Contacts of the helix formed by residues 354 - 361 (chain C) in PDB entry 4EEM
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 GLN 354 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308C TRP* 5.9 1.2 - - - -
352C ASN* 3.0 13.4 + - - +
353C PRO* 1.3 80.9 - - + +
355C ARG* 1.3 62.4 + - - +
356C PHE 3.3 1.1 - - - -
357C ASP* 3.2 17.2 + - + +
358C ARG* 2.7 62.8 + - + +
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Residues in contact with ARG 355 (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 TYR* 4.2 2.4 - - + -
310C TRP* 3.8 17.2 - - - -
311C GLY* 3.7 32.1 - - - +
312C GLY* 4.3 3.6 - - - -
351C PRO* 3.4 29.5 - - - +
352C ASN* 3.0 38.8 + - - +
353C PRO* 3.2 5.3 - - - +
354C GLN* 1.3 76.9 - - - +
356C PHE* 1.3 92.5 + - + +
358C ARG* 3.2 7.4 + - - +
359C ILE* 3.0 34.0 + - - +
2F NAG 2.9 32.1 + - + +
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Residues in contact with PHE 356 (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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353C PRO* 4.3 13.7 - - + +
354C GLN 3.3 0.8 - - - -
355C ARG* 1.3 120.2 - - + +
357C ASP* 1.3 66.1 + - - +
359C ILE* 3.5 14.2 - - + +
360C ALA* 3.4 20.8 + - - +
1F MMA 5.5 11.9 - - - -
2F NAG 4.0 18.6 - - + -
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Residues in contact with ASP 357 (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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353C PRO 5.0 2.1 - - - +
354C GLN* 3.2 19.3 + - + +
356C PHE* 1.3 77.1 - - - +
358C ARG* 1.3 63.5 + - + +
360C ALA* 3.4 9.4 + - - +
361C HIS* 2.9 37.0 + - + +
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Residues in contact with ARG 358 (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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306C ASN* 3.2 52.4 + - - +
307C TYR* 3.2 39.5 + - + +
308C TRP* 5.4 3.8 - - - -
316C ASP* 4.2 0.7 - - - +
352C ASN* 4.4 6.3 - - - +
354C GLN* 2.7 54.2 + - + +
355C ARG 3.5 6.1 - - - +
356C PHE 3.2 0.2 - - - -
357C ASP* 1.3 78.1 - - + +
359C ILE* 1.3 61.7 + - - +
361C HIS* 3.1 17.2 + - - +
362C THR* 3.6 8.0 + - - -
365C THR* 5.0 2.1 + - - +
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Residues in contact with ILE 359 (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 TYR* 3.7 10.3 - - - +
312C GLY* 3.4 31.6 - - - +
315C ASP* 3.9 13.2 - - + -
316C ASP 4.1 1.8 - - - +
319C ASN* 3.1 29.9 + - - +
323C PHE* 5.8 0.5 - - - -
355C ARG 3.0 14.8 + - - +
356C PHE* 3.5 18.2 - - + +
358C ARG* 1.3 73.8 - - - +
360C ALA* 1.3 65.6 + - + +
361C HIS 3.3 0.5 + - - -
362C THR* 3.3 11.0 + - - -
1F MMA 3.9 28.5 - - - -
2F NAG 4.3 11.0 - - + -
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Residues in contact with ALA 360 (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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356C PHE 3.4 9.6 + - - +
357C ASP* 3.4 11.8 + - - +
358C ARG 3.2 1.0 - - - -
359C ILE* 1.3 81.2 - - + +
361C HIS* 1.3 69.9 + - + +
362C THR 3.5 0.6 + - - -
363C LYS 5.3 0.5 + - - -
364C GLU* 4.3 3.3 - - - +
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Residues in contact with HIS 361 (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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357C ASP* 2.9 32.3 + - + +
358C ARG* 3.1 9.9 + - - +
360C ALA* 1.3 87.7 - - + +
362C THR* 1.3 62.6 + - - +
363C LYS 3.3 2.9 - - - -
364C GLU* 3.1 50.5 + - - +
365C THR* 3.1 25.9 + - + -
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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