Contacts of the helix formed by residues 3471 - 3476 (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 GLU3471 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3220C GLU* 3.5 14.6 - - - +
3246C GLU* 2.7 43.4 - - - +
3247C SER* 4.7 3.0 + - - -
3351C ASN* 3.0 23.6 + - - +
3447C TYR* 4.2 11.9 - - + +
3449C PHE* 3.5 38.0 - - + -
3469C GLY* 3.3 9.8 + - - -
3470C ASP* 1.3 72.2 - - - +
3472C LEU* 1.3 73.4 + - - +
3473C PHE 3.3 0.2 - - - -
3474C SER* 3.0 7.4 + - - -
3475C VAL* 3.0 26.8 + - + +
3496C VAL* 6.3 0.4 - - + -
3500C TRP* 5.5 1.1 - - + -
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Residues in contact with LEU3472 (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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3101C PHE* 3.7 49.8 - - + +
3103C ASN* 5.8 0.9 - - - -
3138C TRP* 3.4 36.8 - - + -
3152C TYR* 4.2 8.3 - - + -
3220C GLU* 3.4 19.1 - - + -
3246C GLU* 3.9 2.9 - - - +
3469C GLY* 3.2 18.5 + - - +
3471C GLU* 1.3 89.0 - - - +
3473C PHE* 1.3 58.7 + - + +
3475C VAL* 4.4 3.8 - - + -
3476C PHE* 2.9 45.4 + - + +
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Residues in contact with PHE3473 (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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3100C LEU 3.4 26.2 - - - -
3101C PHE* 4.6 7.6 - + - -
3102C THR 3.5 22.9 - - - -
3103C ASN* 4.8 3.1 - - - -
3453C PRO* 3.8 25.1 - - + -
3455C PHE* 3.5 51.1 - + + -
3456C SER* 5.0 2.5 - - - -
3469C GLY 4.2 11.9 - - - -
3470C ASP* 3.7 20.2 - - - +
3471C GLU 3.3 0.4 - - - -
3472C LEU* 1.3 78.7 - - + +
3474C SER* 1.3 60.3 + - - +
3477C GLY 3.4 0.5 + - - -
3478C ALA* 2.9 43.9 + - + -
3479C PRO* 3.3 8.1 - - + +
3482C LYS* 4.1 2.9 - - - -
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Residues in contact with SER3474 (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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3449C PHE* 4.0 11.0 - - - -
3451C TYR* 5.4 0.7 - - - -
3470C ASP 4.8 1.0 + - - -
3471C GLU 3.0 10.0 + - - -
3473C PHE* 1.3 78.8 - - - +
3475C VAL* 1.3 66.0 + - - +
3477C GLY 3.3 1.4 + - - -
3479C PRO* 5.6 0.4 - - - +
3489C GLU 5.1 1.2 + - - -
3492C LEU* 3.8 23.2 - - - +
3493C SER* 2.8 34.6 + - - +
3496C VAL* 3.8 26.2 - - - -
3497C MET* 3.4 8.3 - - - +
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Residues in contact with VAL3475 (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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3157C LEU* 3.7 14.5 - - + +
3218C PHE* 3.9 15.5 - - + -
3246C GLU* 4.0 15.5 - - - +
3471C GLU* 3.0 22.6 + - + +
3472C LEU* 3.8 5.4 - - - +
3474C SER* 1.3 76.4 - - - +
3476C PHE* 1.3 72.6 + - + +
3477C GLY 3.3 0.2 - - - -
3496C VAL* 3.6 22.9 - - + -
3497C MET* 3.4 19.2 - - - +
3500C TRP* 3.7 40.4 - - + +
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Residues in contact with PHE3476 (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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3103C ASN* 2.9 35.2 + - + +
3138C TRP* 3.3 66.9 - + + -
3152C TYR* 4.0 24.9 - + + -
3153C ASP 3.8 19.9 - - - +
3154C GLY* 4.8 2.9 - - - -
3156C ALA* 3.8 10.1 - - - +
3157C LEU* 4.6 10.3 + - + -
3165C VAL* 4.7 13.2 - - + -
3167C THR* 4.9 2.7 - - + -
3218C PHE* 4.1 11.0 - + - -
3472C LEU* 2.9 23.9 + - + +
3475C VAL* 1.3 86.7 - - + +
3477C GLY* 1.3 60.4 + - - +
3478C ALA 3.3 1.8 - - - -
3497C MET* 4.5 2.9 - - - -
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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