Contacts of the helix formed by residues 308 - 318 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307C PRO* 1.3 74.9 - - + +
309C GLN* 1.3 70.1 + - - +
310C ALA 3.2 0.9 + - - -
311C HIS* 3.4 24.6 + - - +
312C SER* 4.0 6.5 + - - -
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Residues in contact with GLN 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307C PRO* 3.2 10.8 - - - +
308C GLU* 1.3 84.8 + - - +
310C ALA* 1.3 59.6 + - - +
312C SER* 3.1 6.3 + - - -
313C ILE* 2.8 33.7 + - + +
338C TRP* 3.9 41.3 - - + +
339C GLU* 2.6 34.2 + - - +
342C LEU* 4.0 18.6 - - + -
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Residues in contact with ALA 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C LEU* 4.0 15.9 - - + -
295C LEU* 3.9 4.4 - - + +
306C LEU* 4.1 15.5 - - + -
307C PRO 3.2 16.2 + - - +
308C GLU 3.1 0.6 - - - -
309C GLN* 1.3 79.3 - - - +
311C HIS* 1.3 58.8 + - - +
313C ILE* 3.3 3.4 + - - +
314C ILE* 3.0 32.9 + - - +
338C TRP* 3.5 32.4 - - + -
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Residues in contact with HIS 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288C LYS* 2.4 40.1 + - - +
292C LEU* 3.6 37.2 - - + +
303C LYS 5.7 2.2 + - - -
306C LEU* 5.2 8.7 - - + +
307C PRO 4.2 11.2 + - - -
308C GLU* 3.7 16.9 + - - +
309C GLN 3.2 0.6 - - - -
310C ALA* 1.3 77.2 - - + +
312C SER* 1.3 61.4 + - - +
314C ILE 3.5 0.2 + - - -
315C LYS* 3.1 7.3 + - - +
47D PRO* 3.3 41.3 - - + +
48D THR* 3.9 9.4 - - + +
51D GLN* 4.3 5.4 + - - -
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Residues in contact with SER 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308C GLU 4.0 6.4 + - - -
309C GLN* 3.1 5.5 + - - -
311C HIS* 1.3 76.4 - - - +
313C ILE* 1.3 58.6 + - - +
315C LYS* 3.3 10.6 + - - +
316C GLU* 2.9 32.4 + - - +
342C LEU* 3.4 33.2 - - - +
346C GLN* 4.7 5.8 - - - -
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Residues in contact with ILE 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295C LEU* 4.5 10.5 - - + -
309C GLN 2.8 19.6 + - - +
310C ALA* 3.6 5.4 - - - +
312C SER* 1.3 73.9 - - - +
314C ILE* 1.3 62.4 + - + +
316C GLU* 3.2 3.6 + - - +
317C CYS* 3.0 27.4 + - - -
327C ILE* 3.7 27.6 - - + -
331C LEU* 4.1 10.5 - - + -
338C TRP* 3.5 49.1 - - + +
341C TYR* 5.0 2.7 - - + -
342C LEU* 3.8 27.1 - - + +
345C LEU* 3.8 12.1 - - + -
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Residues in contact with ILE 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286C LEU 6.1 0.2 - - - +
287C GLY 5.0 1.1 - - - +
288C LYS* 3.4 41.3 - - + +
291C GLY* 3.6 26.7 - - - +
292C LEU* 3.8 21.5 - - + +
295C LEU* 3.6 15.7 - - + -
310C ALA 3.0 20.0 + - - +
311C HIS 3.9 0.7 - - - +
312C SER 3.3 0.2 - - - -
313C ILE* 1.3 75.3 - - + +
315C LYS* 1.3 65.4 + - - +
317C CYS* 3.0 14.9 + - - +
318C LYS* 3.4 8.1 + - - -
319C GLY* 4.3 8.0 + - - +
324C VAL* 3.7 23.6 - - + -
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Residues in contact with LYS 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288C LYS* 3.5 9.9 - - - +
311C HIS 3.1 14.9 + - - +
312C SER* 3.4 13.0 - - - +
314C ILE* 1.3 76.5 - - - +
316C GLU* 1.3 72.1 + - - +
318C LYS* 3.2 20.8 + - - +
405D ASP* 3.0 35.7 + - - -
406D MET* 4.3 7.3 - - - +
407D GLU* 4.8 12.8 - - + +
467D TYR* 5.2 2.4 + - - -
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Residues in contact with GLU 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312C SER 2.9 18.8 + - - +
313C ILE 3.2 7.8 + - - +
315C LYS* 1.3 87.0 - - - +
317C CYS* 1.3 61.0 + - - +
318C LYS* 3.5 7.4 + - - +
342C LEU* 4.0 8.1 - - + -
345C LEU* 3.5 39.0 - - + +
346C GLN* 3.6 36.3 + - + +
348C LYS* 3.8 20.6 + - - -
363C ALA* 3.5 17.0 - - - +
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Residues in contact with CYS 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313C ILE* 3.0 24.5 + - - -
314C ILE* 3.0 9.8 + - - +
316C GLU* 1.3 75.1 - - - +
318C LYS* 1.3 70.8 + - - +
319C GLY 3.2 1.4 + - - +
320C SER* 3.3 17.0 + - - -
323C VAL* 3.7 30.5 - - + +
324C VAL* 3.6 37.0 - - + -
327C ILE* 4.1 14.1 - - - -
345C LEU* 4.6 3.8 - - - -
363C ALA* 4.2 5.2 - - - +
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Residues in contact with LYS 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C MET* 6.0 2.1 - - - +
284C SER 5.1 1.6 - - - +
285C SER* 4.4 8.3 - - - -
314C ILE 3.4 2.4 + - - -
315C LYS 3.2 17.8 + - - +
316C GLU* 3.2 6.7 - - - +
317C CYS* 1.3 79.1 - - - +
319C GLY* 1.3 58.0 + - - +
320C SER* 3.2 6.3 + - - -
348C LYS* 2.8 25.5 - - - +
360C ASP* 4.0 13.6 + - - +
362C GLU* 2.8 36.4 + - - +
363C ALA* 4.4 8.6 - - + +
466D ARG 6.1 0.9 - - - +
467D TYR* 6.5 0.4 - - + -
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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