Contacts of the helix formed by residues 303 - 320 (chain A) in PDB entry 5LXG
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 303 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A PHE* 6.4 2.5 - + - -
223A TRP* 3.7 29.8 - + - -
298A GLY 5.2 0.9 - - - +
299A GLN* 2.4 33.6 + - + +
300A MET* 3.3 37.7 - - + +
302A TRP* 1.3 69.0 - - + +
304A PHE* 1.3 65.1 + - - +
305A LEU* 3.1 11.6 - - - +
306A MET* 3.1 54.7 + - + +
307A ALA* 4.1 7.7 + - + -
350A VAL* 5.4 2.5 - - + -
351A HIS* 3.5 21.3 - + - -
354A GLY* 5.2 11.9 - - - -
355A VAL 5.4 0.4 - - - -
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Residues in contact with PHE 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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300A MET 2.6 14.4 + - - +
301A GLY* 2.8 24.2 + - - +
303A PHE* 1.3 77.6 - - - +
305A LEU* 1.3 62.6 + - - +
307A ALA* 3.3 14.4 + - + +
308A VAL* 3.1 43.5 + - + +
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Residues in contact with LEU 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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301A GLY 4.2 0.6 + - - -
302A TRP* 2.7 52.2 + - + +
303A PHE* 3.3 12.1 - - - +
304A PHE* 1.3 82.4 - - - +
306A MET* 1.4 69.6 + - - +
308A VAL* 3.2 9.8 + - - +
309A MET* 2.8 44.9 + - + +
350A VAL* 3.2 38.1 - - + -
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Residues in contact with MET 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A SER* 5.9 1.6 - - - -
303A PHE* 3.1 30.6 + - + +
305A LEU* 1.4 82.2 - - + +
307A ALA* 1.3 66.4 + - - +
309A MET* 3.2 15.3 + - + +
310A TYR* 3.0 42.7 + - + -
347A ALA* 3.7 12.3 - - + +
350A VAL* 4.3 3.6 - - + -
351A HIS* 2.9 62.8 - - + +
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Residues in contact with ALA 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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303A PHE* 4.1 7.7 + - + +
304A PHE* 3.3 18.4 + - + +
306A MET* 1.3 79.8 - - - +
308A VAL* 1.4 63.1 + - + +
310A TYR* 3.4 7.1 + - - +
311A ILE* 3.1 30.7 + - + +
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Residues in contact with VAL 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A PHE* 3.1 45.3 + - + +
305A LEU* 3.2 11.4 + - - +
306A MET 3.2 0.4 - - - -
307A ALA* 1.4 76.1 - - + +
309A MET* 1.3 52.5 + - + +
311A ILE* 3.2 8.5 + - - +
312A THR* 2.5 45.9 + - - +
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Residues in contact with MET 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A LEU* 2.8 23.9 + - + +
306A MET* 3.2 27.8 + - - +
308A VAL* 1.3 72.4 - - + +
310A TYR* 1.3 56.4 + - - +
312A THR* 3.2 6.9 + - - -
313A GLY* 2.9 24.6 + - - -
343A LEU* 3.3 38.5 - - + +
346A ALA* 4.6 6.7 - - - -
347A ALA* 3.6 30.5 - - + -
350A VAL* 3.7 22.9 - - + -
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Residues in contact with TYR 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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212A ILE* 6.4 1.3 - - + -
215A LEU* 3.7 29.2 - - + +
216A ILE* 5.1 19.5 - - + -
219A SER* 5.1 3.8 + - - -
306A MET* 3.0 26.9 + - + +
307A ALA* 3.7 10.1 - - - +
308A VAL 3.4 0.2 - - - -
309A MET* 1.3 74.8 - - - +
311A ILE* 1.3 62.6 + - + +
313A GLY* 3.3 2.4 + - - -
314A ALA* 2.9 29.5 + - - +
340A PHE* 5.1 5.0 - - - -
343A LEU* 4.5 2.5 - - - -
344A VAL* 3.7 16.2 + - + -
347A ALA* 2.5 39.7 - - + -
348A ALA* 3.6 17.7 + - - +
351A HIS* 6.0 0.2 - - - +
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Residues in contact with ILE 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ALA* 3.1 16.3 + - + +
308A VAL* 3.6 9.2 - - - +
310A TYR* 1.3 76.0 - - + +
312A THR* 1.4 56.5 + - - +
314A ALA* 3.8 8.9 - - + +
315A GLY* 2.7 34.4 + - - -
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Residues in contact with THR 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A VAL* 2.5 39.0 + - - +
309A MET* 3.2 9.5 + - - -
311A ILE* 1.4 72.7 - - - +
313A GLY* 1.3 53.0 + - - +
315A GLY* 3.9 0.6 - - - -
316A LEU* 2.7 56.0 + - + +
343A LEU* 4.3 8.3 - - + -
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Residues in contact with GLY 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 MET 2.9 10.5 + - - -
310A TYR* 3.7 4.0 - - - -
312A THR* 1.3 76.7 - - - +
314A ALA* 1.4 51.5 + - - +
316A LEU* 3.3 5.5 + - - +
317A TYR* 2.8 37.2 + - - +
340A PHE* 3.6 24.6 - - - +
343A LEU* 3.6 17.8 - - - +
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Residues in contact with ALA 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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271A PHE* 6.4 2.9 - - + -
310A TYR 2.9 19.5 + - - +
311A ILE* 3.8 12.6 - - + +
313A GLY* 1.4 68.6 - - - +
315A GLY* 1.3 65.4 + - - +
317A TYR* 2.7 37.8 - - + -
318A ALA* 3.3 6.1 + - - +
340A PHE* 4.1 8.3 - - + -
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Residues in contact with GLY 315 (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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311A ILE* 2.7 21.7 + - - -
312A THR* 3.9 0.9 - - - -
314A ALA* 1.3 73.4 - - - +
316A LEU* 1.3 61.6 + - - +
318A ALA* 4.0 3.7 - - - +
319A ALA* 3.2 25.9 + - - +
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Residues in contact with LEU 316 (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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312A THR* 2.7 39.5 + - + +
313A GLY* 3.6 6.1 - - - +
315A GLY* 1.3 71.8 - - - +
317A TYR* 1.3 54.2 + - - +
319A ALA* 3.5 1.5 + - - +
320A ARG* 2.8 28.6 + - - -
321A ILE* 3.4 50.0 + - + +
336A SER* 3.8 7.0 - - - +
339A ILE* 4.1 30.1 - - + -
340A PHE* 6.0 0.9 - - + +
343A LEU* 5.4 1.6 - - + -
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Residues in contact with TYR 317 (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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209A TYR* 5.7 0.3 + - - -
313A GLY 2.8 17.0 + - - +
314A ALA* 2.7 38.1 - - + -
316A LEU* 1.3 70.6 - - - +
318A ALA* 1.4 81.5 + - + +
320A ARG* 3.1 37.4 + - - +
336A SER* 3.9 16.0 + - - +
337A HIS* 4.7 18.6 - + - +
340A PHE* 4.1 28.5 - + + -
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Residues in contact with ALA 318 (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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314A ALA 3.3 14.0 + - - +
315A GLY* 4.0 4.5 - - - +
317A TYR* 1.4 93.2 - - + +
319A ALA* 1.3 64.9 + - - +
320A ARG* 3.4 14.4 + - - +
324A ARG* 4.9 1.7 + - - -
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Residues in contact with ALA 319 (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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315A GLY 3.2 16.6 + - - +
316A LEU 3.7 2.0 - - - +
318A ALA* 1.3 75.7 - - - +
320A ARG* 1.3 66.7 + - - +
321A ILE* 3.3 30.4 + - + +
324A ARG* 2.6 35.8 + - - +
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Residues in contact with ARG 320 (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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106A ASP* 3.4 27.3 + - - +
107A ASN* 3.8 27.8 + - - +
108A ASP* 5.2 5.0 + - - -
109A TYR* 4.1 17.0 - - + -
316A LEU 2.8 7.2 + - - -
317A TYR* 3.1 30.6 + - - +
318A ALA* 4.1 10.8 + - - +
319A ALA* 1.3 79.3 - - - +
321A ILE* 1.3 59.5 + - - +
323A GLU* 2.2 36.3 - - - +
324A ARG* 2.9 16.4 + - - +
336A SER* 3.5 11.9 - - - +
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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