Contacts of the helix formed by residues 394 - 399 (chain C) in PDB entry 4EJJ
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 MET 394 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C TYR* 3.6 31.0 - - + +
58C LEU* 3.8 25.8 - - + -
59C MET* 4.8 3.8 - - - -
80C VAL* 3.6 24.5 - - + -
81C LEU 3.0 23.8 + - - +
82C CYS* 4.2 4.7 - - - -
83C GLY 4.8 0.2 + - - -
87C VAL* 4.3 1.0 - - - +
367C PRO 3.8 3.8 - - - +
368C MET* 3.8 35.7 - - + +
392C TYR* 3.9 10.1 - - - +
393C PRO* 1.3 65.8 - - - +
395C LEU* 1.3 67.2 + - - +
396C GLY 3.1 2.2 - - - -
397C SER* 2.9 31.5 + - - +
398C VAL* 3.4 8.2 + - - +
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Residues in contact with LEU 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C VAL* 4.9 9.6 - - + -
366C ILE* 3.7 21.1 - - + +
367C PRO 3.2 3.0 + - - -
369C SER* 3.6 29.8 - - - +
393C PRO* 2.9 22.9 + - + +
394C MET* 1.3 69.4 - - - +
396C GLY* 1.3 59.5 + - - +
398C VAL* 2.8 27.6 + - - +
399C LEU* 2.9 20.6 + - + +
430C VAL* 3.5 35.2 - - + +
431C PRO* 4.4 4.7 - - + +
433C SER* 4.0 20.6 - - - +
434C ILE* 5.9 0.2 - - + -
500C HEM 3.7 18.2 - - + -
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Residues in contact with GLY 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C TYR* 3.5 13.8 + - - -
364C ASP* 2.8 33.7 + - - +
367C PRO 2.9 13.7 + - - -
395C LEU* 1.3 77.9 - - - +
397C SER* 1.3 55.4 + - - +
399C LEU* 3.7 4.6 + - - +
400C ARG* 3.4 29.6 + - - +
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Residues in contact with SER 397 (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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55C TYR* 3.3 16.6 + - - -
59C MET* 4.0 25.1 - - - -
82C CYS* 3.5 6.2 - - - -
83C GLY* 2.8 33.7 + - - -
394C MET* 2.9 19.4 + - - +
396C GLY* 1.3 75.9 - - - +
398C VAL* 1.3 59.4 + - - +
400C ARG* 3.8 5.0 - - - +
401C ASP* 3.1 24.9 + - - +
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Residues in contact with VAL 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C GLY 3.9 7.9 - - - +
84C HIS* 3.6 36.3 - - + +
87C VAL* 4.2 17.5 - - + -
394C MET 3.7 9.6 - - - +
395C LEU* 2.8 14.3 + - - +
397C SER* 1.3 68.6 - - - +
399C LEU* 1.3 59.9 + - - +
400C ARG 2.8 10.8 + - - -
401C ASP* 2.9 16.8 + - - +
405C PHE* 3.8 1.0 - - - -
428C ALA* 3.5 40.7 - - + +
430C VAL* 3.5 20.6 - - + -
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Residues in contact with LEU 399 (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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360C GLN 4.4 8.1 - - - +
361C ARG* 3.0 68.2 + - + +
364C ASP* 3.9 20.2 - - - +
365C VAL 5.8 0.2 - - - +
366C ILE 6.0 0.2 - - - +
395C LEU* 2.9 23.4 + - + +
396C GLY* 3.8 6.7 - - - +
397C SER 3.4 0.2 - - - -
398C VAL* 1.3 77.2 - - - +
400C ARG* 1.3 57.5 + - + +
405C PHE* 3.5 5.3 - - - -
428C ALA 3.4 19.5 - - - +
429C PHE* 4.2 4.7 - - + -
430C VAL* 3.6 17.9 - - + +
431C PRO* 3.9 26.7 - - + -
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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