Contacts of the helix formed by residues 3331 - 3338 (chain C) in PDB entry 2H7C
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 THR3331 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3258C LYS* 5.8 8.5 - - + -
3323C ILE* 3.7 18.3 - - + +
3330C LYS* 1.3 78.0 - - - +
3332C PRO* 1.3 74.5 - - - +
3333C GLU* 3.7 11.6 + - - +
3334C GLU* 3.0 42.9 + - + +
3335C LEU* 3.0 11.3 + - - +
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Residues in contact with PRO3332 (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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3229C VAL* 6.0 0.7 - - + -
3232C LEU* 3.8 24.2 - - + +
3250C ALA* 3.9 33.9 - - + +
3251C LEU* 4.3 10.8 - - + -
3256C VAL* 4.6 15.3 - - + -
3323C ILE* 4.3 9.6 - - + -
3328C LEU* 4.8 10.3 - - + -
3330C LYS 3.7 2.0 - - - +
3331C THR* 1.3 86.4 - - - +
3333C GLU* 1.3 58.6 + - + +
3335C LEU* 3.3 5.8 + - + +
3336C GLN* 2.8 39.3 + - - +
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Residues in contact with GLU3333 (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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3251C LEU* 3.7 25.4 - - + +
3331C THR* 3.1 10.9 + - - +
3332C PRO* 1.3 80.3 - - + +
3334C GLU* 1.3 67.2 + - - +
3336C GLN* 3.5 9.8 + - - +
3337C ALA* 3.2 23.7 + - - +
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Residues in contact with GLU3334 (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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3330C LYS* 3.8 24.2 - - + -
3331C THR* 3.0 32.5 + - + +
3333C GLU* 1.3 78.4 - - - +
3335C LEU* 1.3 61.0 + - - +
3337C ALA* 3.3 7.2 + - - +
3338C GLU* 2.9 31.4 + - - +
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Residues in contact with LEU3335 (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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3232C LEU* 3.7 37.2 - - + +
3328C LEU* 3.9 17.9 - - + -
3329C LEU* 5.0 8.5 - - + +
3330C LYS* 3.3 42.0 - - + +
3331C THR 3.0 12.8 + - - +
3332C PRO* 3.6 9.4 - - + +
3334C GLU* 1.3 77.0 - - - +
3336C GLN* 1.3 62.4 + - - +
3338C GLU* 3.2 19.1 + - - +
3339C ARG 3.0 17.0 + - - -
3340C ASN* 3.1 26.9 + - + +
3341C PHE* 4.0 3.1 - - - -
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Residues in contact with GLN3336 (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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3232C LEU* 4.3 15.9 - - + -
3251C LEU* 3.6 26.4 - - - +
3332C PRO* 2.8 27.8 + - + +
3333C GLU* 3.7 9.3 - - - +
3334C GLU 3.2 0.2 - - - -
3335C LEU* 1.3 77.2 - - - +
3337C ALA* 1.3 57.0 + - - +
3339C ARG* 2.9 32.7 + - - -
3341C PHE* 3.8 12.5 - - + -
3432C ILE* 4.1 0.7 + - - +
3433C VAL* 3.4 43.1 + - - +
3436C ASN* 3.6 33.8 + - + +
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Residues in contact with ALA3337 (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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3333C GLU 3.2 14.6 + - - +
3334C GLU* 3.8 7.4 - - - +
3336C GLN* 1.3 79.4 - - - +
3338C GLU* 1.3 60.4 + - - +
3339C ARG* 3.1 19.3 + - - +
3436C ASN* 4.4 1.1 + - - -
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Residues in contact with GLU3338 (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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3330C LYS* 3.3 29.4 + - - +
3334C GLU 2.9 17.2 + - - +
3335C LEU* 3.4 18.4 - - - +
3336C GLN 3.1 0.2 - - - -
3337C ALA* 1.3 75.4 - - - +
3339C ARG* 1.3 68.1 + - - +
3340C ASN* 2.9 40.5 + - + +
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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