Contacts of the helix formed by residues 308 - 318 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307B PRO* 1.3 74.9 - - - +
309B GLN* 1.3 86.1 + - - +
310B ALA 3.1 1.1 + - - -
311B HIS* 3.4 26.5 + - - +
312B SER* 4.0 6.6 + - - -
339B GLU* 5.3 0.7 - - - +
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Residues in contact with GLN 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B PRO* 3.2 11.0 - - - +
308B GLU* 1.3 98.9 + - + +
310B ALA* 1.3 53.9 + - - +
311B HIS 3.2 0.2 - - - -
312B SER* 3.1 6.1 + - - -
313B ILE* 2.8 37.2 + - + +
338B TRP* 3.8 42.0 - - + +
339B GLU* 2.7 34.7 + - - +
342B LEU* 4.0 18.6 - - + -
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Residues in contact with ALA 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B LEU* 4.0 15.5 - - + -
295B LEU* 4.1 4.8 - - + +
306B LEU* 4.1 15.9 - - + -
307B PRO 3.2 15.5 + - - +
308B GLU 3.1 0.8 - - - -
309B GLN* 1.3 78.5 - - - +
311B HIS* 1.3 59.1 + - + +
313B ILE* 3.2 3.4 + - - +
314B ILE* 2.9 32.2 + - - +
338B TRP* 3.5 32.8 - - + -
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Residues in contact with HIS 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B LYS* 2.4 42.7 + - + +
292B LEU* 3.6 36.1 - - + +
303B LYS 5.7 3.2 + - - -
306B LEU* 5.2 8.5 - - + +
307B PRO 4.3 10.5 + - - -
308B GLU* 3.7 17.7 + - - +
309B GLN 3.2 0.6 - - - -
310B ALA* 1.3 77.2 - - + +
312B SER* 1.3 63.0 + - - +
314B ILE 3.5 0.3 + - - -
315B LYS* 3.1 8.0 + - - +
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Residues in contact with SER 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B GLU 4.0 5.6 + - - -
309B GLN* 3.1 5.8 + - - -
311B HIS* 1.3 76.7 - - - +
313B ILE* 1.3 58.3 + - - +
315B LYS* 3.3 10.7 + - - +
316B GLU* 2.9 32.6 + - - +
342B LEU* 3.5 31.1 - - - +
346B GLN* 4.7 6.1 - - - -
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Residues in contact with ILE 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B LEU* 4.4 13.2 - - + -
309B GLN 2.8 19.4 + - - +
310B ALA* 3.6 4.9 - - - +
312B SER* 1.3 73.6 - - - +
314B ILE* 1.3 59.0 + - + +
316B GLU* 3.2 6.9 + - - +
317B CYS* 3.0 32.8 + - - -
327B ILE* 3.8 26.0 - - + -
331B LEU* 4.2 9.4 - - + -
338B TRP* 3.6 48.2 - - + +
341B TYR* 4.9 2.9 - - + -
342B LEU* 3.9 27.6 - - + +
345B LEU* 4.0 9.0 - - + -
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Residues in contact with ILE 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B GLY 5.0 1.6 - - - +
288B LYS* 3.5 42.6 - - + +
291B GLY* 3.5 28.0 - - - +
292B LEU* 3.7 23.8 - - + +
295B LEU* 3.7 14.8 - - + -
310B ALA 2.9 17.3 + - - +
312B SER 3.4 0.2 - - - -
313B ILE* 1.3 74.1 - - + +
315B LYS* 1.3 68.1 + - - +
317B CYS* 3.0 14.8 + - + +
318B LYS* 3.3 8.3 + - - -
319B GLY* 4.3 8.5 + - - +
324B VAL* 3.8 20.2 - - + -
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Residues in contact with LYS 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B LYS* 3.5 8.8 - - - +
311B HIS 3.1 14.3 + - - +
312B SER* 3.4 13.0 - - - +
314B ILE* 1.3 74.9 - - - +
316B GLU* 1.3 73.7 + - - +
318B LYS* 3.3 21.0 + - - +
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Residues in contact with GLU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B SER 2.9 19.0 + - - +
313B ILE 3.2 7.8 + - - +
315B LYS* 1.3 88.6 - - - +
317B CYS* 1.3 60.6 + - - +
318B LYS* 3.5 8.4 + - - +
342B LEU* 4.1 7.4 - - + -
345B LEU* 3.8 31.7 - - + +
346B GLN* 3.8 36.2 + - + +
348B LYS* 3.7 26.0 + - - +
363B ALA* 3.6 17.0 - - - +
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Residues in contact with CYS 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B ILE* 3.0 24.7 + - - -
314B ILE* 3.0 10.6 + - - +
316B GLU* 1.3 76.0 - - - +
318B LYS* 1.3 70.3 + - - +
319B GLY 4.5 0.7 - - - +
320B SER* 3.2 17.7 + - - -
323B VAL* 3.6 31.3 - - + +
324B VAL* 3.8 35.2 - - + -
327B ILE* 4.2 13.9 - - - -
345B LEU* 4.8 3.8 - - - -
363B ALA* 4.2 4.2 - - - +
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Residues in contact with LYS 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B MET* 5.9 3.1 - - - +
284B SER 5.1 1.4 - - - +
285B SER* 4.4 8.5 - - - -
314B ILE 3.3 2.2 + - - -
315B LYS 3.3 17.8 + - - +
316B GLU* 3.3 8.4 + - - +
317B CYS* 1.3 78.2 - - - +
319B GLY* 1.3 58.2 + - - +
320B SER* 3.2 6.9 + - - -
348B LYS* 3.0 24.7 - - - +
360B ASP* 4.0 18.1 + - - +
362B GLU* 2.9 30.9 + - - +
363B ALA* 4.6 6.7 - - + +
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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