Contacts of the helix formed by residues 321 - 336 (chain A) in PDB entry 2Y4U
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 LYS 321 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285A THR* 3.3 30.7 - - - +
316A PHE* 3.2 27.9 + - + +
317A SER* 4.7 0.4 + - - -
319A ASP* 3.3 31.4 + - + +
320A GLU* 1.3 79.6 - - - +
322A PRO* 1.3 68.3 - - - +
323A VAL 3.4 1.8 - - - -
324A GLU* 3.3 23.4 - - - +
325A ALA* 3.1 22.6 + - - +
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Residues in contact with PRO 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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317A SER* 6.0 0.2 - - - -
320A GLU 3.2 12.3 - - - +
321A LYS* 1.3 82.6 - - - +
323A VAL* 1.3 69.3 + - + +
324A GLU* 4.7 0.4 - - - +
325A ALA* 3.3 7.3 - - + +
326A ILE* 2.8 37.2 + - + +
349A ALA* 3.8 28.9 - - + +
352A ILE* 4.3 23.1 - - + -
353A GLU* 4.1 24.5 - - + +
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Residues in contact with VAL 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LYS 3.4 0.6 - - - -
322A PRO* 1.3 82.9 - - + +
324A GLU* 1.3 69.0 + - + +
326A ILE* 3.3 8.9 + - - +
327A ARG* 3.0 25.2 + - + +
353A GLU* 4.9 11.0 - - - +
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Residues in contact with GLU 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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316A PHE* 3.8 32.5 - - + -
321A LYS* 3.3 34.8 - - - +
322A PRO* 4.7 0.2 - - - +
323A VAL* 1.3 81.8 + - + +
325A ALA* 1.3 69.7 + - - +
327A ARG* 3.0 36.0 + - - +
328A VAL* 3.0 16.8 + - - +
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Residues in contact with ALA 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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313A CYS 4.5 2.2 - - - +
316A PHE* 3.6 10.8 - - - +
317A SER* 3.7 28.9 - - - +
321A LYS 3.1 20.6 + - - +
322A PRO* 3.3 10.5 - - + +
324A GLU* 1.3 77.1 - - - +
326A ILE* 1.3 60.5 + - - +
328A VAL* 3.8 0.9 - - - +
329A CYS* 2.7 36.5 + - - -
346A ARG* 5.3 0.2 - - - -
349A ALA* 4.0 10.3 - - + -
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Residues in contact with ILE 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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322A PRO* 2.8 33.7 + - + +
323A VAL* 3.6 6.5 - - - +
325A ALA* 1.3 71.6 - - - +
327A ARG* 1.3 59.9 - - - +
328A VAL 3.1 1.2 + - - -
329A CYS* 3.5 0.7 + - - +
330A SER* 2.5 40.7 + - - +
346A ARG* 4.1 23.7 - - + +
349A ALA* 4.4 12.8 - - + -
350A TYR* 4.2 37.0 - - + +
353A GLU* 4.9 9.9 - - + -
355A MSE 5.6 2.9 - - + -
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Residues in contact with ARG 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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316A PHE* 4.8 9.3 - - - -
323A VAL* 3.0 14.3 + - + +
324A GLU* 3.0 34.3 + - - +
326A ILE* 1.3 79.5 - - - +
328A VAL* 1.3 77.0 + - - +
330A SER* 3.4 15.6 - - - -
331A GLU* 3.6 10.5 + - - +
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Residues in contact with VAL 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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309A LYS* 3.8 20.9 - - + +
312A ILE* 4.2 7.9 - - + -
313A CYS* 3.6 30.7 - - + +
316A PHE* 4.1 17.9 - - + -
324A GLU 3.0 16.7 + - - +
325A ALA 4.0 1.6 - - - +
327A ARG* 1.3 95.5 - - - +
329A CYS* 1.3 60.1 + - - +
330A SER 3.0 1.3 - - - -
331A GLU* 2.7 34.9 + - + +
332A VAL* 2.9 13.3 + - + +
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Residues in contact with CYS 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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313A CYS* 2.1 46.2 - - - -
325A ALA* 2.7 33.8 + - - +
328A VAL* 1.3 73.7 - - - +
330A SER* 1.3 56.8 + - - +
332A VAL* 4.0 6.1 - - - -
333A LEU* 2.8 39.2 + - + +
342A ALA 4.3 5.8 - - - +
345A ASP 5.1 0.4 - - - -
346A ARG* 3.7 37.2 - - + -
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Residues in contact with SER 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ILE* 2.5 29.2 + - - +
327A ARG* 3.4 10.8 - - - -
328A VAL 3.0 0.6 - - - -
329A CYS* 1.3 77.3 - - - +
331A GLU* 1.3 57.1 + - - +
333A LEU* 3.8 2.5 - - - +
334A GLN* 2.9 38.8 + - - +
346A ARG* 3.5 21.8 + - - +
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Residues in contact with GLU 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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309A LYS* 2.9 39.9 + - + +
327A ARG* 3.6 8.9 + - - +
328A VAL* 2.7 23.2 + - - +
330A SER* 1.3 74.1 - - - +
332A VAL* 1.3 61.3 + - - +
334A GLN* 3.3 18.7 + - - +
335A MSE 3.2 32.5 + - + +
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Residues in contact with VAL 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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306A VAL* 4.8 1.8 - - + +
309A LYS* 3.8 20.6 - - + +
310A GLU* 3.8 31.6 - - + +
313A CYS* 4.5 1.3 - - + -
328A VAL* 2.9 16.6 + - + +
329A CYS* 3.5 13.0 - - - +
331A GLU* 1.3 76.3 - - - +
333A LEU* 1.3 51.9 + - - +
335A MSE 2.8 20.1 + - + +
336A GLU* 2.7 33.2 + - + +
339A ASN* 4.3 19.3 - - + +
342A ALA* 3.7 23.6 - - + -
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Residues in contact with LEU 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 CYS* 2.8 25.0 + - + +
330A SER* 4.1 2.9 - - - +
332A VAL* 1.3 67.7 - - - +
334A GLN* 1.3 66.6 + - - +
336A GLU 2.9 21.1 - - - +
337A PRO* 3.0 35.3 - - + +
339A ASN* 3.7 11.9 - - + +
342A ALA* 3.5 26.7 - - + -
343A LEU* 3.9 30.3 - - + +
346A ARG* 3.5 40.8 - - - +
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Residues in contact with GLN 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 SER* 2.9 25.6 + - - +
331A GLU* 3.3 20.5 - - + +
332A VAL 3.1 0.2 - - - -
333A LEU* 1.3 78.8 - - - +
335A MSE 1.3 60.9 + - + +
337A PRO* 4.8 4.7 - - - +
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Residues in contact with MSE 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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305A THR* 5.5 3.1 - - - -
306A VAL* 3.6 45.5 - - + +
309A LYS* 4.6 12.1 - - + -
331A GLU* 3.4 17.5 - - + +
332A VAL* 2.8 43.6 + - + +
333A LEU 4.1 0.2 - - - -
334A GLN* 1.3 77.1 - - + +
336A GLU* 1.3 69.3 + - + +
337A PRO* 4.2 4.3 - - - +
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Residues in contact with GLU 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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303A GLU* 5.0 0.3 - - - +
306A VAL* 3.3 15.3 - - + +
307A ARG* 2.7 37.5 + - - -
332A VAL* 2.7 12.1 + - - +
333A LEU* 2.9 21.3 - - - +
335A MSE 1.3 82.2 - - + +
337A PRO* 1.4 64.7 - - - +
338A ASP* 3.0 15.7 + - - +
339A ASN* 2.5 51.0 + - + +
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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