - +
324F ALA* 3.5 19.4 - - + +
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Residues in contact with ARG 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F GLN 4.5 5.1 + - - -
47F ILE* 3.8 48.0 + - - +
49F VAL* 4.1 7.7 - - - +
311F LEU 3.1 13.1 + - - -
312F ASN* 2.8 40.4 + - - +
313F ALA 3.2 7.8 - - - +
314F TRP* 1.3 79.6 - - - +
316F GLY* 1.3 55.9 + - - +
317F GLN* 3.2 15.9 + - + -
320F ASN* 4.4 6.3 - - - +
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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