Contacts of the helix formed by residues 2311 - 2323 (chain C) in PDB entry 1G50
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 THR2311 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2309C SER 5.1 2.5 - - - +
2310C LEU* 1.3 72.9 - - - +
2312C ALA* 1.3 55.7 - - - +
2313C ASP* 2.6 24.7 + - - +
2314C GLN* 2.7 65.6 + - - +
2315C MET* 3.0 9.4 + - - +
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Residues in contact with ALA2312 (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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2310C LEU 3.5 3.7 + - - -
2311C THR* 1.3 70.4 - - - +
2313C ASP* 1.3 60.2 + - - +
2315C MET* 3.4 9.6 - - - +
2316C VAL* 3.4 4.3 - - - +
2481C LYS* 4.8 5.2 - - - +
2484C ASP* 4.9 3.6 - - + +
2485C THR* 3.2 36.7 - - - +
2488C HIS* 3.6 37.5 - - + -
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Residues in contact with ASP2313 (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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2311C THR* 2.6 15.8 + - - +
2312C ALA* 1.3 76.5 + - - +
2314C GLN* 1.3 63.1 + - - +
2315C MET 3.1 1.3 - - - -
2316C VAL* 3.3 10.4 + - - +
2317C SER* 3.1 22.0 + - - -
2488C HIS* 3.2 34.1 + - - -
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Residues in contact with GLN2314 (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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2309C SER 5.0 1.8 + - - -
2310C LEU* 3.6 26.7 - - + +
2311C THR* 2.7 58.7 + - + +
2313C ASP* 1.3 70.0 - - + +
2315C MET* 1.3 58.3 + - - +
2317C SER* 3.3 6.6 + - - +
2318C ALA* 2.7 40.4 + - - +
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Residues in contact with MET2315 (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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2307C ALA 5.0 0.7 - - - +
2310C LEU* 4.6 11.7 - - + +
2311C THR 3.0 9.8 + - - +
2312C ALA* 3.4 14.1 - - - +
2314C GLN* 1.3 75.2 - - - +
2316C VAL* 1.3 62.5 + - - +
2318C ALA* 3.0 19.5 - - - +
2319C LEU* 3.0 29.7 + - + +
2365C PRO* 4.2 27.1 - - + -
2478C VAL* 4.7 3.6 - - + +
2481C LYS* 3.2 43.5 - - + -
2482C ILE* 3.7 25.4 - - + -
2485C THR* 3.0 28.7 - - + +
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Residues in contact with VAL2316 (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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2312C ALA 3.4 18.2 - - - +
2313C ASP* 3.3 11.0 + - - +
2314C GLN 3.2 0.4 - - - -
2315C MET* 1.3 71.3 - - - +
2317C SER* 1.3 55.9 + - - +
2318C ALA 2.7 13.7 + - - -
2319C LEU* 3.0 9.5 + - - +
2320C LEU* 2.9 48.2 + - + +
2443C GLU* 4.0 23.1 - - + -
2446C VAL* 4.7 3.3 - - + +
2447C CYS* 5.6 2.5 - - - -
2485C THR* 3.5 16.4 - - + +
2489C LEU* 4.0 17.3 - - + -
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Residues in contact with SER2317 (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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2313C ASP 3.1 12.6 + - - -
2314C GLN* 3.5 5.4 - - - -
2316C VAL* 1.3 79.3 - - - +
2318C ALA* 1.3 56.7 + - - +
2320C LEU* 4.0 13.0 - - - +
2321C ASP* 3.2 24.6 + - - +
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Residues in contact with ALA2318 (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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2310C LEU* 5.3 5.4 - - + -
2314C GLN* 2.7 19.9 + - + +
2315C MET* 3.0 13.5 - - - +
2316C VAL 2.7 1.2 + - - -
2317C SER* 1.3 76.9 - - - +
2319C LEU* 1.3 62.6 + - - +
2320C LEU 3.1 1.1 - - - -
2321C ASP* 3.2 5.7 + - - +
2322C ALA* 3.1 21.8 + - - +
2363C ARG 5.6 2.4 - - - +
2365C PRO* 4.5 17.5 - - + -
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Residues in contact with LEU2319 (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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2315C MET* 3.4 28.3 - - + +
2316C VAL* 3.0 5.2 + - - +
2318C ALA* 1.3 75.5 - - - +
2320C LEU* 1.3 58.6 + - - +
2322C ALA* 3.4 8.6 + - + +
2323C GLU* 3.2 28.4 + - - +
2360C TRP* 4.5 4.3 + - - +
2364C VAL* 4.4 7.4 - - + -
2365C PRO* 3.6 30.5 - - + -
2446C VAL* 3.5 45.5 - - + +
2447C CYS* 4.0 15.5 - - - +
2450C SER* 3.3 24.0 - - - +
2482C ILE* 5.4 3.6 - - + -
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Residues in contact with LEU2320 (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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2316C VAL* 2.9 41.4 + - + +
2317C SER* 4.1 8.5 - - - -
2319C LEU* 1.3 76.6 - - - +
2321C ASP* 1.3 63.9 + - - +
2323C GLU* 3.7 19.0 + - + +
2442C GLY* 4.5 11.9 - - - +
2443C GLU* 4.5 11.4 - - + -
2446C VAL* 3.7 26.2 - - + -
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Residues in contact with ASP2321 (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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2317C SER 3.2 20.9 + - - +
2318C ALA* 3.2 7.0 + - - +
2320C LEU* 1.3 78.2 - - - +
2322C ALA* 1.3 63.2 + - - +
2323C GLU 3.4 6.1 + - - +
2363C ARG* 5.6 3.3 - - - -
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Residues in contact with ALA2322 (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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2318C ALA 3.1 13.6 + - - +
2319C LEU* 3.4 14.1 - - + +
2321C ASP* 1.3 77.0 - - - +
2323C GLU* 1.3 66.7 + - - +
2324C PRO* 3.3 3.6 - - - +
2360C TRP* 3.6 30.2 - - + +
2363C ARG* 3.9 40.4 + - + +
2364C VAL* 5.2 0.9 - - - +
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Residues in contact with GLU2323 (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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2319C LEU 3.2 16.7 + - - +
2320C LEU* 3.7 17.5 - - + +
2321C ASP 3.3 5.8 - - - +
2322C ALA* 1.3 79.2 - - - +
2324C PRO* 1.3 76.5 - - - +
2325C PRO* 4.7 0.3 - - - +
2360C TRP* 4.0 6.1 + - - -
2445C PHE* 4.3 12.1 - - + -
2446C VAL* 3.9 22.0 - - + +
2449C LYS* 2.9 41.9 + - - +
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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