Contacts of the helix formed by residues 289 - 304 (chain B) in PDB entry 5AM8
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 GLN 289 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B GLY 3.6 10.5 - - - +
288B TRP* 1.3 79.9 - - - +
290B ALA* 1.3 69.0 + - - +
291B THR* 3.2 8.5 - - + +
292B HIS* 3.1 31.8 + - + +
293B MET* 3.2 17.8 + - - +
320B GLU* 4.7 9.8 - - - +
351B VAL* 4.0 9.4 - - - +
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Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B GLN* 1.3 72.8 - - - +
291B THR* 1.3 66.1 + - - +
293B MET* 2.9 24.7 + - - +
294B PHE* 3.0 20.4 + - + -
319B LEU* 3.5 32.8 - - + +
320B GLU* 3.7 23.4 + - + +
349B THR* 3.9 13.5 - - + +
351B VAL* 4.6 3.6 - - - +
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Residues in contact with THR 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B GLN* 4.4 6.5 - - + +
290B ALA* 1.3 78.3 - - - +
292B HIS* 1.3 85.9 + - + +
294B PHE* 3.2 7.6 + - - +
295B ARG* 2.9 34.7 + - - +
314B TRP* 4.9 7.7 - - - -
319B LEU* 5.1 8.4 - - - +
320B GLU* 5.4 0.4 + - - -
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Residues in contact with HIS 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B GLY 4.2 7.2 - - - -
288B TRP* 4.0 21.9 - + + -
289B GLN* 3.1 44.6 + - + +
291B THR* 1.3 88.1 - - + +
293B MET* 1.3 57.7 + - - +
295B ARG* 3.2 5.3 + - - +
296B VAL* 2.9 39.4 + - + +
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Residues in contact with MET 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B MET* 4.0 9.2 - - + -
288B TRP* 4.0 20.0 - - + -
289B GLN 3.2 19.0 + - - +
290B ALA* 2.9 7.0 + - - +
292B HIS* 1.3 76.1 - - - +
294B PHE* 1.3 57.9 + - - +
296B VAL* 3.5 1.9 + - - +
297B ALA* 3.0 28.4 + - - +
349B THR* 3.7 23.1 - - + -
350B ARG 3.5 23.3 - - - +
351B VAL* 4.1 10.1 - - - -
352B THR 4.0 6.5 - - - +
355B GLN* 3.8 5.2 - - + +
356B LEU* 3.7 47.8 - - + +
359B VAL* 3.9 11.9 - - + +
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Residues in contact with PHE 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ALA 3.0 26.5 + - - +
291B THR 3.8 5.6 - - - +
293B MET* 1.3 77.3 - - - +
295B ARG* 1.3 56.4 + - - +
297B ALA 3.5 0.2 + - - -
298B GLU* 2.9 25.6 + - - +
313B PHE* 4.0 6.7 - + - -
314B TRP* 3.8 20.4 - - + -
319B LEU* 3.7 35.2 - - + -
345B ILE* 3.7 29.4 - - + -
347B GLN* 3.6 22.0 - - + -
349B THR* 3.5 21.1 - - + -
359B VAL* 3.5 32.1 - - + -
363B MET* 3.4 22.6 - - + +
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Residues in contact with ARG 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B THR* 2.9 28.9 + - - +
292B HIS* 3.9 5.2 - - - +
294B PHE* 1.3 72.4 - - - +
296B VAL* 1.3 62.3 + - + +
298B GLU* 2.9 30.3 + - - +
299B GLU* 2.9 29.1 + - - +
314B TRP* 3.3 54.1 - - + +
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Residues in contact with VAL 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B TRP* 3.7 33.0 - - + -
292B HIS* 2.9 23.5 + - + +
293B MET* 3.8 4.3 - - - +
295B ARG* 1.3 75.8 - - + +
297B ALA* 1.3 66.6 + - - +
299B GLU* 3.2 14.2 + - - +
300B PHE* 3.3 11.8 + - - +
356B LEU* 5.1 7.4 - - + -
360B HIS* 4.7 5.3 + - + +
399B VAL* 6.3 0.9 - - + -
404B HIS* 6.2 0.4 - - - +
408B ILE* 4.4 24.9 - - + -
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B MET 3.0 18.3 + - - +
294B PHE 3.6 5.2 - - - +
296B VAL* 1.3 76.2 - - - +
298B GLU* 1.3 65.3 + - - +
300B PHE* 3.1 14.4 + - - +
301B PHE* 3.3 14.6 + - - -
359B VAL* 3.8 20.0 - - + -
360B HIS* 3.4 33.8 + - + +
363B MET* 3.8 12.3 - - + -
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B PHE 2.9 18.6 + - - +
295B ARG* 2.9 37.4 + - - +
297B ALA* 1.3 76.1 - - - +
299B GLU* 1.3 62.5 + - - +
301B PHE* 3.0 15.7 + - - +
302B THR* 3.0 14.5 + - + +
307B SER 5.4 0.2 - - - +
308B PRO* 3.7 15.6 - - + +
309B MET* 2.9 44.4 + - + +
314B TRP* 3.6 13.4 + - + -
363B MET* 3.4 16.1 - - + -
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Residues in contact with GLU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ARG 2.9 17.3 + - - +
296B VAL* 3.8 7.9 - - - +
297B ALA 3.2 0.4 - - - -
298B GLU* 1.3 75.3 + - - +
300B PHE* 1.3 60.9 + - - +
302B THR* 3.1 11.7 + - - +
303B SER* 2.8 34.3 + - - -
531B TYR* 2.6 38.8 + - - -
532B ARG* 4.7 7.2 + - - -
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Residues in contact with PHE 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B VAL 3.3 9.5 + - - +
297B ALA 3.1 11.7 + - - +
299B GLU* 1.3 75.7 + - - +
301B PHE* 1.3 64.3 + - - +
303B SER* 2.5 26.7 + - - -
304B LEU* 3.4 9.1 + - + +
360B HIS* 4.6 6.5 - - - +
395B LEU* 3.7 34.5 - - + -
398B SER* 3.5 24.5 - - - -
399B VAL* 3.4 31.9 - - + -
404B HIS* 3.7 22.0 - + - -
529B ASP* 3.8 4.0 - - - -
530B ILE* 3.9 14.8 - - + -
531B TYR* 3.6 36.3 - + + -
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Residues in contact with PHE 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ALA 3.3 21.9 + - - -
298B GLU* 3.0 8.5 + - - +
300B PHE* 1.3 79.6 - - - +
302B THR* 1.3 59.8 + - - +
304B LEU* 3.1 11.7 + - - +
306B LEU* 3.1 36.4 + - + +
307B SER 4.3 5.2 - - - +
309B MET* 5.7 0.4 - - + -
360B HIS* 4.2 12.1 - + - -
363B MET* 3.6 32.8 - - + -
364B GLY* 3.6 26.7 - - - -
367B GLN* 3.6 46.9 - - + +
391B ILE* 4.8 8.1 - - + -
392B GLY* 4.8 2.7 - - - -
395B LEU* 3.5 29.4 - - + -
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Residues in contact with THR 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B GLU* 3.0 12.9 + - + +
299B GLU* 3.1 27.3 + - - +
301B PHE* 1.3 70.8 - - - +
303B SER* 1.3 61.3 + - - +
304B LEU 3.0 1.8 - - - -
305B GLU* 2.9 21.8 + - - +
306B LEU 3.7 9.9 - - - +
307B SER 4.2 0.7 - - - -
308B PRO* 3.7 43.1 - - + -
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Residues in contact with SER 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B GLU* 2.8 21.1 + - - -
300B PHE 2.5 19.6 + - - -
302B THR* 1.3 76.9 + - - +
304B LEU* 1.3 61.1 + - - +
305B GLU* 3.3 1.4 + - - +
531B TYR* 3.4 25.4 - - - -
532B ARG* 3.1 47.8 + - - +
534B THR* 4.1 8.3 - - - +
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B PHE* 3.5 29.4 - - + +
301B PHE 3.1 6.7 + - - +
302B THR 3.0 0.6 - - - -
303B SER* 1.3 83.9 - - - +
305B GLU* 1.3 68.1 + - - +
306B LEU* 3.3 20.6 + - + -
395B LEU* 4.3 17.0 - - + -
530B ILE* 3.2 41.3 - - + +
533B SER* 3.5 19.7 - - - +
534B THR* 4.2 7.0 - - - +
536B ALA* 4.9 0.9 - - + -
537B GLY* 3.4 32.2 - - - +
540B LEU* 5.0 3.4 - - + -
541B ARG* 4.2 1.2 + - - -
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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
------------------------------------------------------------
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