Contacts of the helix formed by residues 314 - 327 (chain C) in PDB entry 4X2Q
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 ILE 314 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277C ILE* 4.0 12.1 - - + +
278C PHE 3.4 27.4 - - - +
279C ALA* 3.9 28.3 - - + +
281C ALA 5.5 1.8 - - - +
283C LEU* 4.4 24.0 - - + +
310C VAL* 3.9 16.2 - - + -
311C GLU* 3.3 12.3 + - + +
313C SER* 1.3 80.2 - - - +
315C TYR* 1.3 58.6 + - - +
316C GLU 3.3 2.7 - - - -
317C GLU* 3.4 12.2 + - + +
318C PHE* 2.9 31.3 + - + +
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Residues in contact with TYR 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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310C VAL* 4.0 37.2 - - + -
311C GLU 3.1 12.5 + - - +
312C GLU* 3.7 14.4 - - - +
313C SER 3.6 1.4 - - - -
314C ILE* 1.3 74.7 - - - +
316C GLU* 1.3 67.4 + - - +
318C PHE* 3.5 1.8 + + + +
319C VAL* 3.3 47.6 + - + +
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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 GLU 4.8 2.1 + - - +
313C SER 5.1 3.8 + - - +
314C ILE* 3.3 0.6 - - - +
315C TYR* 1.3 84.8 - - - +
317C GLU* 1.3 73.2 + - + +
318C PHE 3.5 0.2 + - - -
319C VAL* 3.7 5.5 + - - +
320C ARG* 3.6 35.8 + - - +
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Residues in contact with GLU 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C LEU* 3.9 22.5 - - + +
313C SER 5.8 1.6 - - - +
314C ILE* 3.4 14.3 + - + +
316C GLU* 1.3 85.2 - - + +
318C PHE* 1.3 65.0 + - - +
320C ARG* 3.5 33.7 + - - +
321C ARG* 3.2 32.7 + - - +
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Residues in contact with PHE 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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277C ILE* 3.6 38.1 - - + -
283C LEU* 4.2 13.6 - - + +
286C ALA* 5.0 0.2 - - + -
287C VAL* 3.6 36.5 - - + +
290C ALA* 4.5 8.1 - - + -
308C ILE* 4.2 13.5 - - + -
310C VAL* 3.7 32.1 - - + -
314C ILE* 2.9 19.3 + - + +
315C TYR* 3.8 5.6 - + + +
316C GLU 3.3 0.2 - - - -
317C GLU* 1.3 74.9 - - - +
319C VAL* 1.3 67.8 - - + +
321C ARG* 3.3 6.0 + - - +
322C SER* 3.0 44.3 + - - -
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Residues in contact with VAL 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C TYR* 3.3 40.5 + - + +
316C GLU* 4.1 7.0 - - - +
317C GLU 3.4 0.2 - - - -
318C PHE* 1.3 80.3 - - + +
320C ARG* 1.3 58.4 + - + +
322C SER* 3.1 7.2 + - - -
323C VAL* 2.9 44.6 + - + +
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Residues in contact with ARG 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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316C GLU* 3.6 29.4 + - - +
317C GLU* 3.5 37.2 + - - +
319C VAL* 1.3 79.2 - - + +
321C ARG* 1.3 61.5 + - + +
323C VAL* 3.3 20.8 - - + +
324C GLU* 3.1 23.5 - - - +
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Residues in contact with ARG 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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283C LEU* 3.5 33.4 + - + +
284C ASP* 2.9 46.2 + - - +
287C VAL* 3.8 24.1 - - + +
317C GLU* 3.2 21.2 + - - +
318C PHE 3.6 6.7 - - - +
319C VAL 3.2 0.2 - - - -
320C ARG* 1.3 77.4 - - + +
322C SER* 1.3 62.8 + - - +
324C GLU* 3.5 12.5 + - - +
325C ARG* 3.3 25.8 + - - +
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Residues in contact with SER 322 (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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287C VAL* 4.3 9.8 - - - +
291C HIS* 4.9 6.9 - - - -
318C PHE* 3.0 39.8 + - - -
319C VAL* 3.1 7.4 + - - -
321C ARG* 1.3 75.1 - - - +
323C VAL* 1.3 66.9 + - - +
325C ARG* 3.0 16.8 + - - +
326C ALA* 3.2 12.9 + - - +
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Residues in contact with VAL 323 (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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319C VAL* 2.9 32.8 + - + +
320C ARG* 3.3 24.0 - - + +
322C SER* 1.3 76.4 - - - +
324C GLU* 1.3 60.9 + - + +
325C ARG 3.3 0.2 - - - -
326C ALA* 3.4 8.0 + - - +
327C LYS* 3.1 45.6 + - + +
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Residues in contact with GLU 324 (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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320C ARG* 3.1 25.1 + - - +
321C ARG* 3.5 13.3 + - - +
322C SER 3.2 1.0 - - - -
323C VAL* 1.3 81.0 - - + +
325C ARG* 1.3 66.3 + - - +
326C ALA 3.4 0.2 - - - -
327C LYS* 4.1 8.5 - - + +
328C ARG* 3.4 43.9 + - - +
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Residues in contact with ARG 325 (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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287C VAL* 4.7 11.9 - - + +
288C GLU* 3.8 25.8 + - - +
291C HIS* 3.6 33.1 + - + +
321C ARG 3.3 14.3 + - - +
322C SER* 3.0 10.7 + - - +
324C GLU* 1.3 80.9 - - - +
326C ALA* 1.3 58.7 + - - +
327C LYS 3.5 0.2 - - - -
328C ARG* 3.9 21.7 - - - +
329C ARG* 3.2 27.5 + - - +
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Residues in contact with ALA 326 (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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291C HIS* 4.4 6.0 + - + +
295C PHE* 5.3 12.6 - - + -
322C SER 3.2 10.7 + - - +
323C VAL* 3.8 10.5 - - - +
324C GLU 3.4 0.2 - - - -
325C ARG* 1.3 75.8 - - - +
327C LYS* 1.3 60.0 - - + +
328C ARG 3.1 6.0 + - - -
329C ARG* 3.8 16.6 + - - +
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Residues in contact with LYS 327 (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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323C VAL* 3.1 30.6 + - + +
324C GLU* 4.6 8.1 - - + +
325C ARG 3.5 0.2 - - - -
326C ALA* 1.3 77.1 - - + +
328C ARG* 1.3 64.3 + - + +
329C ARG 5.3 0.7 - - - -
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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