Contacts of the helix formed by residues 327 - 343 (chain A) in PDB entry 4COO
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 ASN 327 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A PRO* 6.0 0.9 - - - -
283A GLU* 4.2 25.2 + - + +
303A VAL* 5.1 1.3 - - - -
326A SER* 1.3 77.2 + - - +
328A ASP* 1.3 66.2 + - - +
329A GLU* 3.1 10.6 + - - +
330A GLU* 2.9 45.3 + - - +
331A ALA* 3.1 23.1 + - - +
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Residues in contact with ASP 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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282A PRO* 6.0 0.2 - - - +
301A TYR* 3.5 17.0 - - - +
302A GLU* 2.7 37.8 + - - +
303A VAL* 3.0 33.8 + - - +
327A ASN* 1.3 73.6 - - - +
329A GLU* 1.3 68.0 + - - +
331A ALA* 3.1 1.4 + - - +
332A PHE* 3.0 30.9 + - + -
396A PHE* 3.5 23.0 - - + -
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Residues in contact with GLU 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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327A ASN* 3.1 9.4 + - - +
328A ASP* 1.3 79.8 - - - +
330A GLU* 1.3 55.4 + - - +
332A PHE* 3.9 1.2 - - - +
333A THR* 2.7 44.8 + - - +
391A MET* 5.6 0.2 - - - +
395A GLY 4.8 7.0 - - - +
396A PHE* 4.0 40.4 - - + +
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Residues in contact with GLU 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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325A LYS 4.0 2.4 - - - +
326A SER* 3.2 14.7 - - - -
327A ASN* 2.9 48.6 + - - +
329A GLU* 1.3 75.5 - - - +
331A ALA* 1.3 69.2 + - - +
333A THR* 4.2 5.6 - - - -
334A PHE* 2.9 36.7 + - + +
352A SER* 5.6 0.2 - - - -
355A ALA* 3.8 21.9 - - + +
356A VAL* 5.2 0.7 - - - +
359A LYS* 3.1 31.0 + - - -
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Residues in contact with ALA 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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303A VAL* 3.5 22.0 - - + -
327A ASN 3.1 18.3 + - - +
328A ASP 3.1 1.5 + - - +
330A GLU* 1.3 77.7 - - - +
332A PHE* 1.3 60.3 + - + +
335A ALA* 2.9 26.2 + - - +
348A GLY 3.7 6.1 - - - +
351A GLY* 3.3 9.7 - - - -
352A SER* 3.2 37.2 - - - +
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Residues in contact with PHE 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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302A GLU* 3.9 13.0 - - + -
303A VAL* 3.8 34.3 - - + -
328A ASP* 3.0 22.7 + - + +
329A GLU* 4.3 2.0 - - - +
331A ALA* 1.3 74.4 - - - +
333A THR* 1.3 66.2 + - - +
335A ALA* 3.9 2.8 - - - +
336A ARG* 3.0 31.5 + - - +
348A GLY* 4.2 11.9 - - - -
381A TYR* 6.1 1.8 - + - -
385A PHE* 3.4 35.8 - + + -
390A TRP* 3.7 18.6 - + - -
391A MET* 3.8 20.6 - - + -
396A PHE* 3.6 36.6 - + + -
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Residues in contact with THR 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 GLU* 2.7 32.9 + - - +
330A GLU* 3.7 7.6 - - - -
332A PHE* 1.3 77.5 - - - +
334A PHE* 1.3 63.8 + - + +
336A ARG* 3.4 8.0 + - - +
337A MET* 3.1 42.4 + - + +
391A MET* 4.8 3.8 - - - +
396A PHE 4.8 5.2 + - - -
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Residues in contact with PHE 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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95A ILE* 4.1 11.4 - - + -
99A PHE* 3.5 43.3 - + - -
330A GLU* 2.9 29.3 + - + +
333A THR* 1.3 82.9 - - + +
335A ALA* 1.3 59.9 + - - +
337A MET* 3.6 17.0 - - + +
338A LEU* 2.9 33.1 + - - +
351A GLY* 3.4 22.9 - - - +
354A VAL* 3.9 21.8 - - + -
355A ALA* 3.6 20.4 - - + -
358A VAL* 3.9 24.5 - - + -
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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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331A ALA 2.9 17.5 + - - +
332A PHE* 3.4 4.2 + - - +
334A PHE* 1.3 75.8 - - - +
336A ARG* 1.3 63.1 + - - +
338A LEU* 3.3 8.9 + - - +
339A ILE* 3.2 26.0 + - - +
346A CYS* 4.6 3.9 - - - +
347A GLY 3.5 25.4 - - - +
348A GLY* 4.4 1.8 - - - -
351A GLY* 3.6 6.8 - - - -
385A PHE* 3.7 25.1 - - + -
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Residues in contact with ARG 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 PHE 3.0 22.5 + - - +
333A THR* 3.7 6.5 - - - +
335A ALA* 1.3 76.4 - - - +
337A MET* 1.3 57.3 + - - +
339A ILE* 3.3 10.8 + - + +
340A ALA* 2.9 30.4 + - - +
385A PHE* 2.9 37.6 + - + -
386A LEU* 3.2 20.0 + - + -
387A SER 3.6 1.6 - - - -
388A ASP* 2.6 38.5 + - - +
391A MET* 3.8 23.9 - - - +
397A LEU* 4.5 12.4 - - - +
183B ALA* 4.6 5.6 - - + +
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Residues in contact with MET 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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95A ILE* 3.8 21.5 - - + -
98A LYS* 3.9 14.1 - - - -
99A PHE* 3.8 31.6 - - + -
333A THR* 3.1 33.5 + - + +
334A PHE* 3.6 16.4 - - + +
335A ALA 3.2 0.2 - - - -
336A ARG* 1.3 74.5 - - - +
338A LEU* 1.3 59.7 + - - +
340A ALA* 4.4 4.5 - - - +
341A GLN* 2.8 66.1 + - + +
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Residues in contact with LEU 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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92A ILE* 4.2 10.8 - - + -
95A ILE* 3.6 22.0 - - + -
334A PHE 2.9 22.9 + - - +
335A ALA 3.6 4.7 - - - +
337A MET* 1.3 73.4 - - - +
339A ILE* 1.3 61.7 + - - +
342A GLU* 3.0 20.4 + - + +
343A GLY 3.1 6.9 + - - -
344A LEU* 3.2 30.3 + - + +
346A CYS* 3.6 28.5 - - - -
350A ALA* 3.9 16.2 - - + +
351A GLY 4.2 1.6 - - - +
354A VAL* 3.9 34.8 - - + -
374A LEU* 4.7 4.5 - - + -
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Residues in contact with ILE 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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335A ALA 3.2 14.8 + - - +
336A ARG* 3.6 8.7 - - + +
337A MET 3.2 0.2 - - - -
338A LEU* 1.3 76.4 - - - +
340A ALA* 1.3 58.6 + - - +
343A GLY* 3.0 24.4 + - - -
344A LEU 3.3 21.5 - - - +
345A LEU* 3.9 15.3 - - + -
346A CYS 4.3 4.9 - - - +
378A VAL* 4.0 17.5 - - + -
385A PHE* 4.3 11.0 - - + -
386A LEU* 3.9 25.8 - - + -
159B ALA* 4.7 0.3 - - - +
183B ALA* 3.6 28.3 - - + +
184B LEU* 3.6 20.4 - - + +
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Residues in contact with ALA 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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94A LYS* 4.9 0.2 + - - -
336A ARG 2.9 21.3 + - - +
337A MET* 4.2 4.3 - - - +
339A ILE* 1.3 73.5 - - - +
341A GLN* 1.3 64.2 + - + +
159B ALA* 3.5 22.3 - - - +
183B ALA 3.5 17.7 - - - +
184B LEU* 4.5 9.1 - - - +
185B GLY* 5.4 1.6 - - - +
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Residues in contact with GLN 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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94A LYS* 2.6 66.7 + - + +
95A ILE* 4.2 9.5 - - + +
98A LYS* 3.6 23.9 + - - +
337A MET* 2.8 50.6 + - + +
340A ALA* 1.3 81.9 - - + +
342A GLU* 1.3 60.9 + - - +
343A GLY 3.7 0.2 - - - -
159B ALA 4.1 2.5 - - - +
160B VAL* 4.6 2.1 - - - -
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Residues in contact with GLU 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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91A ARG 4.1 3.5 - - - +
92A ILE* 3.4 19.8 - - + +
93A ASN* 2.9 29.0 + - - +
94A LYS* 2.7 30.5 + - - +
95A ILE* 3.1 33.0 + - + +
338A LEU* 3.0 12.7 + - + +
341A GLN* 1.3 80.1 - - - +
343A GLY* 1.3 63.9 + - - +
344A LEU* 3.4 20.0 + - + +
79B ASP* 6.0 0.2 - - - +
80B ILE* 3.5 18.2 + - - +
160B VAL* 3.6 11.6 - - - +
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Residues in contact with GLY 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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338A LEU 3.1 0.2 + - - -
339A ILE* 3.0 21.0 + - - -
340A ALA 4.7 0.4 - - - -
341A GLN 3.7 0.6 - - - -
342A GLU* 1.3 79.6 - - - +
344A LEU* 1.3 60.3 + - - +
345A LEU* 3.7 5.5 + - - +
80B ILE* 3.6 16.3 - - - +
114B ALA 4.9 1.6 - - - +
156B LEU* 3.7 36.0 - - - +
159B ALA* 5.1 2.1 - - - +
160B VAL* 4.4 3.1 - - - +
184B LEU* 4.2 4.7 - - - -
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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