Contacts of the helix formed by residues 310 - 321 (chain C) in PDB entry 4J1R
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 PRO 310 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155C VAL* 4.1 35.4 - - + -
251C LEU* 5.0 4.7 - - + -
308C ARG 3.3 7.2 - - - +
309C THR* 1.3 90.4 - - + +
311C PRO* 1.3 71.9 - - + +
312C GLU* 3.4 22.2 - - - +
313C ALA* 3.3 19.3 + - + +
314C ILE* 3.3 20.3 + - - +
339C PHE* 5.0 0.2 - - + -
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Residues in contact with PRO 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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309C THR 4.0 3.8 - - - +
310C PRO* 1.3 81.6 - - + +
312C GLU* 1.3 74.6 + - + +
314C ILE* 3.4 12.4 + - + +
315C ALA* 2.8 30.6 + - - +
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Residues in contact with GLU 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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159C LYS* 4.8 10.0 + - - -
310C PRO* 3.4 19.6 - - - +
311C PRO* 1.3 95.3 - - + +
313C ALA* 1.3 60.3 + - - +
315C ALA* 4.1 6.1 - - - -
316C LEU* 3.0 23.6 + - - +
337C HIS* 3.3 14.5 - - + -
338C SER* 4.5 14.8 - - - +
339C PHE* 3.9 31.8 - - - +
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Residues in contact with ALA 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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247C LEU* 4.4 2.2 - - - +
251C LEU* 3.7 26.5 - - + -
309C THR* 4.5 0.7 - - + -
310C PRO* 3.3 24.3 + - + +
312C GLU* 1.3 80.1 + - - +
314C ILE* 1.3 62.3 + - - +
316C LEU* 3.1 6.7 + - - +
317C CYS* 3.0 24.1 + - - +
339C PHE* 3.6 32.0 - - + -
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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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251C LEU* 5.5 0.2 - - + -
301C TRP* 3.8 29.3 - - + -
302C THR* 4.5 23.6 - - + +
305C PHE* 3.8 26.2 - - + -
306C ARG 5.3 1.1 - - - +
309C THR* 3.7 32.1 - - + +
310C PRO 3.3 17.0 + - - +
311C PRO* 3.4 11.2 + - + +
313C ALA* 1.3 74.7 - - - +
315C ALA* 1.3 63.0 + - - +
317C CYS* 3.1 17.9 + - - +
318C SER* 3.1 14.1 + - - -
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Residues in contact with ALA 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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311C PRO 2.8 18.4 + - - +
312C GLU* 3.7 9.6 - - - +
313C ALA 3.2 0.2 - - - -
314C ILE* 1.3 77.5 - - - +
316C LEU* 1.3 58.4 + - - +
318C SER* 2.9 20.6 + - - -
319C ARG* 3.3 16.5 - - - +
337C HIS* 4.1 9.9 + - + +
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Residues in contact with LEU 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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166C PHE* 4.7 4.9 - - + -
247C LEU* 3.7 18.8 - - + -
312C GLU 3.0 14.4 + - - +
313C ALA 3.1 8.7 + - - +
315C ALA* 1.3 76.5 - - - +
317C CYS* 1.3 64.4 + - - +
319C ARG* 3.1 11.4 + - - +
320C LEU* 3.2 20.9 + - + +
329C LEU* 3.8 19.5 - - + -
334C ALA* 4.7 4.7 - - + +
337C HIS* 3.6 32.1 + - + +
339C PHE* 3.6 32.1 - - + -
340C PHE* 3.7 18.8 - - + -
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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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244C GLY 4.4 3.8 - - - -
247C LEU* 3.7 33.0 - - - -
248C ALA* 4.2 14.8 - - - -
251C LEU* 4.2 4.0 - - - -
301C TRP* 4.3 9.6 - - + -
305C PHE* 3.9 30.1 - - + -
313C ALA 3.0 11.6 + - - +
314C ILE 3.1 9.4 + - - +
316C LEU* 1.3 76.5 - - - +
318C SER* 1.3 57.1 + - - +
320C LEU* 3.2 5.4 + - - +
321C LEU* 2.9 36.0 + - + +
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Residues in contact with SER 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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301C TRP* 3.6 39.2 - - - -
314C ILE* 3.1 9.7 + - - -
315C ALA* 2.9 22.0 + - - -
317C CYS* 1.3 78.3 - - - +
319C ARG* 1.3 64.6 + - - +
321C LEU 3.9 6.1 - - - +
322C GLU* 3.1 26.1 - - - +
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Residues in contact with ARG 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 ALA 3.3 15.9 - - - +
316C LEU* 3.1 11.7 + - - +
318C SER* 1.3 83.9 + - - +
320C LEU* 1.3 57.6 + - - +
322C GLU* 3.7 16.0 + - - +
327C ALA 4.0 16.1 + - - +
328C ARG* 3.4 23.7 - - - -
329C LEU* 3.4 48.8 + - + +
337C HIS* 5.0 6.5 - - + +
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Residues in contact with LEU 320 (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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166C PHE* 3.7 32.8 - - + -
240C VAL* 3.7 27.7 - - + +
241C TRP* 4.3 5.7 - - - -
243C ALA 4.5 0.2 - - - -
244C GLY* 3.5 32.5 - - - +
247C LEU* 4.2 16.8 - - + -
316C LEU* 3.2 19.2 + - + +
317C CYS* 3.8 5.2 - - - +
319C ARG* 1.3 78.1 - - - +
321C LEU* 1.3 60.6 + - - +
322C GLU 3.1 7.6 + - - -
328C ARG* 3.3 23.7 - - - +
329C LEU* 4.1 25.1 - - + -
334C ALA* 4.5 1.6 - - + -
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Residues in contact with LEU 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C TRP* 3.3 59.5 - - + +
244C GLY* 3.9 18.6 - - - +
245C CYS* 3.8 10.5 - - - +
248C ALA* 4.8 3.1 - - + -
256C ILE* 4.3 10.5 - - + -
257C PHE* 4.2 18.8 - - + -
273C LEU* 3.7 21.0 - - + +
301C TRP* 3.8 27.9 - - + -
317C CYS* 2.9 19.1 + - + +
318C SER 3.9 6.9 - - - +
320C LEU* 1.3 72.2 - - - +
322C GLU* 1.3 62.0 + - - +
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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