Contacts of the helix formed by residues 317 - 334 (chain A) in PDB entry 4U1D
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 THR 317 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A ARG 5.3 3.6 - - - +
316A ALA* 1.3 76.2 - - - +
318A GLU* 1.3 63.8 + - - +
319A GLU* 3.6 10.7 + - - +
320A GLU* 3.0 41.5 + - - +
321A PHE* 3.2 12.5 - - - -
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Residues in contact with GLU 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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316A ALA 3.7 1.0 + - - -
317A THR* 1.3 74.8 - - - +
319A GLU* 1.3 61.7 + - - +
320A GLU 3.2 0.3 + - - -
321A PHE* 3.2 20.4 + - - +
322A LYS* 3.0 21.7 + - + +
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Residues in contact with GLU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A THR* 3.1 11.3 - - - +
318A GLU* 1.3 79.2 - - - +
320A GLU* 1.3 60.3 + - + +
322A LYS* 3.2 36.8 - - - +
323A THR* 3.3 27.5 + - + +
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Residues in contact with GLU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A TYR* 2.5 34.0 + - + -
315A ARG 4.3 1.4 - - - +
316A ALA* 3.6 0.3 - - - -
317A THR* 3.0 37.9 + - - +
318A GLU 3.1 0.6 - - - -
319A GLU* 1.3 75.5 - - + +
321A PHE* 1.3 56.8 + - - +
322A LYS 3.1 1.6 - - - -
323A THR* 3.0 9.5 + - - +
324A TYR* 2.7 68.3 + - + +
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Residues in contact with PHE 321 (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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307A TYR* 3.3 35.4 - + - +
310A TYR* 3.9 16.4 - + - -
311A SER* 3.7 42.4 - - - -
313A ASN 5.8 0.4 - - - -
316A ALA* 3.6 31.0 - - + -
317A THR 3.2 18.4 - - - -
318A GLU* 3.2 25.9 + - - +
320A GLU* 1.3 77.9 - - + +
322A LYS* 1.3 61.9 + - - +
324A TYR* 4.7 0.7 - - - -
325A SER* 2.7 30.0 + - - -
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Residues in contact with LYS 322 (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 GLU* 3.0 12.7 + - + +
319A GLU* 3.2 39.5 - - - +
320A GLU 3.1 0.2 - - - -
321A PHE* 1.3 79.9 - - - +
323A THR* 1.3 82.1 + - - +
325A SER* 4.0 1.7 - - - -
326A SER* 2.8 35.2 + - - +
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Residues in contact with THR 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A GLU* 3.3 18.3 + - + +
320A GLU* 3.0 14.9 + - - +
322A LYS* 1.3 102.9 - - - +
324A TYR* 1.3 68.8 + - - +
326A SER* 3.6 5.3 - - - -
327A THR* 2.8 34.4 + - - -
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Residues in contact with TYR 324 (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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284A GLU* 4.8 6.0 + - - -
303A TRP* 3.8 24.7 - + + -
306A PHE* 3.5 35.2 - + - -
307A TYR* 3.8 21.5 - + + -
310A TYR* 3.7 29.4 - + - -
320A GLU* 2.7 49.8 + - + +
321A PHE 4.9 0.2 - - - -
323A THR* 1.3 79.6 - - - +
325A SER* 1.3 61.1 + - - +
327A THR* 3.1 7.4 + - - -
328A ILE* 2.8 35.5 + - - +
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Residues in contact with SER 325 (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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307A TYR* 2.7 29.6 + - - -
321A PHE 2.7 21.9 + - - -
322A LYS* 4.0 2.2 - - - -
324A TYR* 1.3 77.5 - - - +
326A SER* 1.3 57.4 + - - +
328A ILE* 3.4 9.6 + - - +
329A PHE* 3.0 28.8 + - - +
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Residues in contact with SER 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A LYS* 2.8 33.2 + - - +
323A THR* 3.6 6.7 - - - -
325A SER* 1.3 74.4 - - - +
327A THR* 1.3 56.4 + - - +
329A PHE* 3.0 7.1 + - - +
330A LEU* 2.7 37.5 + - - +
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Residues in contact with THR 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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299A HIS* 5.5 1.8 - - - +
303A TRP* 3.5 40.2 - - + +
323A THR* 2.8 25.9 + - - -
324A TYR* 3.4 7.2 - - - -
326A SER* 1.3 72.5 - - - +
328A ILE* 1.3 63.2 + - - +
330A LEU* 3.2 7.6 + - - +
331A SER* 2.9 26.1 + - - -
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Residues in contact with ILE 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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300A THR* 3.7 10.8 - - + +
303A TRP* 3.7 36.8 - - + +
304A LYS* 4.0 24.9 - - + +
307A TYR* 3.7 40.6 - - + -
324A TYR 2.8 23.9 + - - +
325A SER* 3.6 9.0 - - - +
327A THR* 1.3 72.9 - - - +
329A PHE* 1.3 61.6 + - - +
331A SER* 2.8 22.8 + - - -
332A ALA* 3.3 9.7 + - - +
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Residues in contact with PHE 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 SER 3.0 17.4 + - - +
326A SER* 3.6 5.2 - - - +
328A ILE* 1.3 74.7 - - - +
330A LEU* 1.3 67.7 + - - +
332A ALA* 3.1 17.9 + - + +
333A ILE* 3.1 43.5 + - + +
367A LEU* 4.3 22.9 - - + -
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Residues in contact with LEU 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 SER 2.7 21.4 + - - +
327A THR* 3.7 7.6 - - - +
329A PHE* 1.3 73.9 - - - +
331A SER* 1.3 57.6 + - - +
333A ILE* 3.2 18.3 + - + +
334A SER* 2.9 37.0 + - - -
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Residues in contact with SER 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A PRO* 4.9 2.4 - - - +
299A HIS* 3.8 28.8 - - - -
300A THR* 2.8 21.9 + - - +
303A TRP* 5.1 1.3 - - - -
327A THR* 2.9 15.7 + - - -
328A ILE* 2.8 19.1 + - - -
330A LEU* 1.3 77.4 - - - +
332A ALA* 1.3 57.7 + - - +
334A SER* 3.8 8.7 - - - -
335A THR* 2.8 23.0 + - - -
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Residues in contact with ALA 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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300A THR* 4.3 13.9 - - + -
328A ILE 3.3 9.4 + - - +
329A PHE* 3.1 16.0 + - + +
331A SER* 1.3 80.0 + - - +
333A ILE* 1.3 63.3 + - - +
334A SER 3.2 0.9 - - - -
335A THR* 3.6 17.4 + - - -
363A ARG* 3.8 13.7 + - - +
366A MET* 4.5 9.4 - - + +
367A LEU* 4.2 27.8 - - + +
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Residues in contact with ILE 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 PHE* 3.1 47.7 + - + +
330A LEU* 3.2 20.8 + - + +
332A ALA* 1.3 76.5 - - - +
334A SER* 1.3 58.9 + - - +
335A THR 3.1 5.7 + - - +
337A LEU* 5.6 0.3 - - - +
363A ARG* 2.9 32.8 + - - +
367A LEU* 5.8 2.2 - - + -
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Residues in contact with SER 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A PRO* 5.5 0.9 - - - +
330A LEU* 2.9 24.9 + - - -
331A SER* 3.9 11.7 - - - -
332A ALA 3.2 0.2 - - - -
333A ILE* 1.3 76.7 - - - +
335A THR* 1.3 60.5 + - - +
336A GLN 3.6 1.4 + - - -
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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