Contacts of the helix formed by residues 307 - 322 (chain C) in PDB entry 4PEI
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 307 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184B GLN* 4.9 6.7 - - - +
212B PRO* 6.2 0.9 - - + -
215B LYS* 3.9 16.6 - - - +
305C LYS 3.4 12.3 + - - +
306C ARG* 1.3 81.6 - - - +
308C LYS* 1.3 56.6 + - - +
309C GLU* 3.6 6.1 + - - +
310C LEU* 3.1 32.8 + - + +
311C ASP* 2.8 38.3 + - - -
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Residues in contact with LYS 308 (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 THR* 1.3 75.5 - - - +
309C GLU* 1.3 75.1 + - + +
311C ASP* 3.7 8.3 - - + +
312C LYS* 3.0 28.8 + - - +
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Residues in contact with GLU 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 THR* 3.2 6.3 + - - +
308C LYS* 1.3 100.5 + - + +
310C LEU* 1.3 68.9 + - + +
312C LYS* 3.3 24.3 + - - +
313C LYS* 3.0 23.4 + - - +
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Residues in contact with LEU 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C MET* 4.0 15.3 - - + -
305C LYS* 3.8 22.0 - - + +
307C THR* 3.1 26.1 + - + +
309C GLU* 1.3 78.5 - - + +
311C ASP* 1.3 55.0 + - - +
313C LYS* 3.0 9.0 + - + +
314C ILE* 2.8 44.5 + - + +
351C LEU* 4.7 19.4 - - + +
353C ILE* 3.9 30.5 - - + -
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Residues in contact with ASP 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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277C CYS* 3.4 21.7 - - - +
306C ARG* 2.9 52.1 + - - +
307C THR 2.8 30.3 + - - +
308C LYS* 3.7 8.1 - - + +
310C LEU* 1.3 72.6 - - - +
312C LYS* 1.3 64.8 + - - +
314C ILE* 3.0 5.6 + - - +
315C ILE* 3.0 28.4 + - + +
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Residues in contact with LYS 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 LYS 3.0 19.9 + - - +
309C GLU* 3.7 24.9 + - - +
310C LEU 3.3 0.4 - - - -
311C ASP* 1.3 77.1 - - - +
313C LYS* 1.3 60.6 + - + +
315C ILE* 3.5 6.2 + - - +
316C GLU* 3.1 31.1 + - + +
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Residues in contact with LYS 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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309C GLU 3.0 12.4 + - - +
310C LEU* 3.0 13.1 + - + +
312C LYS* 1.3 78.6 - - + +
314C ILE* 1.3 61.4 + - - +
316C GLU* 3.1 34.9 + - - +
317C LEU* 2.5 60.4 + - + +
350C GLU* 5.1 9.9 + - - -
351C LEU* 4.0 14.1 - - + -
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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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276C VAL* 3.8 16.4 - - + -
277C CYS* 4.1 22.7 - - + +
280C ILE* 3.5 31.6 - - + -
281C MET* 3.7 37.5 - - + -
310C LEU 2.8 23.3 + - - +
311C ASP* 3.0 8.5 + - - +
313C LYS* 1.3 78.9 - - - +
315C ILE* 1.3 57.8 + - - +
317C LEU* 3.2 6.9 + - - +
318C TRP* 2.8 27.4 + - + +
347C ILE* 4.3 5.1 - - + +
351C LEU* 3.8 21.5 - - + -
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Residues in contact with ILE 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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273C LYS* 3.7 61.2 - - + +
276C VAL* 3.8 21.1 - - + -
277C CYS* 3.9 9.6 - - - -
311C ASP* 3.0 19.7 + - + +
312C LYS* 3.9 6.3 - - - +
314C ILE* 1.3 73.9 - - - +
316C GLU* 1.3 59.9 + - - +
318C TRP* 3.8 2.7 - - - +
319C GLU* 2.9 30.2 + - + +
324C LEU* 4.4 19.9 - - + +
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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 LYS* 3.1 22.4 + - + +
313C LYS* 3.1 39.7 + - - +
314C ILE 3.3 0.2 - - - -
315C ILE* 1.3 77.6 - - - +
317C LEU* 1.3 65.7 + - + +
319C GLU* 3.2 7.5 + - - +
320C LYS* 3.0 21.4 + - + +
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Residues in contact with LEU 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 LYS* 2.5 77.6 + - + +
314C ILE* 4.3 2.2 - - - +
316C GLU* 1.3 80.3 - - + +
318C TRP* 1.3 66.7 + - - +
320C LYS* 3.1 14.8 + - + +
321C TYR* 2.9 41.3 + - + -
347C ILE* 3.8 29.6 - - + -
350C GLU* 3.8 26.7 - - + +
351C LEU* 4.5 5.2 - - + -
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Residues in contact with TRP 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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271C TYR* 3.3 35.2 - + - -
276C VAL* 3.5 34.5 - - + +
279C LEU* 3.8 25.4 - - + -
280C ILE* 3.8 26.5 - - + -
314C ILE 2.8 17.3 + - - +
315C ILE* 3.8 5.8 - - - +
317C LEU* 1.3 76.4 - - - +
319C GLU* 1.3 63.5 + - - +
322C ILE* 2.9 49.8 + - + +
323C GLY 2.9 48.5 + - - -
324C LEU* 3.8 15.9 - - + -
340C ARG* 4.0 11.7 - - - -
344C ILE* 4.3 4.0 - - + -
347C ILE* 3.6 12.7 - - + +
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Residues in contact with GLU 319 (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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315C ILE* 2.9 20.7 + - - +
316C GLU* 3.6 6.7 - - - +
318C TRP* 1.3 79.2 - - - +
320C LYS* 1.3 62.6 + - - +
323C GLY* 3.4 21.7 + - - -
324C LEU* 3.1 37.4 - - + +
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Residues in contact with LYS 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C GLU* 3.0 13.7 + - + +
317C LEU* 3.2 19.5 - - + +
319C GLU* 1.3 81.4 - - - +
321C TYR* 1.3 105.2 + - + +
323C GLY 4.9 0.2 + - - -
350C GLU* 5.3 2.0 + - - -
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Residues in contact with TYR 321 (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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317C LEU* 2.9 43.5 + - + +
320C LYS* 1.3 117.1 + - + +
322C ILE* 1.3 64.2 + - + +
343C TYR* 3.7 46.0 - + + -
346C LYS* 3.6 27.3 + - + -
347C ILE* 3.9 19.1 - - + -
350C GLU* 2.4 31.6 + - - -
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Residues in contact with ILE 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C TYR* 3.9 6.1 - - + +
318C TRP* 2.9 67.2 + - + +
320C LYS 5.2 0.2 - - - -
321C TYR* 1.3 83.6 - - + +
323C GLY* 1.3 59.7 + - - +
325C LYS 4.7 4.5 - - - +
327C ILE* 5.1 10.9 - - - +
340C ARG* 3.8 34.1 - - - +
343C TYR* 3.6 35.2 - - + -
347C ILE* 4.6 4.9 - - + -
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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