Contacts of the helix formed by residues 334 - 350 (chain A) in PDB entry 1XR2
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 PHE 334 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A PRO* 3.6 24.0 - - + -
314A LEU* 4.4 4.0 - - - -
315A PRO* 3.4 46.9 - - + +
317A THR* 3.5 24.0 - - - -
318A LEU* 3.6 28.7 - - + +
321A GLU* 4.3 10.3 - - + -
324A LEU* 6.0 0.2 - - + -
332A LEU* 4.5 4.0 - - + -
333A ALA* 1.3 82.6 - - - +
335A ALA* 1.3 69.8 + - - +
337A GLU* 2.7 20.0 + - - +
338A LYS* 2.8 26.2 + - - +
482A THR* 4.4 8.3 - - + -
485A GLY* 4.6 6.7 - - - -
499A ILE* 4.2 22.0 - - + -
541A TYR* 5.1 1.1 - + - -
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Residues in contact with ALA 335 (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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8A PHE* 4.1 7.4 - - + -
9A PRO* 3.5 32.8 - - + -
311A LEU* 4.0 16.2 - - + +
314A LEU* 4.0 8.9 - - + +
315A PRO 2.9 18.1 + - - +
316A VAL 3.5 4.7 - - - +
334A PHE* 1.3 75.7 - - - +
336A LYS* 1.3 63.6 + - - +
338A LYS* 3.0 20.3 + - - +
339A LEU* 3.1 12.6 + - - +
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Residues in contact with LYS 336 (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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8A PHE* 3.9 12.9 - - + -
13A GLU* 3.2 23.8 + - - -
44A TYR* 4.0 15.1 + - - -
48A ASN* 3.2 27.8 + - - +
52A ASN* 5.7 2.2 - - - +
316A VAL 2.9 20.8 + - - +
317A THR* 4.0 17.0 - - - +
319A GLU* 6.1 0.4 - - + -
334A PHE 3.4 0.2 - - - -
335A ALA* 1.3 72.7 - - - +
337A GLU* 1.3 70.5 + - - +
339A LEU* 3.3 7.6 + - + +
340A GLU* 3.1 39.2 + - + +
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Residues in contact with GLU 337 (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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287A LYS* 6.5 0.2 - - - -
317A THR* 2.8 26.8 + - - -
318A LEU* 3.1 25.0 + - + +
319A GLU* 3.9 3.1 + - - +
332A LEU 5.2 0.7 - - - +
333A ALA* 3.8 14.8 - - + -
334A PHE* 2.7 47.6 + - - +
336A LYS* 1.3 82.3 - - - +
338A LYS* 1.3 57.3 + - - +
340A GLU* 3.3 18.4 + - - +
341A GLU* 2.9 31.9 + - + +
344A MET* 5.2 0.3 - - - +
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Residues in contact with LYS 338 (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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280A ILE* 3.7 15.8 - - + +
281A ASN* 3.0 30.2 + - - +
284A GLN* 2.7 29.4 + - - +
286A TRP 3.5 21.9 + - - +
288A VAL* 5.6 2.0 - - - +
311A LEU* 3.9 17.3 - - + -
314A LEU* 3.7 17.5 - - + -
333A ALA* 3.4 20.6 - - + +
334A PHE 2.8 22.2 + - - +
335A ALA 3.2 6.7 - - - +
337A GLU* 1.3 74.6 - - - +
339A LEU* 1.3 59.7 + - - +
341A GLU* 2.8 35.9 + - - +
342A LEU* 3.0 16.6 + - + +
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Residues in contact with LEU 339 (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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5A ALA* 3.7 25.1 - - + -
8A PHE* 3.5 32.5 - - + -
48A ASN* 3.5 34.5 - - + +
49A TYR* 4.2 11.0 - - + +
52A ASN* 3.4 23.8 - - + +
53A VAL* 5.2 1.1 - - + -
311A LEU* 3.5 29.2 - - + -
335A ALA 3.1 3.5 + - - +
336A LYS* 3.4 10.5 - - + +
338A LYS* 1.3 78.6 - - - +
340A GLU* 1.3 62.7 + - - +
342A LEU* 3.1 19.9 + - + +
343A LYS 3.3 8.0 + - - -
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Residues in contact with GLU 340 (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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52A ASN* 3.4 25.0 + - - +
336A LYS* 3.1 30.4 + - - +
337A GLU* 3.5 26.6 - - - +
338A LYS 3.1 0.4 - - - -
339A LEU* 1.3 77.0 - - - +
341A GLU* 1.3 65.1 + - - +
343A LYS* 3.2 3.9 + - - +
344A MET* 3.1 33.1 + - + +
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Residues in contact with GLU 341 (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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280A ILE* 3.8 35.0 - - + +
286A TRP 4.7 0.2 - - - +
287A LYS* 3.5 30.5 - - - +
288A VAL* 3.9 14.9 + - - +
290A LEU* 4.3 14.1 - - + +
333A ALA* 3.6 16.8 - - + +
337A GLU 2.9 17.8 + - - +
338A LYS* 2.8 19.4 + - - +
340A GLU* 1.3 77.1 - - - +
342A LEU* 1.3 56.7 + - - +
344A MET* 3.5 22.3 + - + +
345A LEU* 3.1 28.4 + - - +
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Residues in contact with LEU 342 (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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3A ALA* 4.8 2.7 - - + +
4A TYR 3.4 21.1 - - - +
5A ALA* 4.3 9.0 - - + -
52A ASN 4.7 1.6 - - - -
53A VAL* 4.3 11.4 - - + -
279A VAL* 5.3 0.2 - - + -
280A ILE* 3.5 28.5 - - + -
305A ILE* 3.6 21.4 - - + +
306A SER* 3.6 26.7 - - - +
307A ASN* 3.9 21.5 - - + +
311A LEU* 5.7 0.7 - - + -
338A LYS* 3.0 14.4 + - + +
339A LEU* 3.1 13.7 + - + +
341A GLU* 1.3 76.2 - - - +
343A LYS* 1.3 59.5 + - - +
345A LEU* 3.5 4.4 + - + -
346A LYS* 2.9 26.7 + - - +
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Residues in contact with LYS 343 (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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51A LYS 4.2 14.4 - - - +
52A ASN* 3.6 39.9 + - - +
339A LEU 3.3 3.0 + - - -
340A GLU* 3.2 9.9 + - - +
342A LEU* 1.3 76.8 - - - +
344A MET* 1.3 62.7 + - + +
346A LYS* 3.0 10.8 + - + +
347A ASP* 2.7 72.7 + - - +
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Residues in contact with MET 344 (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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290A LEU* 4.8 17.7 - - + -
340A GLU* 3.1 14.2 + - + +
341A GLU* 3.6 37.7 - - + +
343A LYS* 1.3 80.2 - - + +
345A LEU* 1.3 57.9 + - - +
347A ASP* 3.3 10.8 + - - +
348A PHE* 2.9 32.4 + - - +
353A THR* 4.3 1.2 + - - -
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Residues in contact with LEU 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A VAL* 3.9 13.9 - - + -
280A ILE* 4.8 5.8 - - + -
290A LEU* 4.0 23.1 - - + +
293A VAL* 3.6 24.7 - - + -
294A ALA* 3.9 35.7 - - + +
297A VAL* 4.4 2.0 - - + -
305A ILE* 3.7 24.2 - - + -
341A GLU 3.1 18.0 + - - +
342A LEU* 3.6 7.9 - - + +
343A LYS 3.2 0.2 - - - -
344A MET* 1.3 77.2 - - - +
346A LYS* 1.3 62.7 + - - +
348A PHE* 4.5 4.9 - - + -
349A LEU* 3.0 38.1 + - + +
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Residues in contact with LYS 346 (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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0A PHE* 3.8 8.5 - - - -
1A THR* 2.8 30.5 + - - +
3A ALA* 4.5 10.3 - - + -
52A ASN 5.1 7.0 - - - +
53A VAL 5.5 0.7 - - - -
54A ASP* 2.8 41.8 + - - +
305A ILE* 4.1 8.5 - - + +
342A LEU 2.9 15.6 + - - +
343A LYS* 3.0 14.3 + - + +
345A LEU* 1.3 78.3 - - - +
347A ASP* 1.3 71.6 + - - +
349A LEU* 3.8 3.4 - - - +
350A GLU* 3.0 54.0 + - - +
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Residues in contact with ASP 347 (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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343A LYS* 2.7 59.6 + - - +
344A MET* 3.7 7.9 - - - +
346A LYS* 1.3 81.2 - - - +
348A PHE* 1.3 64.2 + - - +
350A GLU* 3.1 6.6 + - - +
351A GLY 2.9 3.5 + - - -
352A LYS* 2.9 37.2 + - + +
353A THR* 3.4 28.2 - - + +
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Residues in contact with PHE 348 (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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290A LEU* 5.1 4.7 - - + -
291A ARG* 5.0 12.3 - - + -
294A ALA* 3.8 31.6 - - + -
344A MET 2.9 21.0 + - - +
345A LEU* 3.9 6.3 - - + +
347A ASP* 1.3 71.0 - - - +
349A LEU* 1.3 63.4 + - + +
351A GLY* 2.8 21.8 + - - -
353A THR* 3.1 28.5 + - - +
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Residues in contact with LEU 349 (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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1A THR* 3.6 35.6 + - + +
294A ALA* 4.0 33.7 - - + +
297A VAL* 3.8 25.6 - - + -
298A GLU* 4.9 13.0 - - + +
305A ILE* 4.2 8.5 - - + -
345A LEU* 3.0 32.8 + - + +
346A LYS 3.8 1.6 - - - +
348A PHE* 1.3 82.1 - - + +
350A GLU* 1.3 61.4 + - - +
351A GLY* 3.1 1.3 + - - -
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Residues in contact with GLU 350 (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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0A PHE* 3.3 22.0 - - - +
1A THR* 2.8 36.9 + - - +
346A LYS* 3.0 53.8 + - - +
347A ASP* 3.8 7.7 - - - +
349A LEU* 1.3 75.6 - - - +
351A GLY* 1.3 58.8 + - - +
352A LYS* 3.1 11.3 + - + +
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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
------------------------------------------------------------
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