Contacts of the helix formed by residues 303 - 315 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32L ALA* 3.5 20.4 - - - +
35L GLU* 4.8 2.0 - - - -
43L ARG* 4.2 6.1 - - - -
272L SER* 3.6 7.3 + - - -
301L SER 4.1 1.2 + - - -
302L TYR* 1.3 74.7 - - - +
304L ARG* 1.3 63.6 + - - +
305L ALA 3.3 0.2 - - - -
306L LEU* 3.4 6.4 + - - +
307L GLN* 2.9 28.1 + - - +
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Residues in contact with ARG 304 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43L ARG* 2.8 67.0 - - - +
46L GLN* 2.6 34.8 + - - +
272L SER* 4.0 5.0 + - - +
273L GLY 5.4 6.1 - - - +
275L GLN 5.7 4.9 - - - +
303L GLY* 1.3 68.6 - - - +
305L ALA* 1.3 54.6 + - - +
306L LEU 2.7 17.7 + - - -
307L GLN* 2.8 3.7 + - + -
308L ALA* 2.8 47.9 + - + +
311L LEU* 5.3 5.0 - - + +
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Residues in contact with ALA 305 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272L SER* 3.2 32.4 + - - -
275L GLN 4.8 4.4 + - - +
276L SER 4.6 1.8 - - - +
277L GLU* 3.5 29.9 - - - +
280L ALA* 3.8 13.0 - - + -
302L TYR* 3.4 17.7 - - + -
303L GLY 3.3 0.6 - - - -
304L ARG* 1.3 76.1 - - - +
306L LEU* 1.3 58.1 + - - +
331L ARG* 3.6 15.4 + - - +
335L ASN* 4.0 4.7 + - - -
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Residues in contact with LEU 306 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30L ILE 3.7 15.3 - - - +
31L LEU* 3.7 31.6 - - + -
74L ILE* 4.7 2.5 - - + -
277L GLU* 4.0 6.6 - - - +
300L PHE* 3.8 15.0 - - + -
302L TYR* 3.7 23.8 - - + +
303L GLY 3.4 8.6 + - - +
304L ARG 2.7 5.1 + - - -
305L ALA* 1.3 76.2 - - - +
307L GLN* 1.3 57.5 + - - +
308L ALA 3.7 0.7 - - - -
310L ALA* 4.4 0.5 - - - +
328L PHE* 3.6 32.1 - - + -
331L ARG* 3.7 6.7 - - + +
332L ALA* 3.6 37.7 - - + +
335L ASN* 3.7 17.3 - - - +
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Residues in contact with GLN 307 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31L LEU* 3.8 15.9 - - + +
32L ALA 3.3 15.2 + - - -
33L ALA* 4.2 1.2 - - - +
35L GLU* 3.3 26.8 + - - +
40L MET* 5.6 0.2 - - - +
43L ARG* 4.2 4.9 + - - +
59L TYR* 2.7 45.2 + - - +
60L ARG* 4.8 0.5 + - - -
63L LEU* 3.6 22.1 - - + +
303L GLY 2.9 21.8 + - - +
304L ARG* 2.8 6.9 + - + -
306L LEU* 1.3 80.5 - - - +
308L ALA* 1.3 59.8 + - - +
309L SER 3.6 1.1 - - - -
310L ALA* 3.8 8.7 - - + -
311L LEU* 2.8 33.8 + - + +
328L PHE* 5.5 0.7 - - + -
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Residues in contact with ALA 308 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277L GLU* 3.3 20.2 + - + +
304L ARG* 2.8 40.5 + - + +
307L GLN* 1.3 73.9 - - - +
309L SER* 1.3 59.2 + - - +
311L LEU* 3.5 5.1 - - - +
312L ASN* 2.9 29.9 + - - +
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Residues in contact with SER 309 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277L GLU* 2.8 27.8 + - - -
308L ALA* 1.3 79.0 - - - +
310L ALA* 1.3 59.2 + - - +
312L ASN* 3.1 8.6 + - - +
313L ALA* 2.8 31.7 + - - +
327L GLU* 3.1 27.7 + - - +
331L ARG* 4.0 9.0 - - - +
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Residues in contact with ALA 310 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59L TYR* 4.8 2.7 - - + +
62L VAL* 5.7 0.2 - - + -
63L LEU* 4.6 6.7 - - + -
277L GLU* 4.4 0.2 + - - -
307L GLN* 3.7 19.0 - - + +
308L ALA 3.1 0.2 - - - -
309L SER* 1.3 83.1 + - - +
311L LEU* 1.3 61.2 + - - +
313L ALA* 3.2 0.3 + - - +
314L TRP* 3.0 20.1 + - - +
324L ALA* 3.2 30.3 - - + +
327L GLU* 3.5 11.0 - - - -
328L PHE* 3.8 23.6 - - + +
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Residues in contact with LEU 311 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L MET* 4.9 0.9 - - + -
43L ARG* 4.0 39.5 - - + +
44L LEU* 4.4 5.4 - - + -
47L ILE* 3.6 39.7 - - + +
59L TYR* 3.3 48.6 + - + +
304L ARG* 5.3 5.6 - - + +
307L GLN* 2.8 21.6 + - + +
308L ALA* 3.5 4.9 - - - +
310L ALA* 1.3 76.2 - - - +
312L ASN* 1.3 62.9 + - - +
314L TRP* 3.8 5.2 - - + +
315L ARG 3.1 20.1 + - - -
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Residues in contact with ASN 312 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47L ILE* 4.5 7.1 - - - +
308L ALA 2.9 16.6 + - - +
309L SER* 3.1 10.9 + - - +
311L LEU* 1.3 79.2 - - - +
313L ALA* 1.3 59.9 + - - +
315L ARG* 2.8 51.0 + - - +
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Residues in contact with ALA 313 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309L SER 2.8 15.8 + - - +
310L ALA* 3.5 4.5 - - - +
312L ASN* 1.3 76.4 - - - +
314L TRP* 1.3 69.3 + - - +
315L ARG* 3.2 4.0 + - - +
320L ASN* 3.3 18.4 - - - +
323L ALA* 4.4 10.5 - - + +
324L ALA* 3.8 18.8 - - - +
327L GLU* 4.7 8.3 - - + -
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Residues in contact with TRP 314 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44L LEU* 3.8 20.0 - - + -
47L ILE* 3.7 15.0 - - + -
49L VAL* 4.1 11.7 - - + -
55L ASN* 3.5 22.0 - - + -
58L LEU* 4.0 16.9 + - + +
59L TYR* 3.6 39.7 - + + -
62L VAL* 3.9 22.9 - - + +
310L ALA 3.0 8.8 + - - +
311L LEU* 3.8 3.1 - - + +
313L ALA* 1.3 80.0 - - - +
315L ARG* 1.3 62.2 + - - +
316L GLY* 2.9 40.0 + - - -
317L GLN 2.9 36.6 + - - -
318L ARG* 4.8 2.2 - - - +
320L ASN* 3.3 15.3 - - - +
321L ALA* 4.2 9.9 - - - +
324L ALA* 3.5 19.4 - - + +
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Residues in contact with ARG 315 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46L GLN 4.5 5.3 + - - -
47L ILE* 3.8 47.7 + - - +
49L VAL* 4.1 7.7 - - - +
311L LEU 3.1 13.3 + - - -
312L ASN* 2.8 40.8 + - - +
313L ALA 3.5 8.1 - - - +
314L TRP* 1.3 80.1 - - - +
316L GLY* 1.3 55.5 + - - +
317L GLN* 3.2 15.7 + - + +
320L 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