Contacts of the helix formed by residues 420 - 427 (chain C) in PDB entry 1CX2
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 420 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418C GLY* 4.9 1.4 - - - -
419C LEU* 1.3 76.7 + - - +
421C GLN* 1.3 57.3 + - - +
422C PHE 2.9 0.2 + - - -
423C VAL* 3.1 3.2 + - - +
424C GLU* 2.9 45.1 + - - +
572C VAL* 3.4 14.5 - - + +
573C LYS* 3.6 18.1 - - - +
574C GLY* 3.2 35.0 - - - +
576C PRO* 3.9 17.5 - - + -
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Residues in contact with GLN 421 (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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397C ILE* 3.8 15.0 - - + +
398C GLU* 4.4 19.3 - - - +
417C HIS* 3.2 30.2 + - + +
418C GLY 2.7 16.6 + - - +
419C LEU 3.0 1.0 - - - -
420C THR* 1.3 76.8 + - - +
422C PHE* 1.3 68.9 + - - +
424C GLU* 3.8 21.8 + - - +
425C SER* 2.4 41.5 + - - -
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Residues in contact with PHE 422 (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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296C PRO* 4.0 16.2 - - + -
300C MET* 3.9 20.0 - - + -
397C ILE* 4.1 12.1 - - + -
407C PHE* 4.0 11.2 - + - -
413C ILE* 3.8 29.2 - - + -
414C LEU* 3.6 35.4 - - + -
417C HIS* 4.0 5.4 - - + -
418C GLY 3.2 10.5 - - - +
419C LEU* 2.9 17.3 - - - +
420C THR 2.9 1.4 + - - -
421C GLN* 1.3 88.5 + - - +
423C VAL* 1.3 57.0 + - - +
424C GLU 3.2 0.4 - - - -
425C SER* 3.8 5.8 - - - -
426C PHE* 2.8 77.3 + + - -
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Residues in contact with VAL 423 (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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197C MET* 3.2 25.4 - - + +
300C MET* 3.6 17.7 - - + -
419C LEU* 2.9 25.1 + - - +
420C THR 3.5 4.7 - - - +
422C PHE* 1.3 77.7 - - - +
424C GLU* 1.3 51.4 + - - +
426C PHE 3.7 0.5 - - - -
427C THR* 2.6 37.6 + - - -
568C ILE* 3.9 4.0 - - + -
572C VAL* 3.8 23.1 - - + -
576C PRO* 3.3 29.2 - - + -
577C PHE 4.3 0.9 - - - +
578C THR* 3.5 18.2 - - + +
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Residues in contact with GLU 424 (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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398C GLU* 4.6 2.2 - - + -
420C THR* 2.9 26.7 + - - +
421C GLN* 3.7 22.1 + - - +
423C VAL* 1.3 74.4 - - - +
425C SER* 1.3 65.8 + - - +
427C THR 3.1 5.2 + - - -
428C ARG* 2.8 51.2 + - - +
576C PRO* 3.9 26.8 - - + +
577C PHE 5.4 0.2 + - - -
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Residues in contact with SER 425 (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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396C ASN 3.6 6.5 - - - -
397C ILE* 3.0 36.0 - - - +
398C GLU* 3.0 29.7 + - - +
421C GLN* 2.4 29.8 + - - -
422C PHE 3.4 4.1 + - - -
424C GLU* 1.3 72.6 - - - +
426C PHE* 1.3 62.1 + - - +
428C ARG 2.5 32.2 - - - +
429C GLN* 3.7 4.2 - - - +
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Residues in contact with PHE 426 (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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195C ASN* 3.0 8.5 - - - +
196C MET* 3.0 56.5 + - + -
197C MET* 3.6 30.9 + - - +
200C PHE* 3.4 34.5 - + + -
297C GLY* 4.6 0.9 - - - -
300C MET* 4.3 10.5 - - - -
395C PHE* 5.6 2.0 - - + -
396C ASN 5.3 1.1 - - - -
397C ILE* 3.2 35.7 - - + -
407C PHE* 4.0 4.0 - + - -
422C PHE* 2.8 47.5 + + - +
425C SER* 1.3 74.9 - - - +
427C THR* 1.3 59.2 + - - +
428C ARG 3.1 2.2 + - - -
429C GLN* 3.9 8.6 + - - -
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Residues in contact with THR 427 (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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195C ASN* 3.7 9.4 - - - +
197C MET* 4.8 0.6 - - - +
423C VAL 2.6 22.0 + - - -
424C GLU 3.1 6.7 + - - -
426C PHE* 1.3 77.2 - - - +
428C ARG* 1.3 67.7 + - - +
577C PHE* 3.4 43.4 + - + -
578C THR* 3.4 22.9 - - - +
579C SER 4.4 4.0 - - - +
581C ASN 3.6 6.4 - - - +
582C VAL* 3.3 26.3 - - - -
583C GLN* 4.0 9.4 - - + -
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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