Contacts of the helix formed by residues 289 - 304 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A GLY 3.6 11.0 - - - +
288A TRP* 1.3 80.4 - - - +
290A ALA* 1.3 70.8 + - - +
291A THR* 3.2 9.0 + - - +
292A HIS* 3.0 34.3 + - + +
293A MET* 3.1 17.8 + - - +
320A GLU* 4.7 9.6 + - - +
351A VAL* 4.0 6.1 - - - -
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Residues in contact with ALA 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A GLN* 1.3 72.3 - - - +
291A THR* 1.3 59.3 + - - +
293A MET* 2.9 31.6 + - - +
294A PHE* 3.0 19.0 + - + -
319A LEU* 3.4 32.3 - - + +
320A GLU* 3.6 23.9 + - + +
349A THR* 3.8 15.7 - - + +
351A VAL* 4.5 3.8 - - - +
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Residues in contact with THR 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A GLN* 3.2 6.4 + - - +
290A ALA* 1.3 79.0 - - - +
292A HIS* 1.3 68.2 + - - +
294A PHE* 3.3 7.5 + - - +
295A ARG* 3.0 36.9 + - + +
314A TRP* 4.2 20.9 - - + -
319A LEU* 4.9 9.9 - - + +
320A GLU* 5.2 3.7 + - - -
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Residues in contact with HIS 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A GLN 5.9 0.2 - - - -
287A GLY 3.6 15.6 + - - -
288A TRP* 3.8 16.4 - + + -
289A GLN* 3.0 42.6 + - + +
291A THR* 1.3 81.1 - - - +
293A MET* 1.3 68.0 + - - +
295A ARG* 3.3 7.3 + - - +
296A VAL* 2.9 32.3 + - + +
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Residues in contact with MET 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A MET* 4.1 8.1 - - + -
288A TRP* 3.9 21.5 - - + -
289A GLN 3.1 15.5 + - - +
290A ALA* 2.9 9.5 + - - +
292A HIS* 1.3 77.1 - - - +
294A PHE* 1.3 60.8 + - - +
296A VAL* 3.4 2.1 + - - +
297A ALA* 3.1 22.7 + - - +
349A THR* 3.9 16.4 - - + -
350A ARG 3.5 25.6 - - - +
351A VAL* 4.0 13.9 - - - -
352A THR 3.7 9.4 - - - +
355A GLN* 3.7 6.1 - - + +
356A LEU* 3.5 45.8 - - + +
359A VAL* 3.9 11.3 - - + +
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Residues in contact with PHE 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ALA 3.0 29.4 + - - -
291A THR* 3.3 4.2 + - - +
293A MET* 1.3 77.1 - - - +
295A ARG* 1.3 56.6 + - - +
297A ALA 3.4 0.3 + - - -
298A GLU* 2.9 28.9 + - - +
313A PHE* 4.1 10.3 - + - -
314A TRP* 3.7 23.6 - - + -
319A LEU* 3.7 32.1 - - + -
345A ILE* 3.7 27.8 - - + -
347A GLN* 3.6 21.8 - - + -
349A THR* 3.5 22.7 - - + -
359A VAL* 3.6 31.2 - - + -
363A MET* 3.4 19.1 - - + +
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Residues in contact with ARG 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A THR* 3.0 28.8 + - + +
292A HIS* 3.3 8.0 + - - +
294A PHE* 1.3 71.9 - - - +
296A VAL* 1.3 62.5 + - + +
298A GLU* 3.0 31.0 + - - +
299A GLU* 3.0 29.5 + - - +
314A TRP* 3.4 51.1 - - + +
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Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A TRP* 3.9 31.9 - - + -
292A HIS* 2.9 21.7 + - + +
293A MET 3.8 3.4 - - - +
295A ARG* 1.3 79.0 - - + +
297A ALA* 1.3 62.0 + - - +
299A GLU* 3.3 13.9 + - - +
300A PHE* 3.4 11.4 + - - +
356A LEU* 4.9 7.4 - - + -
360A HIS* 4.7 4.6 + - + -
399A VAL* 6.2 1.6 - - + -
404A HIS* 6.0 1.1 - - - +
408A ILE* 4.5 22.4 - - + -
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Residues in contact with ALA 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A MET 3.1 13.2 + - - +
294A PHE 3.6 7.4 - - - +
296A VAL* 1.3 74.7 - - - +
298A GLU* 1.3 67.6 + - - +
300A PHE* 3.1 12.8 + - - +
301A PHE* 3.3 16.6 + - + -
359A VAL* 3.9 16.4 - - + -
360A HIS* 3.4 37.6 + - + +
363A MET* 3.8 12.6 - - + -
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Residues in contact with GLU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A PHE 2.9 20.5 + - - +
295A ARG* 3.0 35.5 + - - +
297A ALA* 1.3 73.0 - - - +
299A GLU* 1.3 62.3 + - - +
301A PHE* 3.0 8.6 + - - +
302A THR* 3.0 22.2 + - + +
307A SER 5.3 0.2 - - - +
308A PRO* 3.7 16.0 - - + +
309A MET* 2.8 46.7 + - + +
314A TRP* 3.6 12.8 + - + -
363A MET* 3.4 16.5 - - + -
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Residues in contact with GLU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ARG 3.0 16.9 + - - +
296A VAL* 3.8 7.2 - - - +
297A ALA 3.1 0.6 - - - -
298A GLU* 1.3 74.7 - - - +
300A PHE* 1.3 59.3 + - - +
302A THR* 2.9 13.3 + - - +
303A SER* 2.8 34.8 + - - -
531A TYR* 2.5 37.9 + - - -
532A ARG* 4.8 6.5 + - - -
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Residues in contact with PHE 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A VAL 3.4 7.9 + - - +
297A ALA 3.1 9.5 + - - +
299A GLU* 1.3 78.1 + - - +
301A PHE* 1.3 62.1 + - - +
303A SER* 2.7 24.2 + - - -
304A LEU* 3.2 11.3 + - + +
360A HIS* 4.7 6.7 - - - +
395A LEU* 3.6 34.3 - - + -
398A SER* 3.5 24.7 - - - -
399A VAL* 3.5 28.0 - - + -
404A HIS* 3.5 26.0 - + - -
529A ASP* 3.9 3.6 - - - -
530A ILE* 3.9 14.6 - - + -
531A TYR* 3.5 36.1 - + + -
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Residues in contact with PHE 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ALA 3.3 21.7 + - - -
298A GLU* 3.0 8.8 + - + +
300A PHE* 1.3 78.2 - - - +
302A THR* 1.3 61.4 + - - +
304A LEU* 3.1 10.8 + - - +
306A LEU* 3.0 36.9 + - + +
307A SER 4.2 4.7 - - - +
309A MET* 5.7 0.2 - - + -
360A HIS* 4.4 11.2 - + - -
363A MET* 3.5 33.9 - - + -
364A GLY* 3.7 26.0 - - - -
367A GLN* 3.5 47.3 - - + +
391A ILE* 4.7 6.1 - - + -
392A GLY* 4.8 3.8 - - - -
395A LEU* 3.6 32.1 - - + -
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Residues in contact with THR 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A GLU* 3.0 13.8 + - + +
299A GLU* 2.9 30.5 + - - +
301A PHE* 1.3 72.0 - - - +
303A SER* 1.3 59.1 + - - +
305A GLU* 2.9 21.8 + - - +
306A LEU 3.5 9.0 - - - +
307A SER 4.2 0.4 - - - -
308A PRO* 3.7 44.2 - - + -
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Residues in contact with SER 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A GLU* 2.8 25.1 + - - -
300A PHE 2.7 15.8 + - - -
301A PHE 3.2 0.2 - - - -
302A THR* 1.3 75.8 + - - +
304A LEU* 1.3 58.2 + - - +
305A GLU* 3.1 3.7 + - - +
531A TYR* 3.4 23.7 - - - -
532A ARG* 3.0 48.8 + - - +
534A THR* 4.2 8.3 - - - +
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Residues in contact with LEU 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 PHE* 3.4 30.7 - - + +
301A PHE 3.1 9.0 + - - +
303A SER* 1.3 79.6 + - - +
305A GLU* 1.3 68.3 + - - +
306A LEU* 3.2 15.6 - - + +
395A LEU* 4.1 22.4 - - + -
530A ILE* 3.3 41.1 - - + +
532A ARG 4.1 0.2 - - - +
533A SER 3.4 21.3 - - - +
534A THR* 4.4 4.2 - - - +
536A ALA* 4.8 0.7 - - + -
537A GLY* 3.3 30.4 - - - +
540A LEU* 4.7 4.9 - - + -
541A ARG* 3.9 2.9 + - - -
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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
------------------------------------------------------------
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