Contacts of the helix formed by residues 308 - 317 (chain A) in PDB entry 1Z6T
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 GLU 308 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307A PRO* 1.3 68.9 - - - +
309A GLN* 1.3 67.7 + - - +
310A ALA 3.1 2.5 - - - -
311A HIS* 2.8 30.9 + - + +
312A SER* 4.2 6.8 + - - -
47B PRO* 5.3 11.7 - - + -
407B GLU* 5.2 0.2 - - - +
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Residues in contact with GLN 309 (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 PRO* 3.2 20.1 - - - +
308A GLU* 1.3 81.7 + - + +
310A ALA* 1.3 59.8 + - - +
312A SER* 3.1 6.2 + - - -
313A ILE* 2.8 32.4 + - + +
338A TRP* 3.5 39.7 - - + +
339A GLU* 3.7 26.6 + - + +
342A LEU* 3.6 27.4 - - + -
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Residues in contact with ALA 310 (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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292A LEU* 3.9 18.6 - - + -
295A LEU* 3.9 4.7 - - + +
306A LEU* 3.9 15.5 - - + -
307A PRO 3.2 17.3 + - - +
308A GLU 3.1 0.8 - - - -
309A GLN* 1.3 78.7 - - - +
311A HIS* 1.3 59.4 + - - +
313A ILE* 3.3 4.2 + - - +
314A ILE* 3.0 32.7 + - - +
338A TRP* 3.6 27.2 - - + -
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Residues in contact with HIS 311 (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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292A LEU* 3.7 24.1 - - + +
303A LYS 5.4 1.8 + - - -
306A LEU* 4.6 7.6 + - - +
307A PRO 3.2 24.9 + - - -
308A GLU* 2.8 24.3 + - - +
310A ALA* 1.3 72.3 - - - +
312A SER* 1.3 60.3 + - - +
314A ILE* 3.6 4.9 + - - +
315A LYS* 3.2 21.7 + - - +
47B PRO* 3.5 29.9 - - + +
48B THR* 3.0 34.8 - - + +
51B GLN* 4.2 5.7 + - - -
407B GLU* 3.0 30.1 - - - +
409B GLU* 6.5 0.2 - - - -
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Residues in contact with SER 312 (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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308A GLU 4.2 5.6 + - - -
309A GLN* 3.1 11.0 + - - -
311A HIS* 1.3 75.0 - - - +
313A ILE* 1.3 58.1 + - - -
315A LYS* 3.4 10.1 + - - +
316A GLU* 3.0 32.6 + - - +
342A LEU* 3.5 27.7 - - - +
346A GLN* 4.9 4.9 + - - -
407B GLU* 2.7 21.9 + - - -
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Residues in contact with ILE 313 (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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295A LEU* 4.5 11.7 - - + -
309A GLN 2.8 17.8 + - - +
310A ALA* 3.3 8.9 + - - +
312A SER* 1.3 69.6 - - - +
314A ILE* 1.3 66.6 + - + +
316A GLU* 3.2 7.3 + - - +
317A CYS* 3.0 27.7 + - - -
327A ILE* 3.6 27.4 - - + -
331A LEU* 3.9 14.6 - - + -
338A TRP* 3.7 45.8 - - + +
341A TYR* 5.2 1.3 - - + -
342A LEU* 4.1 25.1 - - + +
345A LEU* 4.0 9.4 - - + -
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Residues in contact with ILE 314 (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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287A GLY 5.2 0.4 - - - +
288A LYS* 3.9 35.7 - - + +
291A GLY* 3.6 27.4 - - - +
292A LEU* 3.9 22.4 - - + +
295A LEU* 3.7 16.8 - - + -
310A ALA 3.0 20.6 + - - +
311A HIS* 3.8 7.0 - - - +
312A SER 3.3 0.2 - - - -
313A ILE* 1.3 76.8 - - - +
315A LYS* 1.3 64.4 + - - +
317A CYS* 3.0 17.3 + - - +
318A LYS* 3.4 7.1 + - - -
319A GLY* 4.4 5.6 + - - +
324A VAL* 3.8 22.0 - - + -
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Residues in contact with LYS 315 (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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311A HIS 3.2 13.9 + - - +
312A SER* 3.5 12.8 - - - +
314A ILE* 1.3 77.3 - - - +
316A GLU* 1.3 84.9 + - - +
318A LYS* 3.3 27.4 + - - +
346A GLN* 5.6 2.6 - - - +
398B LYS* 6.3 0.2 - - - +
405B ASP* 2.5 49.2 + - - -
406B MET* 3.7 4.9 - - - +
407B GLU* 3.7 38.6 - - + +
467B TYR* 3.4 15.1 + - + +
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Residues in contact with GLU 316 (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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312A SER 3.0 18.3 + - - +
313A ILE 3.2 8.2 + - - +
315A LYS* 1.3 102.8 + - - +
317A CYS* 1.3 59.7 + - - +
318A LYS* 3.3 18.7 + - - +
342A LEU* 4.2 7.2 - - + -
345A LEU* 4.0 29.0 - - + +
346A GLN* 3.4 38.5 + - + +
348A LYS* 4.0 17.0 + - - -
363A ALA* 3.4 17.8 - - - +
405B ASP* 4.5 5.3 - - - +
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Residues in contact with CYS 317 (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 ILE* 3.0 26.4 + - - -
314A ILE* 3.0 12.0 + - - +
316A GLU* 1.3 76.0 - - - +
318A LYS* 1.3 69.2 + - - +
319A GLY 3.2 0.7 - - - +
320A SER* 3.2 19.9 + - - -
323A VAL* 3.6 30.0 - - + +
324A VAL* 3.8 35.4 - - + -
327A ILE* 4.2 14.4 - - - -
345A LEU* 4.7 2.7 - - - -
363A ALA* 4.3 4.1 - - - +
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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