Contacts of the helix formed by residues 325 - 338 (chain A) in PDB entry 1U9J
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 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A GLY 4.6 1.3 + - - -
323A VAL 2.9 7.7 + - - -
324A ASN* 1.3 75.8 - - - +
326A PHE* 1.3 60.1 + - - +
327A ILE 3.6 1.3 - - - -
328A GLY 4.0 2.5 - - - -
329A ASN* 2.9 32.6 + - - +
352A ALA* 4.0 12.9 - - - +
353A ILE* 4.8 0.2 - - - +
497A ARG* 4.6 3.6 - - - -
499A ASP* 3.3 11.4 - - - -
505A ARG* 5.1 4.3 - - - -
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Residues in contact with PHE 326 (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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325A GLY* 1.3 71.9 - - - +
327A ILE* 1.3 68.6 + - + +
329A ASN* 3.9 1.7 - - - +
330A HIS* 3.2 41.3 + + - -
493A TRP* 3.7 18.8 - + + -
494A MET* 3.8 16.4 - - - -
495A GLY 4.0 12.1 - - - -
496A PRO 3.4 18.8 - - - -
497A ARG 3.4 26.8 + - - +
498A LEU* 4.1 2.2 - - + -
499A ASP* 2.7 29.8 + - - +
507A GLY* 3.6 4.9 - - - -
508A SER* 3.3 28.7 - - - -
540A ILE* 3.5 36.6 - - + -
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Residues in contact with ILE 327 (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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325A GLY 3.6 0.2 - - - -
326A PHE* 1.3 82.7 - - + +
328A GLY* 1.3 55.9 + - - +
330A HIS* 4.9 0.4 - - - -
331A LEU* 2.8 38.0 + - + +
387A LEU* 4.5 1.8 - - + -
389A LEU* 3.5 35.7 - - + -
488A PHE* 4.7 9.2 - - + -
490A PRO* 5.4 1.6 - - + -
493A TRP* 3.8 31.4 - - + -
506A ILE* 3.6 26.9 + - + +
507A GLY* 3.7 19.1 - - - -
540A ILE* 5.4 0.4 - - - -
544A ILE* 4.1 6.9 - - + +
547A LEU* 4.2 20.4 - - + -
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Residues in contact with GLY 328 (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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320A ILE* 4.5 9.0 - - - -
322A GLY 5.1 0.6 + - - -
323A VAL* 3.3 37.0 + - - +
325A GLY 3.5 3.4 + - - -
326A PHE 3.3 0.8 - - - -
327A ILE* 1.3 77.8 - - - +
329A ASN* 1.3 61.6 + - - +
331A LEU* 4.8 1.8 - - - -
332A THR* 2.7 33.0 + - - -
353A ILE* 4.2 0.4 - - - -
389A LEU* 4.2 3.2 - - - +
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Residues in contact with ASN 329 (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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325A GLY 2.9 20.1 + - - +
326A PHE* 3.9 3.4 - - - +
328A GLY* 1.3 76.4 - - - +
330A HIS* 1.3 71.3 + - - +
333A GLU* 3.1 24.0 + - - +
352A ALA* 2.9 22.1 - - + +
353A ILE* 3.8 14.9 - - + +
355A ARG* 5.9 1.0 - - - +
356A PHE* 3.7 23.5 - - - -
497A ARG* 3.2 41.8 + - + +
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Residues in contact with HIS 330 (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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326A PHE* 3.2 34.0 + + - +
329A ASN* 1.3 84.3 + - - +
331A LEU* 1.3 65.7 + - - +
333A GLU* 3.4 6.9 + - + +
334A ARG* 3.1 22.2 + - - +
496A PRO* 2.9 41.7 + - + +
497A ARG* 4.4 11.7 - - + -
540A ILE* 3.7 31.3 - - + +
541A ARG* 6.3 1.6 - - + -
544A ILE* 3.8 26.8 - - + +
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Residues in contact with LEU 331 (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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318A VAL* 5.1 0.9 - - + -
320A ILE* 3.9 17.0 - - + -
327A ILE* 2.8 23.4 + - + +
328A GLY 4.3 1.3 - - - +
330A HIS* 1.3 72.9 - - - +
332A THR* 1.3 57.7 + - - +
334A ARG* 3.1 7.6 + - + +
335A LEU* 2.8 44.9 + - + +
387A LEU* 3.3 35.2 - - + -
544A ILE* 3.7 12.4 - - + +
547A LEU* 3.6 19.5 - - + -
548A TYR* 4.7 11.2 - - - -
551A ILE* 3.7 32.1 - - + -
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Residues in contact with THR 332 (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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320A ILE* 3.7 16.1 - - - +
323A VAL* 3.9 7.6 - - - +
328A GLY 2.7 24.5 + - - -
329A ASN* 3.9 3.1 - - - -
331A LEU* 1.3 74.9 - - - +
333A GLU* 1.3 64.0 + - - +
335A LEU* 4.6 6.7 - - - +
336A LEU* 2.9 47.0 + - + +
343A VAL* 3.8 9.2 - - + +
353A ILE* 5.5 0.4 - - - -
356A PHE* 3.9 15.5 - - + -
362A PHE* 3.5 22.5 - - + -
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Residues in contact with GLU 333 (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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329A ASN* 3.1 20.6 + - - +
330A HIS* 3.7 9.2 - - + +
331A LEU 3.3 0.2 - - - -
332A THR* 1.3 76.6 - - - +
334A ARG* 1.3 63.7 + - - +
336A LEU* 3.9 2.1 - - - +
337A ARG* 2.7 60.2 + - - +
356A PHE* 3.7 23.5 - - + -
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Residues in contact with ARG 334 (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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330A HIS 3.1 10.3 + - - +
331A LEU* 3.3 16.6 - - + +
333A GLU* 1.3 83.3 + - - +
335A LEU* 1.3 65.0 + - - +
337A ARG* 3.0 52.2 - - - +
338A GLU* 2.6 36.0 + - - +
544A ILE* 4.3 19.7 - - + +
545A GLU* 2.6 40.2 + - - -
548A TYR* 3.4 40.9 - - + -
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Residues in contact with LEU 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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318A VAL* 4.1 25.8 - - + -
320A ILE* 4.6 4.0 - - + -
331A LEU* 2.8 42.8 + - + +
332A THR 4.1 0.7 - - - +
334A ARG* 1.3 72.7 - - - +
336A LEU* 1.3 58.9 + - - +
337A ARG 3.0 0.2 - - - -
338A GLU* 2.9 29.8 + - - +
341A TYR* 3.7 47.8 - - + +
343A VAL* 4.0 27.4 - - + -
548A TYR* 4.0 15.7 - - + -
551A ILE* 4.2 12.6 - - + -
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Residues in contact with LEU 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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332A THR* 2.9 39.7 + - + +
333A GLU* 4.0 3.8 - - - +
335A LEU* 1.3 76.6 - - - +
337A ARG* 1.3 61.5 + - - +
338A GLU 3.2 9.5 - - - +
341A TYR* 4.8 5.6 - - - +
343A VAL* 3.5 27.6 - - + +
356A PHE* 3.7 20.0 - - + -
359A HIS* 3.7 41.3 + - + +
361A HIS* 4.0 22.7 - - + +
362A PHE* 4.2 7.9 - - + -
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Residues in contact with ARG 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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333A GLU* 2.7 44.5 + - - +
334A ARG* 3.0 55.0 + - - +
335A LEU 3.0 0.2 - - - -
336A LEU* 1.3 79.2 - - - +
338A GLU* 1.3 63.9 + - - +
544A ILE* 6.1 0.8 - - - +
545A GLU* 5.4 0.6 + - - -
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Residues in contact with GLU 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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315A ARG* 4.1 6.4 + - - -
334A ARG* 2.6 31.1 + - - +
335A LEU 2.9 17.7 + - - +
336A LEU* 3.2 13.7 - - - +
337A ARG* 1.3 86.4 - - - +
339A ASP* 1.3 61.6 + - - +
340A HIS* 3.4 22.9 + - + +
341A TYR* 4.0 5.1 + - + +
548A TYR* 3.1 35.2 + - + +
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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
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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